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Besterman AD, Jeste SS. Dual orexin receptor antagonists for insomnia in youth with neurodevelopmental disorders: a case series and review. Eur Child Adolesc Psychiatry 2023; 32:527-531. [PMID: 34611728 PMCID: PMC10038945 DOI: 10.1007/s00787-021-01883-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/23/2021] [Indexed: 11/24/2022]
Abstract
Insomnia is a common, impairing, and difficult-to-treat comorbidity in children with neurodevelopmental disorders (NDDs). Behavioral interventions can be challenging because of developmental and behavioral features that interfere with treatment. Medication management also can be difficult due to a high burden of side effects, a high rate of paradoxical responses, and frequent treatment resistance. Therefore, new treatment options for insomnia in children with NDDs are needed. Dual orexin receptor antagonists (DORAs) are a relatively new class of pharmacotherapeutics that induce sleep by inhibiting the orexin signaling pathway. To date, there is little safety or efficacy data on the use of DORAs in children with NDDs. We present four patients with NDDs and insomnia that we treated with the DORA, suvorexant. We found that patients had a wide range of responses, with one patient displaying a robust improvement in sleep onset and maintenance, while another had significant improvement in insomnia symptoms on combination therapy with trazodone. Our final two patients had mild or no benefit from suvorexant therapy. Further research is necessary to establish the safety and efficacy of DORAs in this population and to identify predictive factors, such as specific neurogenetic diagnoses or clinical features, of a positive treatment response.
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Affiliation(s)
- Aaron D Besterman
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA.
- Rady Children's Hospital of San Diego, 3020 Children's Way, San Diego, CA, 92123, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angles, Los Angeles, CA, USA.
| | - Shafali S Jeste
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angles, Los Angeles, CA, USA
- Division of Child Neurology, Department of Pediatrics, UCLA David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Departments of Neurology and Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Neurology and Neurological Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
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2
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Hunt ET, Armstrong B, Beets MW, Turner-McGrievy G, Weaver RG. Interpersonal and Environmental Protective Factors and Their Associations With Children's Weight Status. J Prim Care Community Health 2023; 14:21501319231182304. [PMID: 37350438 PMCID: PMC10291400 DOI: 10.1177/21501319231182304] [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] [Received: 04/13/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/24/2023] Open
Abstract
Both external structure (ie, participating in extracurricular activities) and family factors (ie, parental emotional support) have separately been linked with children's physical health and well-being, however, their combined effects are less well known. The current study examined the longitudinal associations between participating in structured out-of-school activities and parent reports of warmth/emotional support with children's weight status (ie, zBMI) over time. Utilizing longitudinal data from the United States-based Early Childhood Longitudinal Study, Kindergarten Class of 2010 to 2011 (ECLS-K:2011), we employed a confirmatory factor analysis (CFA) and a latent variable cross-lagged path analysis to examine if emotional supportiveness and participation in structured activities predicted lower zBMI over the course of 1 year. The final sample included 18 135 participants. Mean age of the participants was 8.12 years (±0.38 years), and 51% of children were male. Mean zBMI was 0.54 (±1.12). Structure at baseline predicted increased zBMI in year 2 (β = .03, P = .02) but did not predict parent emotional supportiveness at year 2 (β = -.05, P = .09). Parent emotional supportiveness at baseline predicted greater zBMI at year 2 (β = .02, P = <.01) but did not predict structure at year 2 (β = .02, P = .39). zBMI at baseline did not predict structure (β = .02, P = .25) or parent emotional supportiveness at year 2 (β = -.01, P = .55). Our findings were inconsistent with our hypothesis with regard to directionality. Continued refinement about the role of internal structure (ie, family, and parenting practices) may inform public health prevention strategies to support the well-being of children and families.
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Affiliation(s)
- Ethan T. Hunt
- School of Public Health, University of Texas Health Science Center at Houston, Austin, TX, USA
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Bhandari R, Alexander T, Annie FH, Kaleem U, Irfan A, Balla S, Wiener RC, Cook C, Nanjundappa A, Bates M, Thompson E, Smith GS, Feinberg J, Fisher MA. Steep rise in drug use-associated infective endocarditis in West Virginia: Characteristics and healthcare utilization. PLoS One 2022; 17:e0271510. [PMID: 35839224 PMCID: PMC9286279 DOI: 10.1371/journal.pone.0271510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 07/01/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction Life-threatening infections such as infective endocarditis (IE) are increasing simultaneously with the injection drug use epidemic in West Virginia (WV). We utilized a newly developed, statewide database to describe epidemiologic characteristics and healthcare utilization among patients with (DU-IE) and without (non-DU-IE) drug use-associated IE in WV over five years. Materials and methods This retrospective, observational study, incorporating manual review of electronic medical records, included all patients aged 18–90 years who had their first admission for IE in any of the four university-affiliated referral hospitals in WV during 2014–2018. IE was identified using ICD-10-CM codes and confirmed by chart review. Demographics, clinical characteristics, and healthcare utilization were compared between patients with DU-IE and non-DU-IE using Chi-square/Fisher’s exact test or Wilcoxon rank sum test. Multivariable logistic regression analysis was conducted with discharge against medical advice/in-hospital mortality vs. discharge alive as the outcome variable and drug use as the predictor variable. Results Overall 780 unique patients had confirmed first IE admission, with a six-fold increase during study period (p = .004). Most patients (70.9%) had used drugs before hospital admission, primarily by injection. Compared to patients with non-DU-IE, patients with DU-IE were significantly younger (median age: 33.9 vs. 64.1 years; p < .001); were hospitalized longer (median: 25.5 vs. 15 days; p < .001); had a higher proportion of methicillin-resistant Staphylococcus aureus (MRSA) isolates (42.7% vs. 29.9%; p < .001), psychiatric disorders (51.2% vs. 17.3%; p < .001), cardiac surgeries (42.9% vs. 26.6%; p < .001), and discharges against medical advice (19.9% vs. 1.4%; p < .001). Multivariable regression analysis showed drug use was an independent predictor of the combined outcome of discharge against medical advice/in-hospital mortality (OR: 2.99; 95% CI: 1.67–5.64). Discussion and conclusion This multisite study reveals a 681% increase in IE admissions in WV over five years primarily attributable to injection drug use, underscoring the urgent need for both prevention efforts and specialized strategies to improve outcomes.
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Affiliation(s)
- Ruchi Bhandari
- School of Public Health, West Virginia University, Morgantown, West Virginia, United States of America
- * E-mail:
| | - Talia Alexander
- School of Public Health, West Virginia University, Morgantown, West Virginia, United States of America
| | - Frank H. Annie
- Health Education and Research Institute, Charleston Area Medical Center, Charleston, West Virginia, United States of America
| | - Umar Kaleem
- Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, United States of America
| | - Affan Irfan
- Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, United States of America
| | - Sudarshan Balla
- School of Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - R. Constance Wiener
- School of Dentistry, West Virginia University, Morgantown, West Virginia, United States of America
| | - Chris Cook
- School of Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Aravinda Nanjundappa
- Department of Cardiovascular Medicine, Charleston Area Medical Center, Charleston, West Virginia, United States of America
| | - Mark Bates
- Department of Cardiovascular Medicine, Charleston Area Medical Center, Charleston, West Virginia, United States of America
| | - Ellen Thompson
- Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, United States of America
| | - Gordon S. Smith
- School of Public Health, West Virginia University, Morgantown, West Virginia, United States of America
| | - Judith Feinberg
- School of Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Melanie A. Fisher
- School of Medicine, West Virginia University, Morgantown, West Virginia, United States of America
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Blumberg S, Lu P, Kwan AT, Hoover CM, Lloyd-Smith JO, Sears D, Bertozzi SM, Worden L. Modeling scenarios for mitigating outbreaks in congregate settings. PLoS Comput Biol 2022; 18:e1010308. [PMID: 35857774 PMCID: PMC9342784 DOI: 10.1371/journal.pcbi.1010308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/01/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022] Open
Abstract
The explosive outbreaks of COVID-19 seen in congregate settings such as prisons and nursing homes, has highlighted a critical need for effective outbreak prevention and mitigation strategies for these settings. Here we consider how different types of control interventions impact the expected number of symptomatic infections due to outbreaks. Introduction of disease into the resident population from the community is modeled as a stochastic point process coupled to a branching process, while spread between residents is modeled via a deterministic compartmental model that accounts for depletion of susceptible individuals. Control is modeled as a proportional decrease in the number of susceptible residents, the reproduction number, and/or the proportion of symptomatic infections. This permits a range of assumptions about the density dependence of transmission and modes of protection by vaccination, depopulation and other types of control. We find that vaccination or depopulation can have a greater than linear effect on the expected number of cases. For example, assuming a reproduction number of 3.0 with density-dependent transmission, we find that preemptively reducing the size of the susceptible population by 20% reduced overall disease burden by 47%. In some circumstances, it may be possible to reduce the risk and burden of disease outbreaks by optimizing the way a group of residents are apportioned into distinct residential units. The optimal apportionment may be different depending on whether the goal is to reduce the probability of an outbreak occurring, or the expected number of cases from outbreak dynamics. In other circumstances there may be an opportunity to implement reactive disease control measures in which the number of susceptible individuals is rapidly reduced once an outbreak has been detected to occur. Reactive control is most effective when the reproduction number is not too high, and there is minimal delay in implementing control. We highlight the California state prison system as an example for how these findings provide a quantitative framework for understanding disease transmission in congregate settings. Our approach and accompanying interactive website (https://phoebelu.shinyapps.io/DepopulationModels/) provides a quantitative framework to evaluate the potential impact of policy decisions governing infection control in outbreak settings.
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Affiliation(s)
- Seth Blumberg
- University of California San Francisco, Francis I. Proctor Foundation, San Francisco, California, United States of America
- Modeling Infectious Diseases in Healthcare Network, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- University of California San Francisco, Department of Medicine, San Francisco, California, United States of America
| | - Phoebe Lu
- University of California San Francisco, Francis I. Proctor Foundation, San Francisco, California, United States of America
- Modeling Infectious Diseases in Healthcare Network, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ada T. Kwan
- University of California San Francisco, Department of Medicine, San Francisco, California, United States of America
| | - Christopher M. Hoover
- University of California San Francisco, Francis I. Proctor Foundation, San Francisco, California, United States of America
- Modeling Infectious Diseases in Healthcare Network, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James O. Lloyd-Smith
- University of California Los Angeles, Department of Ecology and Evolutionary Biology, Los Angeles, California, United States of America
| | - David Sears
- University of California San Francisco, Department of Medicine, San Francisco, California, United States of America
| | - Stefano M. Bertozzi
- University of California Berkeley, School of Public Health, Berkeley, California, United States of America
- University of Washington, Department of Global Health, Seattle, Washington, United States of America
- National Institute of Public Health of Mexico, Cuernavaca, Mexico
| | - Lee Worden
- University of California San Francisco, Francis I. Proctor Foundation, San Francisco, California, United States of America
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Ukawuba I, Shaman J. Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission. PLoS Comput Biol 2022; 18:e1010161. [PMID: 35679241 PMCID: PMC9182318 DOI: 10.1371/journal.pcbi.1010161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Given the crucial role of climate in malaria transmission, many mechanistic models of malaria represent vector biology and the parasite lifecycle as functions of climate variables in order to accurately capture malaria transmission dynamics. Lower dimension mechanistic models that utilize implicit vector dynamics have relied on indirect climate modulation of transmission processes, which compromises investigation of the ecological role played by climate in malaria transmission. In this study, we develop an implicit process-based malaria model with direct climate-mediated modulation of transmission pressure borne through the Entomological Inoculation Rate (EIR). The EIR, a measure of the number of infectious bites per person per unit time, includes the effects of vector dynamics, resulting from mosquito development, survivorship, feeding activity and parasite development, all of which are moderated by climate. We combine this EIR-model framework, which is driven by rainfall and temperature, with Bayesian inference methods, and evaluate the model’s ability to simulate local transmission across 42 regions in Rwanda over four years. Our findings indicate that the biologically-motivated, EIR-model framework is capable of accurately simulating seasonal malaria dynamics and capturing of some of the inter-annual variation in malaria incidence. However, the model unsurprisingly failed to reproduce large declines in malaria transmission during 2018 and 2019 due to elevated anti-malaria measures, which were not accounted for in the model structure. The climate-driven transmission model also captured regional variation in malaria incidence across Rwanda’s diverse climate, while identifying key entomological and epidemiological parameters important to seasonal malaria dynamics. In general, this new model construct advances the capabilities of implicitly-forced lower dimension dynamical malaria models by leveraging climate drivers of malaria ecology and transmission. Climate plays a fundamental and complex role in malaria transmission, by acting on multiple aspects of mosquito ecology and parasite transmissibility. However, to express malaria transmission pressure, malaria models with implicit vector dynamics have relied on indirect predictors of vector ecology, such as temporal seasonality or interpolations of rainfall/temperature, instead of entomological processes directly informed by ambient conditions. This approach obscures the specific influence of environmental conditions on relevant vector and parasite ecology, as well as meaningful interpretation of climate variability within these models. Here, we demonstrate that both interpretability and ecological effect from climate can be instantiated in lower dimension dynamical models through representation of transmission pressures via a climate-driven Entomological Inoculation Rate (EIR). This process-based model framework is driven by local rainfall and temperature, which regulate multiple aspects of the EIR, namely mosquito density, host-seeking activity, and parasite infectivity. Our results indicate that the climate-driven model construct is able to reproduce regional and local malaria transmission at seasonal and inter-annual time scales, while enabling identification of key entomological determinants of transmission.
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Affiliation(s)
- Israel Ukawuba
- Columbia University, Mailman School of Public Health, New York, New York, United States of America
- * E-mail:
| | - Jeffrey Shaman
- Columbia University, Mailman School of Public Health, New York, New York, United States of America
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6
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Murray JI, Preston E, Crawford JP, Rumley JD, Amom P, Anderson BD, Sivaramakrishnan P, Patel SD, Bennett BA, Lavon TD, Hsiao E, Peng F, Zacharias AL. The anterior Hox gene ceh-13 and elt-1/GATA activate the posterior Hox genes nob-1 and php-3 to specify posterior lineages in the C. elegans embryo. PLoS Genet 2022; 18:e1010187. [PMID: 35500030 PMCID: PMC9098060 DOI: 10.1371/journal.pgen.1010187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 05/12/2022] [Accepted: 04/04/2022] [Indexed: 12/18/2022] Open
Abstract
Hox transcription factors play a conserved role in specifying positional identity during animal development, with posterior Hox genes typically repressing the expression of more anterior Hox genes. Here, we dissect the regulation of the posterior Hox genes nob-1 and php-3 in the nematode C. elegans. We show that nob-1 and php-3 are co-expressed in gastrulation-stage embryos in cells that previously expressed the anterior Hox gene ceh-13. This expression is controlled by several partially redundant transcriptional enhancers. These enhancers act in a ceh-13-dependant manner, providing a striking example of an anterior Hox gene positively regulating a posterior Hox gene. Several other regulators also act positively through nob-1/php-3 enhancers, including elt-1/GATA, ceh-20/ceh-40/Pbx, unc-62/Meis, pop-1/TCF, ceh-36/Otx, and unc-30/Pitx. We identified defects in both cell position and cell division patterns in ceh-13 and nob-1;php-3 mutants, suggesting that these factors regulate lineage identity in addition to positional identity. Together, our results highlight the complexity and flexibility of Hox gene regulation and function and the ability of developmental transcription factors to regulate different targets in different stages of development.
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Affiliation(s)
- John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Elicia Preston
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jeremy P. Crawford
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jonathan D. Rumley
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Prativa Amom
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Breana D. Anderson
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Priya Sivaramakrishnan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shaili D. Patel
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Barrington Alexander Bennett
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Teddy D. Lavon
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Erin Hsiao
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Felicia Peng
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Amanda L. Zacharias
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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Lai B, Qian S, Zhang H, Zhang S, Kozlova A, Duan J, Xu J, He X. Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning. PLoS Comput Biol 2022; 18:e1010011. [PMID: 35576194 PMCID: PMC9135341 DOI: 10.1371/journal.pcbi.1010011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/26/2022] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
Genomewide association studies (GWAS) have identified a large number of loci associated with neuropsychiatric traits, however, understanding the molecular mechanisms underlying these loci remains difficult. To help prioritize causal variants and interpret their functions, computational methods have been developed to predict regulatory effects of non-coding variants. An emerging approach to variant annotation is deep learning models that predict regulatory functions from DNA sequences alone. While such models have been trained on large publicly available dataset such as ENCODE, neuropsychiatric trait-related cell types are under-represented in these datasets, thus there is an urgent need of better tools and resources to annotate variant functions in such cellular contexts. To fill this gap, we collected a large collection of neurodevelopment-related cell/tissue types, and trained deep Convolutional Neural Networks (ResNet) using such data. Furthermore, our model, called MetaChrom, borrows information from public epigenomic consortium to improve the accuracy via transfer learning. We show that MetaChrom is substantially better in predicting experimentally determined chromatin accessibility variants than popular variant annotation tools such as CADD and delta-SVM. By combining GWAS data with MetaChrom predictions, we prioritized 31 SNPs for Schizophrenia, suggesting potential risk genes and the biological contexts where they act. In summary, MetaChrom provides functional annotations of any DNA variants in the neuro-development context and the general method of MetaChrom can also be extended to other disease-related cell or tissue types.
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Affiliation(s)
- Boqiao Lai
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Sheng Qian
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Hanwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
| | - Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
| | - Alena Kozlova
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, United States of America
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, United States of America
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, Illinois, United States of America
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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Abstract
Recent progress in deep learning has greatly improved the prediction of RNA splicing from DNA sequence. Here, we present Pangolin, a deep learning model to predict splice site strength in multiple tissues. Pangolin outperforms state-of-the-art methods for predicting RNA splicing on a variety of prediction tasks. Pangolin improves prediction of the impact of genetic variants on RNA splicing, including common, rare, and lineage-specific genetic variation. In addition, Pangolin identifies loss-of-function mutations with high accuracy and recall, particularly for mutations that are not missense or nonsense, demonstrating remarkable potential for identifying pathogenic variants.
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Affiliation(s)
- Tony Zeng
- The College, University of Chicago, Chicago, 60637, IL, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, 60637, IL, USA.
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Samuels EA, Khatri UG, Snyder H, Wightman RS, Tofighi B, Krawczyk N. Buprenorphine Telehealth Treatment Initiation and Follow-Up During COVID-19. J Gen Intern Med 2022; 37:1331-1333. [PMID: 34981357 PMCID: PMC8722662 DOI: 10.1007/s11606-021-07249-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/25/2021] [Indexed: 12/01/2022]
Affiliation(s)
- Elizabeth A Samuels
- Department of Emergency Medicine, Alpert Medical School of Brown University, Providence, RI, USA.
| | - Utsha G Khatri
- Department of Emergency Medicine, Perelman School of Medicine, National Clinician Scholars Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Hannah Snyder
- Department of Family and Community Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel S Wightman
- Department of Emergency Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| | - Babak Tofighi
- Department of Population Health, New York University Grossman School of Medicine, New York City, NY, USA
| | - Noa Krawczyk
- Center for Opioid Epidemiology and Policy, Department of Population Health, New York University Grossman School of Medicine, New York City, NY, USA
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Krohannon A, Srivastava M, Rauch S, Srivastava R, Dickinson BC, Janga SC. CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion. BMC Genomics 2022; 23:172. [PMID: 35236300 PMCID: PMC8889671 DOI: 10.1186/s12864-022-08366-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/06/2021] [Accepted: 02/03/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recent discovery of the gene editing system - CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas), has resulted in its widespread use for improved understanding of a variety of biological systems. Cas13, a lesser studied Cas protein, has been repurposed to allow for efficient and precise editing of RNA molecules. The Cas13 system utilizes base complementarity between a crRNA/sgRNA (crispr RNA or single guide RNA) and a target RNA transcript, to preferentially bind to only the target transcript. Unlike targeting the upstream regulatory regions of protein coding genes on the genome, the transcriptome is significantly more redundant, leading to many transcripts having wide stretches of identical nucleotide sequences. Transcripts also exhibit complex three-dimensional structures and interact with an array of RBPs (RNA Binding Proteins), both of which may impact the effectiveness of transcript depletion of target sequences. However, our understanding of the features and corresponding methods which can predict whether a specific sgRNA will effectively knockdown a transcript is very limited. RESULTS Here we present a novel machine learning and computational tool, CASowary, to predict the efficacy of a sgRNA. We used publicly available RNA knockdown data from Cas13 characterization experiments for 555 sgRNAs targeting the transcriptome in HEK293 cells, in conjunction with transcriptome-wide protein occupancy information. Our model utilizes a Decision Tree architecture with a set of 112 sequence and target availability features, to classify sgRNA efficacy into one of four classes, based upon expected level of target transcript knockdown. After accounting for noise in the training data set, the noise-normalized accuracy exceeds 70%. Additionally, highly effective sgRNA predictions have been experimentally validated using an independent RNA targeting Cas system - CIRTS, confirming the robustness and reproducibility of our model's sgRNA predictions. Utilizing transcriptome wide protein occupancy map generated using POP-seq in HeLa cells against publicly available protein-RNA interaction map in Hek293 cells, we show that CASowary can predict high quality guides for numerous transcripts in a cell line specific manner. CONCLUSIONS Application of CASowary to whole transcriptomes should enable rapid deployment of CRISPR/Cas13 systems, facilitating the development of therapeutic interventions linked with aberrations in RNA regulatory processes.
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Affiliation(s)
- Alexander Krohannon
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), 535 West Michigan St, Indianapolis, IN, 46202, USA
| | - Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), 535 West Michigan St, Indianapolis, IN, 46202, USA
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637, USA
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), 535 West Michigan St, Indianapolis, IN, 46202, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), 535 West Michigan St, Indianapolis, IN, 46202, USA.
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translation Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN, 46202, USA.
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Irrgang ME, Davis C, Kasson PM. gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support. PLoS Comput Biol 2022; 18:e1009835. [PMID: 35157693 PMCID: PMC8880871 DOI: 10.1371/journal.pcbi.1009835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 02/25/2022] [Accepted: 01/16/2022] [Indexed: 11/19/2022] Open
Abstract
Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is enabled by default in current versions of the software. Here we describe gmxapi 0.3 and later. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, the API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages.
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Affiliation(s)
- M. Eric Irrgang
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Caroline Davis
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Peter M. Kasson
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- * E-mail:
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12
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Hernandez-Castro LE, Villacís AG, Jacobs A, Cheaib B, Day CC, Ocaña-Mayorga S, Yumiseva CA, Bacigalupo A, Andersson B, Matthews L, Landguth EL, Costales JA, Llewellyn MS, Grijalva MJ. Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting. PLoS Genet 2022; 18:e1010019. [PMID: 35120121 PMCID: PMC8849464 DOI: 10.1371/journal.pgen.1010019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/16/2022] [Accepted: 01/06/2022] [Indexed: 12/19/2022] Open
Abstract
Accurate prediction of vectors dispersal, as well as identification of adaptations that allow blood-feeding vectors to thrive in built environments, are a basis for effective disease control. Here we adopted a landscape genomics approach to assay gene flow, possible local adaptation, and drivers of population structure in Rhodnius ecuadoriensis, an important vector of Chagas disease. We used a reduced-representation sequencing technique (2b-RADseq) to obtain 2,552 SNP markers across 272 R. ecuadoriensis samples from 25 collection sites in southern Ecuador. Evidence of high and directional gene flow between seven wild and domestic population pairs across our study site indicates insecticide-based control will be hindered by repeated re-infestation of houses from the forest. Preliminary genome scans across multiple population pairs revealed shared outlier loci potentially consistent with local adaptation to the domestic setting, which we mapped to genes involved with embryogenesis and saliva production. Landscape genomic models showed elevation is a key barrier to R. ecuadoriensis dispersal. Together our results shed early light on the genomic adaptation in triatomine vectors and facilitate vector control by predicting that spatially-targeted, proactive interventions would be more efficacious than current, reactive approaches. Re-infestation of recently insecticide-treated houses by wild/secondary triatomine, their potential adaptation to this new environment and capabilities to geographically disperse across multiple human communities jeopardise sustainable Chagas disease control. This is the first study in Chagas disease vectors that identifies genomic regions possibly linked to adaptations to the built environment and describes landscape drivers for accurate prediction of geographic dispersal. We sampled multiple domestic and wild Rhodnius ecuadoriensis population pairs across a mountainous terrain in southern Ecuador. We evidenced that triatomine movement from forest to built enviroments does occur at a high rate. In these highly connected population pairs we detected loci possibly linked to local adaptation among the genomic makers we evaluated and in doing so we pave the way for future triatomine genomic research. We highlighted that current haphazardous vector control in the zone will be hindered by reinfestation of triatomines from the forest. Instead, we recommend frequent and spatially-targeted vector control and provided a landacape genomic model that identifies highly connected and isolated triatomine populations to facilitate efficient vector control.
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Affiliation(s)
- Luis E. Hernandez-Castro
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- The Epidemiology, Economics and Risk Assessment Group, The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Midlothian, United Kingdom
- * E-mail: (LEH-C); (MSL)
| | - Anita G. Villacís
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- Department of Natural Resources and the Environment, Cornell University, Ithaca, New York, United States of America
| | - Bachar Cheaib
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Casey C. Day
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
| | - Sofía Ocaña-Mayorga
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Cesar A. Yumiseva
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Antonella Bacigalupo
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Louise Matthews
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Erin L. Landguth
- Computational Ecology Lab, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
- Center for Population Health Research, School of Public and Community Health Sciences, University of Montana, Missoula, Montana, United States of America
| | - Jaime A. Costales
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Martin S. Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (LEH-C); (MSL)
| | - Mario J. Grijalva
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Infectious and Tropical Disease Institute, Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, United States of America
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13
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Zhang M, Liu S, Miao Z, Han F, Gottardo R, Sun W. IDEAS: individual level differential expression analysis for single-cell RNA-seq data. Genome Biol 2022; 23:33. [PMID: 35073995 PMCID: PMC8784862 DOI: 10.1186/s13059-022-02605-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 07/15/2021] [Accepted: 01/06/2022] [Indexed: 12/29/2022] Open
Abstract
We consider an increasingly popular study design where single-cell RNA-seq data are collected from multiple individuals and the question of interest is to find genes that are differentially expressed between two groups of individuals. Towards this end, we propose a statistical method named IDEAS (individual level differential expression analysis for scRNA-seq). For each gene, IDEAS summarizes its expression in each individual by a distribution and then assesses whether these individual-specific distributions are different between two groups of individuals. We apply IDEAS to assess gene expression differences of autism patients versus controls and COVID-19 patients with mild versus severe symptoms.
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Affiliation(s)
- Mengqi Zhang
- Public Health Science Division, Fred Hutchison Cancer Research Center, Seattle, USA
- Present Address: University of Pennsylvania, Philadelphia, 19104, USA
| | - Si Liu
- Public Health Science Division, Fred Hutchison Cancer Research Center, Seattle, USA
| | - Zhen Miao
- Department of Statistics, University of Washington, Seattle, USA
| | - Fang Han
- Department of Statistics, University of Washington, Seattle, USA
| | - Raphael Gottardo
- Biomedical Data Sciences Center, Lausanne University Hospital, Lausanne, Switzerland
| | - Wei Sun
- Public Health Science Division, Fred Hutchison Cancer Research Center, Seattle, USA.
- Department of Biostatistics, University of Washington, Seattle, USA.
- Department of Biostatistics, University of North Carolina, Chapel Hill, USA.
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14
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Collins MD, Cui EH, Hyun SW, Wong WK. A model-based approach to designing developmental toxicology experiments using sea urchin embryos. Arch Toxicol 2022; 96:919-932. [PMID: 35022802 PMCID: PMC8850257 DOI: 10.1007/s00204-021-03201-1] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/09/2021] [Indexed: 11/28/2022]
Abstract
The key aim of this paper is to suggest a more quantitative approach to designing a dose–response experiment, and more specifically, a concentration–response experiment. The work proposes a departure from the traditional experimental design to determine a dose–response relationship in a developmental toxicology study. It is proposed that a model-based approach to determine a dose–response relationship can provide the most accurate statistical inference for the underlying parameters of interest, which may be estimating one or more model parameters or pre-specified functions of the model parameters, such as lethal dose, at maximal efficiency. When the design criterion or criteria can be determined at the onset, there are demonstrated efficiency gains using a more carefully selected model-based optimal design as opposed to an ad-hoc empirical design. As an illustration, a model-based approach was theoretically used to construct efficient designs for inference in a developmental toxicity study of sea urchin embryos exposed to trimethoprim. This study compares and contrasts the results obtained using model-based optimal designs versus an ad-hoc empirical design.
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Affiliation(s)
- Michael D Collins
- Department of Environment Health Sciences and Molecular Toxicology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Elvis Han Cui
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Seung Won Hyun
- Research Biostatistics, Johnson and Johnson Medical Devices, Irvine, CA, 92618, USA
| | - Weng Kee Wong
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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15
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Elorbany R, Popp JM, Rhodes K, Strober BJ, Barr K, Qi G, Gilad Y, Battle A. Single-cell sequencing reveals lineage-specific dynamic genetic regulation of gene expression during human cardiomyocyte differentiation. PLoS Genet 2022; 18:e1009666. [PMID: 35061661 PMCID: PMC8809621 DOI: 10.1371/journal.pgen.1009666] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 02/02/2022] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
Dynamic and temporally specific gene regulatory changes may underlie unexplained genetic associations with complex disease. During a dynamic process such as cellular differentiation, the overall cell type composition of a tissue (or an in vitro culture) and the gene regulatory profile of each cell can both experience significant changes over time. To identify these dynamic effects in high resolution, we collected single-cell RNA-sequencing data over a differentiation time course from induced pluripotent stem cells to cardiomyocytes, sampled at 7 unique time points in 19 human cell lines. We employed a flexible approach to map dynamic eQTLs whose effects vary significantly over the course of bifurcating differentiation trajectories, including many whose effects are specific to one of these two lineages. Our study design allowed us to distinguish true dynamic eQTLs affecting a specific cell lineage from expression changes driven by potentially non-genetic differences between cell lines such as cell composition. Additionally, we used the cell type profiles learned from single-cell data to deconvolve and re-analyze data from matched bulk RNA-seq samples. Using this approach, we were able to identify a large number of novel dynamic eQTLs in single cell data while also attributing dynamic effects in bulk to a particular lineage. Overall, we found that using single cell data to uncover dynamic eQTLs can provide new insight into the gene regulatory changes that occur among heterogeneous cell types during cardiomyocyte differentiation.
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Affiliation(s)
- Reem Elorbany
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, Illinois, United States of America
| | - Joshua M. Popp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Katherine Rhodes
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Benjamin J. Strober
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kenneth Barr
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - Guanghao Qi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
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16
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Flynn ED, Tsu AL, Kasela S, Kim-Hellmuth S, Aguet F, Ardlie KG, Bussemaker HJ, Mohammadi P, Lappalainen T. Transcription factor regulation of eQTL activity across individuals and tissues. PLoS Genet 2022; 18:e1009719. [PMID: 35100260 PMCID: PMC8830792 DOI: 10.1371/journal.pgen.1009719] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 02/10/2022] [Accepted: 01/06/2022] [Indexed: 11/18/2022] Open
Abstract
Tens of thousands of genetic variants associated with gene expression (cis-eQTLs) have been discovered in the human population. These eQTLs are active in various tissues and contexts, but the molecular mechanisms of eQTL variability are poorly understood, hindering our understanding of genetic regulation across biological contexts. Since many eQTLs are believed to act by altering transcription factor (TF) binding affinity, we hypothesized that analyzing eQTL effect size as a function of TF level may allow discovery of mechanisms of eQTL variability. Using GTEx Consortium eQTL data from 49 tissues, we analyzed the interaction between eQTL effect size and TF level across tissues and across individuals within specific tissues and generated a list of 10,098 TF-eQTL interactions across 2,136 genes that are supported by at least two lines of evidence. These TF-eQTLs were enriched for various TF binding measures, supporting with orthogonal evidence that these eQTLs are regulated by the implicated TFs. We also found that our TF-eQTLs tend to overlap genes with gene-by-environment regulatory effects and to colocalize with GWAS loci, implying that our approach can help to elucidate mechanisms of context-specificity and trait associations. Finally, we highlight an interesting example of IKZF1 TF regulation of an APBB1IP gene eQTL that colocalizes with a GWAS signal for blood cell traits. Together, our findings provide candidate TF mechanisms for a large number of eQTLs and offer a generalizable approach for researchers to discover TF regulators of genetic variant effects in additional QTL datasets.
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Affiliation(s)
- Elise D. Flynn
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
| | - Athena L. Tsu
- New York Genome Center, New York, New York, United States of America
- Department of Biomedical Engineering, Columbia University, New York, New York, United States of America
| | - Silva Kasela
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
| | - Sarah Kim-Hellmuth
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kristin G. Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Harmen J. Bussemaker
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (PM); (TL)
| | - Tuuli Lappalainen
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- New York Genome Center, New York, New York, United States of America
- KTH Royal Institute of Technology, Stockholm, Sweden
- * E-mail: (PM); (TL)
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17
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Colonnetta MM, Goyal Y, Johnson HE, Syal S, Schedl P, Deshpande G. Preformation and epigenesis converge to specify primordial germ cell fate in the early Drosophila embryo. PLoS Genet 2022; 18:e1010002. [PMID: 34986144 PMCID: PMC8765614 DOI: 10.1371/journal.pgen.1010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/18/2022] [Accepted: 12/17/2021] [Indexed: 11/24/2022] Open
Abstract
A critical step in animal development is the specification of primordial germ cells (PGCs), the precursors of the germline. Two seemingly mutually exclusive mechanisms are implemented across the animal kingdom: epigenesis and preformation. In epigenesis, PGC specification is non-autonomous and depends on extrinsic signaling pathways. The BMP pathway provides the key PGC specification signals in mammals. Preformation is autonomous and mediated by determinants localized within PGCs. In Drosophila, a classic example of preformation, constituents of the germ plasm localized at the embryonic posterior are thought to be both necessary and sufficient for proper determination of PGCs. Contrary to this longstanding model, here we show that these localized determinants are insufficient by themselves to direct PGC specification in blastoderm stage embryos. Instead, we find that the BMP signaling pathway is required at multiple steps during the specification process and functions in conjunction with components of the germ plasm to orchestrate PGC fate. Proper specification of primordial germ cells (PGCs) is crucial as PGCs serve as the precursors of germline stem cells. To specify PGC fate, invertebrates rely upon cell autonomous preformation involving maternally deposited germ plasm. In Drosophila melanogaster, to insulate newly formed PGCs from the adverse effects of the cell-cell signaling pathways, germ plasm determinants silence transcription and attenuate the cell cycle. However, our data on the BMP signaling pathway challenge this long-held view of PGC specification and suggest that appropriate specification of embryonic PGCs is sensitive to the BMP ligand, decapentaplegic (dpp), and its cognate receptor, thickveins. We find that PGCs are not only capable of responding to BMP signals from the soma, but also that these signals impact the proper determination of the germ cells. Based on these unanticipated similarities between mammals and flies, we propose a model integrating contribution of both the cell-autonomous (preformation) and non-autonomous (epigenesis) pathways during PGC determination. Consistent with the model, we have observed dominant genetic interactions between, oskar, the maternal determinant of PGC fate, and the BMP pathway ligand dpp.
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Affiliation(s)
- Megan M. Colonnetta
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Yogesh Goyal
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Heath E. Johnson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Sapna Syal
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Girish Deshpande
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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18
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Ivanov SS, Castore R, Juarez Rodriguez MD, Circu M, Dragoi AM. Neisseria gonorrhoeae subverts formin-dependent actin polymerization to colonize human macrophages. PLoS Pathog 2021; 17:e1010184. [PMID: 34962968 PMCID: PMC8746766 DOI: 10.1371/journal.ppat.1010184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/10/2022] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Dynamic reorganization of the actin cytoskeleton dictates plasma membrane morphogenesis and is frequently subverted by bacterial pathogens for entry and colonization of host cells. The human-adapted bacterial pathogen Neisseria gonorrhoeae can colonize and replicate when cultured with human macrophages, however the basic understanding of how this process occurs is incomplete. N. gonorrhoeae is the etiological agent of the sexually transmitted disease gonorrhea and tissue resident macrophages are present in the urogenital mucosa, which is colonized by the bacteria. We uncovered that when gonococci colonize macrophages, they can establish an intracellular or a cell surface-associated niche that support bacterial replication independently. Unlike other intracellular bacterial pathogens, which enter host cells as single bacterium, establish an intracellular niche and then replicate, gonococci invade human macrophages as a colony. Individual diplococci are rapidly phagocytosed by macrophages and transported to lysosomes for degradation. However, we found that surface-associated gonococcal colonies of various sizes can invade macrophages by triggering actin skeleton rearrangement resulting in plasma membrane invaginations that slowly engulf the colony. The resulting intracellular membrane-bound organelle supports robust bacterial replication. The gonococci-occupied vacuoles evaded fusion with the endosomal compartment and were enveloped by a network of actin filaments. We demonstrate that gonococcal colonies invade macrophages via a process mechanistically distinct from phagocytosis that is regulated by the actin nucleating factor FMNL3 and is independent of the Arp2/3 complex. Our work provides insights into the gonococci life-cycle in association with human macrophages and defines key host determinants for macrophage colonization. During infection, the human-adapted bacterial pathogen Neisseria gonorrhoeae and causative agent of gonorrhea can invade the submucosa of the urogenital tract where it encounters tissue-resident innate immune sentinels, such as macrophages and neutrophils. Instead of eliminating gonococci, macrophages support robust bacterial replication. Here, we detail the life cycle of N. gonorrhoeae in association with macrophages and define key regulators that govern the colonization processes. We uncovered that N. gonorrhoeae establishes two distinct subcellular niches that support bacterial replication autonomously–one niche was on the macrophage surface and another one was intracellular. Gonococci subverted the host actin cytoskeleton through the actin nucleating factor FMNL3 to invade colonized macrophages and occupy a membrane-bound intracellular organelle. We propose that N. gonorrhoeae ability to occupy distinct subcellular niches when colonizing macrophages likely confers broad protection against multiple host defense responses.
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Affiliation(s)
- Stanimir S. Ivanov
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center—Shreveport, Shreveport, Louisiana, United States of America
- * E-mail: (SSI); (AMD)
| | - Reneau Castore
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center—Shreveport, Shreveport, Louisiana, United States of America
| | - Maria Dolores Juarez Rodriguez
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center—Shreveport, Shreveport, Louisiana, United States of America
| | - Magdalena Circu
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center—Shreveport, Shreveport, Louisiana, United States of America
| | - Ana-Maria Dragoi
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center—Shreveport, Shreveport, Louisiana, United States of America
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center—Shreveport, Shreveport, Louisiana, United States of America
- * E-mail: (SSI); (AMD)
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19
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Vallejos MJ, Eadaim A, Hahm ET, Tsunoda S. Age-related changes in Kv4/Shal and Kv1/Shaker expression in Drosophila and a role for reactive oxygen species. PLoS One 2021; 16:e0261087. [PMID: 34932577 PMCID: PMC8691634 DOI: 10.1371/journal.pone.0261087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
Age-related changes in ion channel expression are likely to affect neuronal signaling. Here, we examine how age affects Kv4/Shal and Kv1/Shaker K+ channel protein levels in Drosophila. We show that Kv4/Shal protein levels decline sharply from 3 days to 10 days, then more gradually from 10 to 40 days after eclosion. In contrast, Kv1/Shaker protein exhibits a transient increase at 10 days that then stabilizes and eventually declines at 40 days. We present data that begin to show a relationship between reactive oxygen species (ROS), Kv4/Shal, and locomotor performance. We show that Kv4/Shal levels are negatively affected by ROS, and that over-expression of Catalase or RNAi knock-down of the ROS-generating enzyme, Nicotinamide Adenine Dinucleotide Phosphate (NADPH) Oxidase (NOX), can attenuate the loss of Kv4/Shal protein. Finally, we compare levels of Kv4.2 and Kv4.3 in the hippocampus, olfactory bulb, cerebellum, and motor cortex of mice aged 6 weeks and 1 year. While there was no global decline in Kv4.2/4.3 that parallels what we report in Drosophila, we did find that Kv4.2/4.3 are differentially affected in various brain regions; this survey of changes may help inform mammalian studies that examine neuronal function with age.
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Affiliation(s)
- Maximiliano J. Vallejos
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Abdunaser Eadaim
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Eu-Teum Hahm
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Susan Tsunoda
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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20
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Chang T, Draper JM, Van den Bout A, Kephart E, Maul-Newby H, Vasquez Y, Woodbury J, Randi S, Pedersen M, Nave M, La S, Gallagher N, McCabe MM, Dhillon N, Bjork I, Luttrell M, Dang F, MacMillan JB, Green R, Miller E, Kilpatrick AM, Vaske O, Stone MD, Sanford JR. A method for campus-wide SARS-CoV-2 surveillance at a large public university. PLoS One 2021; 16:e0261230. [PMID: 34919584 PMCID: PMC8682906 DOI: 10.1371/journal.pone.0261230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
The systematic screening of asymptomatic and pre-symptomatic individuals is a powerful tool for controlling community transmission of infectious disease on college campuses. Faced with a paucity of testing in the beginning of the COVID-19 pandemic, many universities developed molecular diagnostic laboratories focused on SARS-CoV-2 diagnostic testing on campus and in their broader communities. We established the UC Santa Cruz Molecular Diagnostic Lab in early April 2020 and began testing clinical samples just five weeks later. Using a clinically-validated laboratory developed test (LDT) that avoided supply chain constraints, an automated sample pooling and processing workflow, and a custom laboratory information management system (LIMS), we expanded testing from a handful of clinical samples per day to thousands per day with the testing capacity to screen our entire campus population twice per week. In this report we describe the technical, logistical, and regulatory processes that enabled our pop-up lab to scale testing and reporting capacity to thousands of tests per day.
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Affiliation(s)
- Terren Chang
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jolene M. Draper
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Anouk Van den Bout
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ellen Kephart
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Hannah Maul-Newby
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Yvonne Vasquez
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jason Woodbury
- Thirdwave Analytics, San Francisco, California, United States of America
| | - Savanna Randi
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Martina Pedersen
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Maeve Nave
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Scott La
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Natalie Gallagher
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Molly M. McCabe
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Namrita Dhillon
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Isabel Bjork
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael Luttrell
- Business and Accounting Services, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Frank Dang
- University of California Davis, Davis, California, United States of America
| | - John B. MacMillan
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Ralph Green
- University of California Davis, Davis, California, United States of America
| | - Elizabeth Miller
- Student Health Services, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Auston M. Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Olena Vaske
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Michael D. Stone
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jeremy R. Sanford
- Colligan Clinical Diagnostic Laboratory, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, California, United States of America
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21
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Hinkle ER, Essader TO, Gentile GM, Giudice J. ViaFuse: Fiji macros to calculate skeletal muscle cell viability and fusion index. Skelet Muscle 2021; 11:28. [PMID: 34915930 PMCID: PMC8675483 DOI: 10.1186/s13395-021-00284-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/03/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Measuring biological features of skeletal muscle cells is difficult because of their unique morphology and multinucleate nature upon differentiation. Here, we developed a new Fiji macro package called ViaFuse (that stands for viability and fusion) to measure skeletal muscle cell viability and differentiation. To test ViaFuse, we utilized immunofluorescence images of differentiated myotubes where the capping actin protein of muscle z-line subunit beta (CAPZB) was depleted in comparison with control cells. RESULTS We compared the values achieved using the ViaFuse macros first with manual quantification performed by researchers and second with those obtained utilizing the MATLAB muscle-centric software MyoCount. We observed a high degree of correlation between all methods of quantification. CONCLUSIONS ViaFuse can detect the borders of myotubes and identify nuclear clumps which have been limitations of previous muscle-centric imaging software. The ViaFuse macros require little computer power or space to run and user inputs to the ViaFuse macros are minimal, thereby automating the analysis process in a quick, easy, and accurate fashion. Additionally, the ViaFuse macros work with Fiji, an existing imaging software widely used by skeletal muscle researchers. Furthermore, ViaFuse is compatible with many computer systems, has a very intuitive interface, and does not require prior complex mathematical knowledge. Therefore, we propose ViaFuse as a robust and meticulous method to quantify skeletal muscle cell viability and differentiation.
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Affiliation(s)
- Emma Rose Hinkle
- Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Tasneem Omar Essader
- Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gabrielle Marie Gentile
- Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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22
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Chu TH, Khairallah C, Shieh J, Cho R, Qiu Z, Zhang Y, Eskiocak O, Thanassi DG, Kaplan MH, Beyaz S, Yang VW, Bliska JB, Sheridan BS. γδ T cell IFNγ production is directly subverted by Yersinia pseudotuberculosis outer protein YopJ in mice and humans. PLoS Pathog 2021; 17:e1010103. [PMID: 34871329 PMCID: PMC8648121 DOI: 10.1371/journal.ppat.1010103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
Yersinia pseudotuberculosis is a foodborne pathogen that subverts immune function by translocation of Yersinia outer protein (Yop) effectors into host cells. As adaptive γδ T cells protect the intestinal mucosa from pathogen invasion, we assessed whether Y. pseudotuberculosis subverts these cells in mice and humans. Tracking Yop translocation revealed that the preferential delivery of Yop effectors directly into murine Vγ4 and human Vδ2+ T cells inhibited anti-microbial IFNγ production. Subversion was mediated by the adhesin YadA, injectisome component YopB, and translocated YopJ effector. A broad anti-pathogen gene signature and STAT4 phosphorylation levels were inhibited by translocated YopJ. Thus, Y. pseudotuberculosis attachment and translocation of YopJ directly into adaptive γδ T cells is a major mechanism of immune subversion in mice and humans. This study uncovered a conserved Y. pseudotuberculosis pathway that subverts adaptive γδ T cell function to promote pathogenicity. Unconventional γδ T cells are a dynamic immune population important for mucosal protection of the intestine against invading pathogens. We determined that the foodborne pathogen Y. pseudotuberculosis preferentially targets an adaptive subset of these cells to subvert immune function. We found that direct injection of Yersinia outer proteins (Yop) into adaptive γδ T cells inhibited their anti-pathogen functions. We screened all Yop effectors and identified YopJ as the sole effector to inhibit adaptive γδ T cell production of IFNγ. We determined that adaptive γδ T cell subversion occurred by limiting activation of the transcription factor STAT4. When we infected mice with Y. pseudotuberculosis expressing an inactive YopJ, this enhanced the adaptive γδ T cell response and led to greater cytokine production from this subset of cells to aid mouse recovery. This mechanism of immune evasion appears conserved in humans as direct injection of Y. pseudotuberculosis YopJ into human γδ T cells inhibited cytokine production. This suggested to us that Y. pseudotuberculosis actively inhibits the adaptive γδ T cell response through YopJ as a mechanism to evade immune surveillance at the site of pathogen invasion.
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Affiliation(s)
- Timothy H. Chu
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Camille Khairallah
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Jason Shieh
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Rhea Cho
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Zhijuan Qiu
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Yue Zhang
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Onur Eskiocak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - David G. Thanassi
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - Mark H. Kaplan
- Department of Microbiology and Immunology, School of Medicine, Indiana University, Indianapolis, Indiana, United States of America
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Vincent W. Yang
- Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
| | - James B. Bliska
- Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Dartmouth, New Hampshire, United States of America
| | - Brian S. Sheridan
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- Center for Infectious Diseases, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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23
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Osheroff N. The COVID-19 Pandemic: a Year Lost, or a Year Found? Med Sci Educ 2021; 31:21-26. [PMID: 34466278 PMCID: PMC8390108 DOI: 10.1007/s40670-021-01392-x] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
This commentary is based on the Leadership Plenary at the IAMSE 2021 Virtual Conference and describes the response of the International Association of Medical Science Educators (IAMSE) to the COVID-19 pandemic.
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Affiliation(s)
- Neil Osheroff
- Departments of Biochemistry and Medicine (Hematology/Oncology), Vanderbilt University School of Medicine, Nashville, TN 37232 USA
- VA Tennessee Valley Healthcare System, Nashville, TN 37212 USA
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24
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Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B. recount3: summaries and queries for large-scale RNA-seq expression and splicing. Genome Biol 2021; 22:323. [PMID: 34844637 PMCID: PMC8628444 DOI: 10.1186/s13059-021-02533-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio .
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Affiliation(s)
- Christopher Wilks
- Department of Computer Science, Johns Hopkins University, Baltimore, USA
| | - Shijie C Zheng
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | | | - Rone Charles
- Department of Computer Science, Johns Hopkins University, Baltimore, USA
| | - Brad Solomon
- Thomas M. Siebel Center for Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan P Ling
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Eddie Luidy Imada
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - David Zhang
- Institute of Child Health, University College London (UCL), London, UK
| | | | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Andrew E Jaffe
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
- Lieber Institute for Brain Development, Baltimore, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Abhinav Nellore
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
- Department of Surgery, Oregon Health & Science University, Portland, OR, USA
| | | | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA.
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA.
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, USA.
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25
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Zimmermann RC, Sardiu ME, Manton CA, Miah MS, Banks CAS, Adams MK, Koestler DC, Hurst DR, Edmonds MD, Washburn MP, Welch DR. Perturbation of BRMS1 interactome reveals pathways that impact metastasis. PLoS One 2021; 16:e0259128. [PMID: 34788285 PMCID: PMC8598058 DOI: 10.1371/journal.pone.0259128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/12/2021] [Indexed: 11/25/2022] Open
Abstract
Breast Cancer Metastasis Suppressor 1 (BRMS1) expression is associated with longer patient survival in multiple cancer types. Understanding BRMS1 functionality will provide insights into both mechanism of action and will enhance potential therapeutic development. In this study, we confirmed that the C-terminus of BRMS1 is critical for metastasis suppression and hypothesized that critical protein interactions in this region would explain its function. Phosphorylation status at S237 regulates BRMS1 protein interactions related to a variety of biological processes, phenotypes [cell cycle (e.g., CDKN2A), DNA repair (e.g., BRCA1)], and metastasis [(e.g., TCF2 and POLE2)]. Presence of S237 also directly decreased MDA-MB-231 breast carcinoma migration in vitro and metastases in vivo. The results add significantly to our understanding of how BRMS1 interactions with Sin3/HDAC complexes regulate metastasis and expand insights into BRMS1's molecular role, as they demonstrate BRMS1 C-terminus involvement in distinct protein-protein interactions.
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Affiliation(s)
- Rosalyn C. Zimmermann
- Department of Cancer Biology, The Kansas University Medical Center, Kansas City, KS, United States of America
| | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biostatistics and Data Science, The Kansas University Medical Center, Kansas City, KS, United States of America
- The University of Kansas Cancer Center, Kansas City, KS, United States of America
| | - Christa A. Manton
- Department of Cancer Biology, The Kansas University Medical Center, Kansas City, KS, United States of America
- Pathology Department, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Biology, Baker University, Baldwin City, KS, United States of America
| | - Md. Sayem Miah
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, University of Arkansas for Health Sciences, Little Rock, AR, United States of America
| | - Charles A. S. Banks
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Mark K. Adams
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Devin C. Koestler
- Department of Biostatistics and Data Science, The Kansas University Medical Center, Kansas City, KS, United States of America
- The University of Kansas Cancer Center, Kansas City, KS, United States of America
| | - Douglas R. Hurst
- Pathology Department, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Mick D. Edmonds
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael P. Washburn
- Department of Cancer Biology, The Kansas University Medical Center, Kansas City, KS, United States of America
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- The University of Kansas Cancer Center, Kansas City, KS, United States of America
| | - Danny R. Welch
- Department of Cancer Biology, The Kansas University Medical Center, Kansas City, KS, United States of America
- The University of Kansas Cancer Center, Kansas City, KS, United States of America
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26
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Rivera-Ortiz J, Pla-Tenorio J, Cruz ML, Colon K, Perez-Morales J, Rodriguez JA, Martinez-Sicari J, Noel RJ. Blockade of beta adrenergic receptors protects the blood brain barrier and reduces systemic pathology caused by HIV-1 Nef protein. PLoS One 2021; 16:e0259446. [PMID: 34784367 PMCID: PMC8594844 DOI: 10.1371/journal.pone.0259446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/19/2021] [Indexed: 01/14/2023] Open
Abstract
Combination antiretroviral therapy (cART) targets viral replication, but early viral protein production by astrocytes may still occur and contribute to the progression of HIV-1 associated neurocognitive disorders and secondary complications seen in patients receiving cART. In prior work with our model, astrocytic HIV-1 Nef expression exhibits neurotoxic effects leading to neurological damage, learning impairment, and immune upregulation that induces inflammation in the lungs and small intestine (SI). In this follow-up study, we focus on the sympathetic nervous system (SNS) as the important branch for peripheral inflammation resulting from astrocytic Nef expression. Male and female Sprague Dawley rats were infused with transfected astrocytes to produce Nef. The rats were divided in four groups: Nef, Nef + propranolol, propranolol and naïve. The beta-adrenergic blocker, propranolol, was administered for 3 consecutive days, starting one day prior to surgery. Two days after the surgery, the rats were sacrificed, and then blood, brain, small intestine (SI), and lung tissues were collected. Levels of IL-1β were higher in both male and female rats, and treatment with propranolol restored IL-1β to basal levels. We observed that Nef expression decreased staining of the tight junction protein claudin-5 in brain tissue while animals co-treated with propranolol restored claudin-5 expression. Lungs and SI of rats in the Nef group showed histological signs of damage including larger Peyer's Patches, increased tissue thickness, and infiltration of immune cells; these findings were abrogated by propranolol co-treatment. Results suggest that interruption of the beta adrenergic signaling reduces the peripheral organ inflammation caused after Nef expression in astrocytes of the brain.
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Affiliation(s)
- Jocelyn Rivera-Ortiz
- HIV-1 Immunopathogenesis Laboratory, The Wistar Institute, Philadelphia, PA, United States of America
| | - Jessalyn Pla-Tenorio
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
| | - Myrella L. Cruz
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
| | - Krystal Colon
- HIV-1 Immunopathogenesis Laboratory, The Wistar Institute, Philadelphia, PA, United States of America
| | - Jaileene Perez-Morales
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
| | - Julio A. Rodriguez
- Cooper University Hospital Department of Orthopaedic Surgery, Camden, NJ, United States of America
| | - Jorge Martinez-Sicari
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
| | - Richard J. Noel
- Department of Basic Sciences, Ponce Health Sciences University, Ponce Research Institute, Ponce, Puerto Rico
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27
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Kurosaki T, Sakano H, Pröschel C, Wheeler J, Hewko A, Maquat LE. NMD abnormalities during brain development in the Fmr1-knockout mouse model of fragile X syndrome. Genome Biol 2021; 22:317. [PMID: 34784943 PMCID: PMC8597091 DOI: 10.1186/s13059-021-02530-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 07/16/2021] [Accepted: 10/28/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Fragile X syndrome (FXS) is an intellectual disability attributable to loss of fragile X protein (FMRP). We previously demonstrated that FMRP binds mRNAs targeted for nonsense-mediated mRNA decay (NMD) and that FMRP loss results in hyperactivated NMD and inhibition of neuronal differentiation in human stem cells. RESULTS We show here that NMD is hyperactivated during the development of the cerebral cortex, hippocampus, and cerebellum in the Fmr1-knockout (KO) mouse during embryonic and early postnatal periods. Our findings demonstrate that NMD regulates many neuronal mRNAs that are important for mouse brain development. CONCLUSIONS We reveal the abnormal regulation of these mRNAs in the Fmr1-KO mouse, a model of FXS, and highlight the importance of early intervention.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642 USA
- Center for RNA Biology, University of Rochester, Rochester, NY 14642 USA
| | - Hitomi Sakano
- Center for RNA Biology, University of Rochester, Rochester, NY 14642 USA
- Department of Otolaryngology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642 USA
| | - Christoph Pröschel
- Department of Biomedical Genetics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642 USA
- Stem Cell and Regenerative Medicine Institute, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642 USA
| | - Jason Wheeler
- Center for RNA Biology, University of Rochester, Rochester, NY 14642 USA
- Department of Otolaryngology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642 USA
| | - Alexander Hewko
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642 USA
- Center for RNA Biology, University of Rochester, Rochester, NY 14642 USA
| | - Lynne E. Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642 USA
- Center for RNA Biology, University of Rochester, Rochester, NY 14642 USA
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28
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De La Rosa-Reyes V, Duprey-Díaz MV, Blagburn JM, Blanco RE. Retinoic acid treatment recruits macrophages and increases axonal regeneration after optic nerve injury in the frog Rana pipiens. PLoS One 2021; 16:e0255196. [PMID: 34739478 PMCID: PMC8570512 DOI: 10.1371/journal.pone.0255196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/21/2021] [Indexed: 11/18/2022] Open
Abstract
Retinoic acid (RA) plays major roles during nervous system development, and during regeneration of the adult nervous system. We have previously shown that components of the RA signaling pathway are upregulated after optic nerve injury, and that exogenous application of all-trans retinoic acid (ATRA) greatly increases the survival of axotomized retinal ganglion cells (RGCs). The objective of the present study is to investigate the effects of ATRA application on the macrophages in the optic nerve after injury, and to determine whether this affects axonal regeneration. The optic nerve was crushed and treated with PBS, ATRA and/or clodronate-loaded liposomes. Nerves were examined at one and two weeks after axotomy with light microscopy, immunocytochemistry and electron microscopy. ATRA application to the optic nerve caused transient increases in the number of macrophages and microglia one week after injury. The macrophages are consistently labeled with M2-type markers, and have considerable phagocytic activity. ATRA increased ultrastructural features of ongoing phagocytic activity in macrophages at one and two weeks. ATRA treatment also significantly increased the numbers of regenerating GAP-43-labeled axons. Clodronate liposome treatment depleted macrophage numbers by 80%, completely eliminated the ATRA-mediated increase in axonal regeneration, and clodronate treatment alone decreased axonal numbers by 30%. These results suggest that the success of axon regeneration is partially dependent on the presence of debris-phagocytosing macrophages, and that the increases in regeneration caused by ATRA are in part due to their increased numbers. Further studies will examine whether macrophage depletion affects RGC survival.
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Affiliation(s)
- Valeria De La Rosa-Reyes
- Department of Anatomy and Neurobiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States of America
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, United States of America
| | - Mildred V. Duprey-Díaz
- Department of Anatomy and Neurobiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States of America
| | - Jonathan M. Blagburn
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, United States of America
| | - Rosa E. Blanco
- Department of Anatomy and Neurobiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States of America
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, United States of America
- * E-mail:
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29
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Schwartz ML, Davis MW, Rich MS, Jorgensen EM. High-efficiency CRISPR gene editing in C. elegans using Cas9 integrated into the genome. PLoS Genet 2021; 17:e1009755. [PMID: 34748534 PMCID: PMC8601624 DOI: 10.1371/journal.pgen.1009755] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/18/2021] [Accepted: 10/16/2021] [Indexed: 11/24/2022] Open
Abstract
Gene editing in C. elegans using plasmid-based CRISPR reagents requires microinjection of many animals to produce a single edit. Germline silencing of plasmid-borne Cas9 is a major cause of inefficient editing. Here, we present a set of C. elegans strains that constitutively express Cas9 in the germline from an integrated transgene. These strains markedly improve the success rate for plasmid-based CRISPR edits. For simple, short homology arm GFP insertions, 50-100% of injected animals typically produce edited progeny, depending on the target locus. Template-guided editing from an extrachromosomal array is maintained over multiple generations. We have built strains with the Cas9 transgene on multiple chromosomes. Additionally, each Cas9 locus also contains a heatshock-driven Cre recombinase for selectable marker removal and a bright fluorescence marker for easy outcrossing. These integrated Cas9 strains greatly reduce the workload for producing individual genome edits.
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Affiliation(s)
- Matthew L. Schwartz
- Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - M. Wayne Davis
- Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew S. Rich
- Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Erik M. Jorgensen
- Howard Hughes Medical Institute and School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
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30
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Ho EKH, Bellis ES, Calkins J, Adrion JR, Latta IV LC, Schaack S. Engines of change: Transposable element mutation rates are high and variable within Daphnia magna. PLoS Genet 2021; 17:e1009827. [PMID: 34723969 PMCID: PMC8594854 DOI: 10.1371/journal.pgen.1009827] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/16/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) represent a major portion of most eukaryotic genomes, yet little is known about their mutation rates or how their activity is shaped by other evolutionary forces. Here, we compare short- and long-term patterns of genome-wide mutation accumulation (MA) of TEs among 9 genotypes from three populations of Daphnia magna from across a latitudinal gradient. While the overall proportion of the genome comprised of TEs is highly similar among genotypes from Finland, Germany, and Israel, populations are distinguishable based on patterns of insertion site polymorphism. Our direct rate estimates indicate TE movement is highly variable (net rates ranging from -11.98 to 12.79 x 10-5 per copy per generation among genotypes), differing both among populations and TE families. Although gains outnumber losses when selection is minimized, both types of events appear to be highly deleterious based on their low frequency in control lines where propagation is not limited to random, single-progeny descent. With rate estimates 4 orders of magnitude higher than base substitutions, TEs clearly represent a highly mutagenic force in the genome. Quantifying patterns of intra- and interspecific variation in TE mobility with and without selection provides insight into a powerful mechanism generating genetic variation in the genome.
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Affiliation(s)
- Eddie K. H. Ho
- Department of Biology, Reed College, Portland, Oregon, United States of America
| | - Emily S. Bellis
- Department of Biology, Reed College, Portland, Oregon, United States of America
- Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America
| | - Jaclyn Calkins
- Department of Biology, Reed College, Portland, Oregon, United States of America
- College of Human Medicine, Michigan State University, East Lansing, Michigan, United States of America
| | - Jeffrey R. Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Leigh C. Latta IV
- Department of Biology, Reed College, Portland, Oregon, United States of America
- Lewis-Clark State College, Lewiston, Idaho, United States of America
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, Oregon, United States of America
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31
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Bates DA, Bates CE, Earl AS, Skousen C, Fetbrandt AN, Ritchie J, Bodily PM, Johnson SM. Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis. PLoS One 2021; 16:e0258737. [PMID: 34673804 PMCID: PMC8530345 DOI: 10.1371/journal.pone.0258737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
The most basic level of eukaryotic gene regulation is the presence or absence of nucleosomes on DNA regulatory elements. In an effort to elucidate in vivo nucleosome patterns, in vitro studies are frequently used. In vitro, short DNA fragments are more favorable for nucleosome formation, increasing the likelihood of nucleosome occupancy. This may in part result from the fact that nucleosomes prefer to form on the terminal ends of linear DNA. This phenomenon has the potential to bias in vitro reconstituted nucleosomes and skew results. If the ends of DNA fragments are known, the reads falling close to the ends are typically discarded. In this study we confirm the phenomenon of end bias of in vitro nucleosomes. We describe a method in which nearly identical libraries, with different known ends, are used to recover nucleosomes which form towards the terminal ends of fragmented DNA. Finally, we illustrate that although nucleosomes prefer to form on DNA ends, it does not appear to skew results or the interpretation thereof.
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Affiliation(s)
- David A. Bates
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Charles E. Bates
- Qubit Software LLC, Spanish Fork, Utah, United States of America
| | - Andrew S. Earl
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Colin Skousen
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Ashley N. Fetbrandt
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Jordon Ritchie
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
| | - Paul M. Bodily
- Computer Science Department, Idaho State University, Pocatello, Idaho, United States of America
| | - Steven M. Johnson
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, United States of America
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32
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Ge X, Chen YE, Song D, McDermott M, Woyshner K, Manousopoulou A, Wang N, Li W, Wang LD, Li JJ. Clipper: p-value-free FDR control on high-throughput data from two conditions. Genome Biol 2021; 22:288. [PMID: 34635147 PMCID: PMC8504070 DOI: 10.1186/s13059-021-02506-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
High-throughput biological data analysis commonly involves identifying features such as genes, genomic regions, and proteins, whose values differ between two conditions, from numerous features measured simultaneously. The most widely used criterion to ensure the analysis reliability is the false discovery rate (FDR), which is primarily controlled based on p-values. However, obtaining valid p-values relies on either reasonable assumptions of data distribution or large numbers of replicates under both conditions. Clipper is a general statistical framework for FDR control without relying on p-values or specific data distributions. Clipper outperforms existing methods for a broad range of applications in high-throughput data analysis.
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Affiliation(s)
- Xinzhou Ge
- Department of Statistics, University of California, Los Angeles, 90095, CA, USA
| | - Yiling Elaine Chen
- Department of Statistics, University of California, Los Angeles, 90095, CA, USA
| | - Dongyuan Song
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, 90095, CA, USA
| | - MeiLu McDermott
- Beckman Research Institute, City of Hope National Medical Center, Duarte, 91010, CA, USA
- The Quantitative and Computational Biology section, University of Southern California, Los Angeles, 90089, CA, USA
| | - Kyla Woyshner
- Beckman Research Institute, City of Hope National Medical Center, Duarte, 91010, CA, USA
| | - Antigoni Manousopoulou
- Beckman Research Institute, City of Hope National Medical Center, Duarte, 91010, CA, USA
| | - Ning Wang
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, 90095, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, 92697, CA, USA
| | - Leo D Wang
- Beckman Research Institute, City of Hope National Medical Center, Duarte, 91010, CA, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, 90095, CA, USA.
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, 90095, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, 90095, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, 90095, CA, USA.
- Department of Biostatistics, University of California, Los Angeles, 90095, CA, USA.
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Zhang S, Holmes AP, Dick A, Rashad AA, Enríquez Rodríguez L, Canziani GA, Root MJ, Chaiken IM. Altered Env conformational dynamics as a mechanism of resistance to peptide-triazole HIV-1 inactivators. Retrovirology 2021; 18:31. [PMID: 34627310 PMCID: PMC8501640 DOI: 10.1186/s12977-021-00575-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/09/2021] [Accepted: 09/20/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND We previously developed drug-like peptide triazoles (PTs) that target HIV-1 Envelope (Env) gp120, potently inhibit viral entry, and irreversibly inactivate virions. Here, we investigated potential mechanisms of viral escape from this promising class of HIV-1 entry inhibitors. RESULTS HIV-1 resistance to cyclic (AAR029b) and linear (KR13) PTs was obtained by dose escalation in viral passaging experiments. High-level resistance for both inhibitors developed slowly (relative to escape from gp41-targeted C-peptide inhibitor C37) by acquiring mutations in gp120 both within (Val255) and distant to (Ser143) the putative PT binding site. The similarity in the resistance profiles for AAR029b and KR13 suggests that the shared IXW pharmacophore provided the primary pressure for HIV-1 escape. In single-round infectivity studies employing recombinant virus, V255I/S143N double escape mutants reduced PT antiviral potency by 150- to 3900-fold. Curiously, the combined mutations had a much smaller impact on PT binding affinity for monomeric gp120 (four to ninefold). This binding disruption was entirely due to the V255I mutation, which generated few steric clashes with PT in molecular docking. However, this minor effect on PT affinity belied large, offsetting changes to association enthalpy and entropy. The escape mutations had negligible effect on CD4 binding and utilization during entry, but significantly altered both binding thermodynamics and inhibitory potency of the conformationally-specific, anti-CD4i antibody 17b. Moreover, the escape mutations substantially decreased gp120 shedding induced by either soluble CD4 or AAR029b. CONCLUSIONS Together, the data suggest that the escape mutations significantly modified the energetic landscape of Env's prefusogenic state, altering conformational dynamics to hinder PT-induced irreversible inactivation of Env. This work therein reveals a unique mode of virus escape for HIV-1, namely, resistance by altering the intrinsic conformational dynamics of the Env trimer.
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Affiliation(s)
- Shiyu Zhang
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, USA
| | - Andrew P Holmes
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Alexej Dick
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Adel A Rashad
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | | | - Gabriela A Canziani
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Michael J Root
- Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, OH, Columbus, USA.
| | - Irwin M Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA.
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Nazario-Yepiz NO, Fernández Sobaberas J, Lyman R, Campbell MR, Shankar V, Anholt RRH, Mackay TFC. Physiological and metabolomic consequences of reduced expression of the Drosophila brummer triglyceride Lipase. PLoS One 2021; 16:e0255198. [PMID: 34547020 PMCID: PMC8454933 DOI: 10.1371/journal.pone.0255198] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/07/2021] [Indexed: 11/18/2022] Open
Abstract
Disruption of lipolysis has widespread effects on intermediary metabolism and organismal phenotypes. Defects in lipolysis can be modeled in Drosophila melanogaster through genetic manipulations of brummer (bmm), which encodes a triglyceride lipase orthologous to mammalian Adipose Triglyceride Lipase. RNAi-mediated knock-down of bmm in all tissues or metabolic specific tissues results in reduced locomotor activity, altered sleep patterns and reduced lifespan. Metabolomic analysis on flies in which bmm is downregulated reveals a marked reduction in medium chain fatty acids, long chain saturated fatty acids and long chain monounsaturated and polyunsaturated fatty acids, and an increase in diacylglycerol levels. Elevated carbohydrate metabolites and tricarboxylic acid intermediates indicate that impairment of fatty acid mobilization as an energy source may result in upregulation of compensatory carbohydrate catabolism. bmm downregulation also results in elevated levels of serotonin and dopamine neurotransmitters, possibly accounting for the impairment of locomotor activity and sleep patterns. Physiological phenotypes and metabolomic changes upon reduction of bmm expression show extensive sexual dimorphism. Altered metabolic states in the Drosophila model are relevant for understanding human metabolic disorders, since pathways of intermediary metabolism are conserved across phyla.
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Affiliation(s)
- Nestor O. Nazario-Yepiz
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Jaime Fernández Sobaberas
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Roberta Lyman
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Marion R. Campbell
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Vijay Shankar
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Robert R. H. Anholt
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
| | - Trudy F. C. Mackay
- Department of Biochemistry and Genetics and Center for Human Genetics, Clemson University, Greenwood, South Carolina, United States of America
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35
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Teng Y, Loveless R, Benson EM, Sun L, Shull AY, Shay C. SHOX2 cooperates with STAT3 to promote breast cancer metastasis through the transcriptional activation of WASF3. J Exp Clin Cancer Res 2021; 40:274. [PMID: 34465361 PMCID: PMC8406721 DOI: 10.1186/s13046-021-02083-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 05/26/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metastasis is most often the root cause of cancer-related death. Human short stature homeobox 2 (SHOX2), a homeodomain transcription factor, is a novel inducer of epithelial-to-mesenchymal transition in breast cancer cells, though its exact role and underlying mechanisms in metastasis are not well understood. METHODS TCGA analysis was performed to identify the clinical relevance of SHOX2 in breast cancer. Gene depletion was achieved by short hairpin RNA and small interfering RNA. Molecular regulations and alterations were assessed by Western blotting, immunoprecipitation, immunohistochemistry, qRT-PCR, chromatin immunoprecipitation coupled with qPCR (ChIP-qPCR), and ChIP/re-ChIP. The impact of SHOX2 signaling on tumor growth and metastasis was evaluated in orthotopic breast tumor mice. RESULTS The expression level of SHOX2 is strongly associated with poor distant metastasis-free survival in breast cancer patients and inactivation of SHOX2 suppresses breast tumor growth and metastasis in mice. In breast cancer cells, SHOX2 directly activates Wiskott-Aldridge syndrome protein family member 3 (WASF3), a metastasis-promoting gene, at the transcriptional level, leading to a significant increase in metastatic potential. Mechanistically, SHOX2 activates signal transducer and activator of transcription 3 (STAT3) and recruits it to the WASF3 promoter, where STAT3 cooperates with SHOX2 to form a functional immunocomplex to promote WASF3 transcriptional activity in breast cancer cells. WASF3 knockdown abrogates SHOX2-induced metastasis, but not SHOX2-dependent tumorigenesis. CONCLUSIONS These findings provide a critical link between the SHOX2-STAT3-WASF3 signaling axis and metastasis and suggest that the targeting of this signaling node may represent a valuable alternative strategy for combating breast cancer metastasis.
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Affiliation(s)
- Yong Teng
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, 201 Dowman Dr, GA, 30322, Atlanta, USA.
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, 30912, Augusta, GA, USA.
| | - Reid Loveless
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, 30912, Augusta, GA, USA
| | - Elayne M Benson
- Department of Biology, Presbyterian College, 29325, Clinton, SC, USA
| | - Li Sun
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, 30912, Augusta, GA, USA
| | - Austin Y Shull
- Department of Biology, Presbyterian College, 29325, Clinton, SC, USA
| | - Chloe Shay
- Emory Children's Center, Emory University School of Medicine, 30322, Atlanta, GA, USA
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Abstract
BACKGROUND A critical step in the HIV-1 replication cycle is the assembly of Gag proteins to form virions at the plasma membrane. Virion assembly and maturation are facilitated by the cellular polyanion inositol hexaphosphate (IP6), which is proposed to stabilize both the immature Gag lattice and the mature capsid lattice by binding to rings of primary amines at the center of Gag or capsid protein (CA) hexamers. The amino acids comprising these rings are critical for proper virion formation and their substitution results in assembly deficits or impaired infectiousness. To better understand the nature of the deficits that accompany IP6 binding deficiency, we passaged HIV-1 mutants that had substitutions in IP6 coordinating residues to select for compensatory mutations. RESULTS We found a mutation, a threonine to isoleucine substitution at position 371 (T371I) in Gag, that restored replication competence to an IP6-binding-deficient HIV-1 mutant. Notably, unlike wild-type HIV-1, the assembly and infectiousness of resulting virus was not impaired when IP6 biosynthetic enzymes were genetically ablated. Surprisingly, we also found that the maturation inhibitor Bevirimat (BVM) could restore the assembly and replication of an IP6-binding deficient mutant. Moreover, using BVM-dependent mutants we were able to image BVM-induced assembly of individual HIV-1 particles assembly in living cells. CONCLUSIONS Overall these results suggest that IP6-Gag and Gag-Gag contacts are finely tuned to generate a Gag lattice of optimal stability, and that under certain conditions BVM can rescue IP6 deficiency. Additionally, our work identifies an inducible virion assembly system that can be utilized to visualize HIV-1 assembly events using live cell microscopy.
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Affiliation(s)
- Daniel Poston
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Trinity Zang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Paul Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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Abstract
Ciliate genomes are replete with "junk" DNA insertions that require DNA splicing for their removal. What is the evolutionary source of these insertions? This Primer explores a new study in PLOS Biology that supports a classic model of transposon origins.
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Affiliation(s)
- Yi Feng
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, New York, United States of America
| | - Laura F. Landweber
- Departments of Biochemistry & Molecular Biophysics and Biological Sciences, Columbia University, New York, New York, United States of America
- * E-mail:
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Hanspers K, Kutmon M, Coort SL, Digles D, Dupuis LJ, Ehrhart F, Hu F, Lopes EN, Martens M, Pham N, Shin W, Slenter DN, Waagmeester A, Willighagen EL, Winckers LA, Evelo CT, Pico AR. Ten simple rules for creating reusable pathway models for computational analysis and visualization. PLoS Comput Biol 2021; 17:e1009226. [PMID: 34411100 PMCID: PMC8375987 DOI: 10.1371/journal.pcbi.1009226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Kristina Hanspers
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
| | - Martina Kutmon
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Susan L. Coort
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Daniela Digles
- Department of Pharmaceutical Sciences, Division of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Lauren J. Dupuis
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Finterly Hu
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Elisson N. Lopes
- Instituto de Ciencias Biologicas, Departamento de Bioquimica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marvin Martens
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Nhung Pham
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Woosub Shin
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Denise N. Slenter
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | | | - Egon L. Willighagen
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Laurent A. Winckers
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
| | - Chris T. Evelo
- Department of Bioinformatics—BiGCaT, NUTRIM, Maastricht University, Maastricht, the Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Alexander R. Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
- * E-mail:
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Williams ZJ, Gotham KO. Improving the measurement of alexithymia in autistic adults: a psychometric investigation of the 20-item Toronto Alexithymia Scale and generation of a general alexithymia factor score using item response theory. Mol Autism 2021; 12:56. [PMID: 34376227 PMCID: PMC8353782 DOI: 10.1186/s13229-021-00463-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 06/03/2021] [Accepted: 07/31/2021] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Alexithymia, a personality trait characterized by difficulties interpreting emotional states, is commonly elevated in autistic adults, and a growing body of literature suggests that this trait underlies several cognitive and emotional differences previously attributed to autism. Although questionnaires such as the 20-item Toronto Alexithymia Scale (TAS-20) are frequently used to measure alexithymia in the autistic population, few studies have investigated the psychometric properties of these questionnaires in autistic adults, including whether differential item functioning (I-DIF) exists between autistic and general population adults. METHODS This study is a revised version of a previous article that was retracted due to copyright concerns (Williams and Gotham in Mol Autism 12:1-40). We conducted an in-depth psychometric analysis of the TAS-20 in a large sample of 743 cognitively able autistic adults recruited from the Simons Foundation SPARK participant pool and 721 general population controls enrolled in a large international psychological study. The factor structure of the TAS-20 was examined using confirmatory factor analysis, and item response theory was used to generate a subset of the items that were strong indicators of a "general alexithymia" factor. Correlations between alexithymia and other clinical outcomes were used to assess the nomological validity of the new alexithymia score in the SPARK sample. RESULTS The TAS-20 did not exhibit adequate model fit in either the autistic or general population samples. Empirically driven item reduction was undertaken, resulting in an 8-item general alexithymia factor score (GAFS-8, with "TAS" no longer referenced due to copyright) with sound psychometric properties and practically ignorable I-DIF between diagnostic groups. Correlational analyses indicated that GAFS-8 scores, as derived from the TAS-20, meaningfully predict autistic trait levels, repetitive behaviors, and depression symptoms, even after controlling for trait neuroticism. The GAFS-8 also presented no meaningful decrement in nomological validity over the full TAS-20 in autistic participants. LIMITATIONS Limitations of the current study include a sample of autistic adults that was majority female, later diagnosed, and well educated; clinical and control groups drawn from different studies with variable measures; only 16 of the TAS-20 items being administered to the non-autistic sample; and an inability to test several other important psychometric characteristics of the GAFS-8, including sensitivity to change and I-DIF across multiple administrations. CONCLUSIONS These results indicate the potential of the GAFS-8 to robustly measure alexithymia in both autistic and non-autistic adults. A free online score calculator has been created to facilitate the use of norm-referenced GAFS-8 latent trait scores in research applications (available at https://asdmeasures.shinyapps.io/alexithymia ).
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Affiliation(s)
- Zachary J. Williams
- Medical Scientist Training Program, Vanderbilt University School of Medicine, 1215 21st Avenue South, Medical Center East, Room 8310, Nashville, TN 37232 USA
- Department of Hearing and Speech Sciences, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN USA
- Frist Center for Autism and Innovation, Vanderbilt University, Nashville, TN USA
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Mitra D, Hasan MH, Bates JT, Bierdeman MA, Ederer DR, Parmar RC, Fassero LA, Liang Q, Qiu H, Tiwari V, Zhang F, Linhardt RJ, Sharp JS, Wang L, Tandon R. The degree of polymerization and sulfation patterns in heparan sulfate are critical determinants of cytomegalovirus entry into host cells. PLoS Pathog 2021; 17:e1009803. [PMID: 34352038 PMCID: PMC8384199 DOI: 10.1371/journal.ppat.1009803] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/24/2021] [Accepted: 07/15/2021] [Indexed: 01/10/2023] Open
Abstract
Several enveloped viruses, including herpesviruses attach to host cells by initially interacting with cell surface heparan sulfate (HS) proteoglycans followed by specific coreceptor engagement which culminates in virus-host membrane fusion and virus entry. Interfering with HS-herpesvirus interactions has long been known to result in significant reduction in virus infectivity indicating that HS play important roles in initiating virus entry. In this study, we provide a series of evidence to prove that specific sulfations as well as the degree of polymerization (dp) of HS govern human cytomegalovirus (CMV) binding and infection. First, purified CMV extracellular virions preferentially bind to sulfated longer chain HS on a glycoarray compared to a variety of unsulfated glycosaminoglycans including unsulfated shorter chain HS. Second, the fraction of glycosaminoglycans (GAG) displaying higher dp and sulfation has a larger impact on CMV titers compared to other fractions. Third, cell lines deficient in specific glucosaminyl sulfotransferases produce significantly reduced CMV titers compared to wild-type cells and virus entry is compromised in these mutant cells. Finally, purified glycoprotein B shows strong binding to heparin, and desulfated heparin analogs compete poorly with heparin for gB binding. Taken together, these results highlight the significance of HS chain length and sulfation patterns in CMV attachment and infectivity.
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Affiliation(s)
- Dipanwita Mitra
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Mohammad H. Hasan
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - John T. Bates
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Michael A. Bierdeman
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Dallas R. Ederer
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Rinkuben C. Parmar
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Lauren A. Fassero
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Quntao Liang
- Biomolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi, United States of America
- College of Biological Science and Engineering, University of Fuzhou, Fujian, China
| | - Hong Qiu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Vaibhav Tiwari
- Department of Microbiology and Immunology, Midwestern University, Downers Grove, Illinois, United States of America
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Robert J. Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Joshua S. Sharp
- Biomolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi, United States of America
| | - Lianchun Wang
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, Florida, United States of America
| | - Ritesh Tandon
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
- Biomolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi, United States of America
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Lavin RC, Johnson C, Ahn YM, Kremiller KM, Sherwood M, Patel JS, Pan Y, Russo R, MacGilvary NJ, Giacalone D, Kevorkian YL, Zimmerman MD, Glickman JF, Freundlich JS, Tan S. Targeting Mycobacterium tuberculosis response to environmental cues for the development of effective antitubercular drugs. PLoS Biol 2021; 19:e3001355. [PMID: 34319985 PMCID: PMC8351955 DOI: 10.1371/journal.pbio.3001355] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 08/09/2021] [Accepted: 07/08/2021] [Indexed: 11/28/2022] Open
Abstract
Sensing and response to environmental cues, such as pH and chloride (Cl−), is critical in enabling Mycobacterium tuberculosis (Mtb) colonization of its host. Utilizing a fluorescent reporter Mtb strain in a chemical screen, we have identified compounds that dysregulate Mtb response to high Cl− levels, with a subset of the hits also inhibiting Mtb growth in host macrophages. Structure–activity relationship studies on the hit compound “C6,” or 2-(4-((2-(ethylthio)pyrimidin-5-yl)methyl)piperazin-1-yl)benzo[d]oxazole, demonstrated a correlation between compound perturbation of Mtb Cl− response and inhibition of bacterial growth in macrophages. C6 accumulated in both bacterial and host cells, and inhibited Mtb growth in cholesterol media, but not in rich media. Subsequent examination of the Cl− response of Mtb revealed an intriguing link with bacterial growth in cholesterol, with increased transcription of several Cl−-responsive genes in the simultaneous presence of cholesterol and high external Cl− concentration, versus transcript levels observed during exposure to high external Cl− concentration alone. Strikingly, oral administration of C6 was able to inhibit Mtb growth in vivo in a C3HeB/FeJ murine infection model. Our work illustrates how Mtb response to environmental cues can intersect with its metabolism and be exploited in antitubercular drug discovery. Responding to environmental cues such as pH and chloride is critical in enabling Mycobacterium tuberculosis to colonize its host. A chemical screen using an M. tuberculosis strain bearing a fluorescent reporter identifies a compound that perturbs the bacterial response to chloride and inhibits its growth in a murine infection model.
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Affiliation(s)
- Richard C. Lavin
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Calvin Johnson
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Yong-Mo Ahn
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University–New Jersey Medical School, Newark, New Jersey, United States of America
| | - Kyle M. Kremiller
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University–New Jersey Medical School, Newark, New Jersey, United States of America
| | - Matthew Sherwood
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University–New Jersey Medical School, Newark, New Jersey, United States of America
| | - Jimmy S. Patel
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University–New Jersey Medical School, Newark, New Jersey, United States of America
| | - Yan Pan
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, United States of America
| | - Riccardo Russo
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University–New Jersey Medical School, Newark, New Jersey, United States of America
| | - Nathan J. MacGilvary
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Yuzo L. Kevorkian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Matthew D. Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, United States of America
| | - J. Fraser Glickman
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, New York, United States of America
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University–New Jersey Medical School, Newark, New Jersey, United States of America
- Division of Infectious Disease, Department of Medicine and the Ruy V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University–New Jersey Medical School, Newark, New Jersey, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
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Avery L, Ingalls B, Dumur C, Artyukhin A. A Keller-Segel model for C elegans L1 aggregation. PLoS Comput Biol 2021; 17:e1009231. [PMID: 34324494 PMCID: PMC8354456 DOI: 10.1371/journal.pcbi.1009231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 08/10/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022] Open
Abstract
We describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a longer range repellent. This model takes the mathematical form of three coupled partial differential equations, one that describes the movement of the worms and one for each of the chemical signals. Numerical solution of these equations produced a pattern of aggregates that resembled that of worm aggregates observed in experiments. We also describe the identification of a sensory receptor gene, srh-2, whose expression is induced under conditions that promote L1 aggregation. Worms whose srh-2 gene has been knocked out form irregularly shaped aggregates. Our model suggests this phenotype may be explained by the mutant worms slowing their movement more quickly than the wild type.
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Affiliation(s)
- Leon Avery
- Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario, Canada
| | - Brian Ingalls
- Department of Applied Mathematics, University of Waterloo, Waterloo, Ontario, Canada
| | - Catherine Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Alexander Artyukhin
- Chemistry Department, State University of New York, College of Environmental Science and Forestry, Syracuse, New York, United States of America
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Abstract
BACKGROUND: The number of persons diagnosed with dementia is projected to triple to 14 million by 2050. The significance of these projections is particularly relevant to older women (>65 years), who are more likely to provide dementia caregiving for a husband than vice versa. Research has identified consistent themes around the impact of caregiving during the caregiving experience, yet there is limited research exploring the ongoing impact during the transition to widowhood. Moreover, there is a paucity of research examining differences between rural and urban spousal dementia caregivers. AIMS: The aims were to compare differences between older rural and urban spousal caregivers on physical and mental health factors affecting the transition from caregiver to widow and to identify resources the women used during this transition over 12 months. METHOD: This mixed-methods longitudinal study recruited 13 urban and nine rural female spousal caregivers. Participants were interviewed three times over 12 months. The dependent variables were depression (measured using Center for Epidemiologic Studies Depression Scale), physical and mental functioning (measured using the 12-item Medical Outcomes Study-Short Form Health Survey Version 2). RESULTS: No statistically significant differences were detected between rural and urban female caregivers on the dependent variables. However, rural caregivers scored higher on depression and lower on both physical and mental functioning compared to their urban counterparts. CONCLUSIONS: The findings have clinical and research implications. Psychiatric nurses are well positioned to provide education related to dementia information deficits; implement interventions that facilitate bereavement, resilience, self-care, and identity; advocate for additional services; and conduct larger scale studies with a more diverse sample of female spousal caregivers.
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Affiliation(s)
- Carla J. Groh
- Carla J. Groh, PhD, PMHNP-BC, FAAN, University of Detroit Mercy, Detroit, MI, USA
| | - Mitzi M. Saunders
- Mitzi M. Saunders, PhD, APRN, CNS-C, University of Detroit Mercy, Detroit, MI, USA
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