1
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Chitwood MH, Colijn C, Yang C, Crudu V, Ciobanu N, Codreanu A, Kim J, Rancu I, Rhee K, Cohen T, Sobkowiak B. The recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova. Nat Commun 2024; 15:2962. [PMID: 38580642 PMCID: PMC10997638 DOI: 10.1038/s41467-024-47282-9] [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: 11/29/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
The projected trajectory of multidrug resistant tuberculosis (MDR-TB) epidemics depends on the reproductive fitness of circulating strains of MDR M. tuberculosis (Mtb). Previous efforts to characterize the fitness of MDR Mtb have found that Mtb strains of the Beijing sublineage (Lineage 2.2.1) may be more prone to develop resistance and retain fitness in the presence of resistance-conferring mutations than other lineages. Using Mtb genome sequences from all culture-positive cases collected over two years in Moldova, we estimate the fitness of Ural (Lineage 4.2) and Beijing strains, the two lineages in which MDR is concentrated in the country. We estimate that the fitness of MDR Ural strains substantially exceeds that of other susceptible and MDR strains, and we identify several mutations specific to these MDR Ural strains. Our findings suggest that MDR Ural Mtb has been transmitting efficiently in Moldova and poses a substantial risk of spreading further in the region.
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Affiliation(s)
- Melanie H Chitwood
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA.
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, 8888 University Drive West, Burnaby, BC, Canada
| | - Chongguang Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 132 Outer Ring East Road, Guangzhou University Town Guangdong, Guangdong, PR China
| | - Valeriu Crudu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Alexandru Codreanu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Jaehee Kim
- Department of Computational Biology, Cornell University, 237 Tower Road, Ithaca, NY, USA
| | - Isabel Rancu
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA.
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA
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2
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Batten SR, Bang D, Kopell BH, Davis AN, Heflin M, Fu Q, Perl O, Ziafat K, Hashemi A, Saez I, Barbosa LS, Twomey T, Lohrenz T, White JP, Dayan P, Charney AW, Figee M, Mayberg HS, Kishida KT, Gu X, Montague PR. Dopamine and serotonin in human substantia nigra track social context and value signals during economic exchange. Nat Hum Behav 2024; 8:718-728. [PMID: 38409356 PMCID: PMC11045309 DOI: 10.1038/s41562-024-01831-w] [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: 04/28/2023] [Accepted: 01/16/2024] [Indexed: 02/28/2024]
Abstract
Dopamine and serotonin are hypothesized to guide social behaviours. In humans, however, we have not yet been able to study neuromodulator dynamics as social interaction unfolds. Here, we obtained subsecond estimates of dopamine and serotonin from human substantia nigra pars reticulata during the ultimatum game. Participants, who were patients with Parkinson's disease undergoing awake brain surgery, had to accept or reject monetary offers of varying fairness from human and computer players. They rejected more offers in the human than the computer condition, an effect of social context associated with higher overall levels of dopamine but not serotonin. Regardless of the social context, relative changes in dopamine tracked trial-by-trial changes in offer value-akin to reward prediction errors-whereas serotonin tracked the current offer value. These results show that dopamine and serotonin fluctuations in one of the basal ganglia's main output structures reflect distinct social context and value signals.
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Affiliation(s)
- Seth R Batten
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA.
| | - Dan Bang
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA.
- Center of Functionally Integrative Neuroscience, Aarhus University, Aarhus, Denmark.
- Wellcome Centre for Human Neuroimaging, University College London, London, UK.
- Department of Experimental Psychology, University of Oxford, Oxford, UK.
| | - Brian H Kopell
- Nash Family Center for Advanced Circuit Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Neuromodulation, Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arianna N Davis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Computational Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Matthew Heflin
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Computational Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Qixiu Fu
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Computational Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ofer Perl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Computational Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kimia Ziafat
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice Hashemi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ignacio Saez
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leonardo S Barbosa
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA
| | - Thomas Twomey
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA
| | - Terry Lohrenz
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA
| | - Jason P White
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA
| | - Peter Dayan
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- University of Tübingen, Tübingen, Germany
| | - Alexander W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Martijn Figee
- Nash Family Center for Advanced Circuit Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Neuromodulation, Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Helen S Mayberg
- Nash Family Center for Advanced Circuit Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Neuromodulation, Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kenneth T Kishida
- Department of Translational Neuroscience, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Department of Neurosurgery, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Xiaosi Gu
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Computational Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - P Read Montague
- Fralin Biomedical Research Institute at VTC, Virginia Tech, Roanoke, VA, USA.
- Wellcome Centre for Human Neuroimaging, University College London, London, UK.
- Department of Physics, Virginia Tech, Blacksburg, VA, USA.
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3
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Hawks ZW, Beck ED, Jung L, Fonseca LM, Sliwinski MJ, Weinstock RS, Grinspoon E, Xu I, Strong RW, Singh S, Van Dongen HPA, Frumkin MR, Bulger J, Cleveland MJ, Janess K, Kudva YC, Pratley R, Rickels MR, Rizvi SR, Chaytor NS, Germine LT. Dynamic associations between glucose and ecological momentary cognition in Type 1 Diabetes. NPJ Digit Med 2024; 7:59. [PMID: 38499605 PMCID: PMC10948782 DOI: 10.1038/s41746-024-01036-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 02/14/2024] [Indexed: 03/20/2024] Open
Abstract
Type 1 diabetes (T1D) is a chronic condition characterized by glucose fluctuations. Laboratory studies suggest that cognition is reduced when glucose is very low (hypoglycemia) and very high (hyperglycemia). Until recently, technological limitations prevented researchers from understanding how naturally-occurring glucose fluctuations impact cognitive fluctuations. This study leveraged advances in continuous glucose monitoring (CGM) and cognitive ecological momentary assessment (EMA) to characterize dynamic, within-person associations between glucose and cognition in naturalistic environments. Using CGM and EMA, we obtained intensive longitudinal measurements of glucose and cognition (processing speed, sustained attention) in 200 adults with T1D. First, we used hierarchical Bayesian modeling to estimate dynamic, within-person associations between glucose and cognition. Consistent with laboratory studies, we hypothesized that cognitive performance would be reduced at low and high glucose, reflecting cognitive vulnerability to glucose fluctuations. Second, we used data-driven lasso regression to identify clinical characteristics that predicted individual differences in cognitive vulnerability to glucose fluctuations. Large glucose fluctuations were associated with slower and less accurate processing speed, although slight glucose elevations (relative to person-level means) were associated with faster processing speed. Glucose fluctuations were not related to sustained attention. Seven clinical characteristics predicted individual differences in cognitive vulnerability to glucose fluctuations: age, time in hypoglycemia, lifetime severe hypoglycemic events, microvascular complications, glucose variability, fatigue, and neck circumference. Results establish the impact of glucose on processing speed in naturalistic environments, suggest that minimizing glucose fluctuations is important for optimizing processing speed, and identify several clinical characteristics that may exacerbate cognitive vulnerability to glucose fluctuations.
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Affiliation(s)
- Z W Hawks
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
| | - E D Beck
- Department of Psychology, University of California Davis, Davis, CA, USA
| | - L Jung
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
| | - L M Fonseca
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
- Programa Terceira Idade (PROTER, Old Age Research Group), Department and Institute of Psychiatry, University of São Paulo School of Medicine, São Paulo, Brazil
| | - M J Sliwinski
- Department of Human Development and Family Studies, Center for Healthy Aging, Pennsylvania State University, State College, PA, USA
| | | | - E Grinspoon
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
| | - I Xu
- Department of Psychology, University of Notre Dame, Notre Dame, IN, USA
| | - R W Strong
- The Many Brains Project, Belmont, MA, USA
| | - S Singh
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - H P A Van Dongen
- Sleep and Performance Research Center & Department of Translational Medicine and Physiology, Washington State University, Spokane, WA, USA
| | - M R Frumkin
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Department of Psychological & Brain Sciences, Washington University in St. Louis, St. Louis, MO, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - J Bulger
- SUNY Upstate Medical University, Syracuse, NY, USA
| | - M J Cleveland
- Department of Human Development, Washington State University, Pullman, WA, USA
| | - K Janess
- Jaeb Center for Health Research, Tampa, FL, USA
| | - Y C Kudva
- Division of Endocrinology, Diabetes and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - R Pratley
- AdventHealth Translational Research Institute, Orlando, FL, USA
| | - M R Rickels
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - S R Rizvi
- Division of Endocrinology, Diabetes and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - N S Chaytor
- Elson S. Floyd College of Medicine, Washington State University, Spokane, WA, USA
| | - L T Germine
- Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
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4
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García Bulle Bueno B, Horn AL, Bell BM, Bahrami M, Bozkaya B, Pentland A, de la Haye K, Moro E. Effect of mobile food environments on fast food visits. Nat Commun 2024; 15:2291. [PMID: 38480685 PMCID: PMC10937966 DOI: 10.1038/s41467-024-46425-2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/26/2024] [Indexed: 03/17/2024] Open
Abstract
Poor diets are a leading cause of morbidity and mortality. Exposure to low-quality food environments saturated with fast food outlets is hypothesized to negatively impact diet. However, food environment research has predominantly focused on static food environments around home neighborhoods and generated mixed findings. In this work, we leverage population-scale mobility data in the U.S. to examine 62M people's visits to food outlets and evaluate how food choice is influenced by the food environments people are exposed to as they move through their daily routines. We find that a 10% increase in exposure to fast food outlets in mobile environments increases individuals' odds of visitation by 20%. Using our results, we simulate multiple policy strategies for intervening on food environments to reduce fast-food outlet visits. This analysis suggests that optimal interventions are informed by spatial, temporal, and behavioral features and could have 2x to 4x larger effect than traditional interventions focused on home food environments.
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Affiliation(s)
| | - Abigail L Horn
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Industrial and Systems Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90089, USA
- Information Sciences Institute, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, 90292, USA
| | - Brooke M Bell
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90089, USA
- Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Mohsen Bahrami
- Institute for Data, Systems, and Society, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Burçin Bozkaya
- Sabanci Business School, Sabanci University, 34956, Tuzla, Istanbul, Turkey
| | - Alex Pentland
- Institute for Data, Systems, and Society, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kayla de la Haye
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA, 90089, USA
| | - Esteban Moro
- Institute for Data, Systems, and Society, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Department of Mathematics and GISC, Universidad Carlos III de Madrid, 28911, Leganés, Spain.
- Network Science Institute, Northeastern University, Boston, MA, 02115, USA.
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5
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Mehdi SMA, Costa AP, Svob C, Pan L, Dartora WJ, Talati A, Gameroff MJ, Wickramaratne PJ, Weissman MM, McIntire LBJ. Depression and cognition are associated with lipid dysregulation in both a multigenerational study of depression and the National Health and Nutrition Examination Survey. Transl Psychiatry 2024; 14:142. [PMID: 38467624 PMCID: PMC10928164 DOI: 10.1038/s41398-024-02847-6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/15/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Chronic dysregulation of peripheral lipids has been found to be associated with depression and cognition, but their interaction has not been investigated. Growing evidence has highlighted the association between peripheral lipoprotein levels with depression and cognition with inconsistent results. We assessed the association between peripheral lipids, depression, and cognition while evaluating their potential interactions using robust clinically relevant predictors such as lipoprotein levels and chronic medical disorders that dysregulate lipoproteins. We report an association between peripheral lipids, depression, and cognition, suggesting a common underlying biological mechanism driven by lipid dysregulation in two independent studies. Analysis of a longitudinal study of a cohort at high or low familial risk for major depressive disorder (MDD) (n = 526) found metabolic diseases, including diabetes, hypertension, and other cardiovascular diseases, were associated with MDD and cognitive outcomes. Investigating a cross-sectional population survey of adults in the National Health and Nutrition Examination Survey 2011-2014 (NHANES) (n = 2377), depression was found to be associated with high density lipoprotein (HDL) and cognitive assessments. In the familial risk study, medical conditions were found to be associated with chronic lipid dysregulation and were significantly associated with MDD using the structural equation model. A positive association between chronic lipid dysregulation and cognitive scores was found in an exploratory analysis of the familial risk study. In a complementary study, analysis of NHANES revealed a positive association of HDL levels with cognition. Further analysis of the NHANES cohort indicated that depression status mediated the interaction between HDL levels and cognitive tests. Importantly, the protective effect of HDL on cognition was absent in those with depressive symptoms, which may ultimately result in worse outcomes leading to cognitive decline. These findings highlight the potential for the early predictive value of medical conditions with chronic lipid dyshomeostasis for the risk of depression and cognitive decline.
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Affiliation(s)
- S M A Mehdi
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - A P Costa
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
- Brain Health Imaging Institute, New York, NY, USA
| | - C Svob
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - L Pan
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - W J Dartora
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA
- Brain Health Imaging Institute, New York, NY, USA
| | - A Talati
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - M J Gameroff
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - P J Wickramaratne
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - M M Weissman
- Mailman School of Public Health, Columbia University, New York, NY, USA.
- Division of Translational Epidemiology and Mental Health Equity, New York State Psychiatric Institute, New York, NY, USA.
- Department of Psychiatry, Columbia University, New York, NY, USA.
| | - L B J McIntire
- Department of Radiology, Weill Cornell Medicine, New York, NY, USA.
- Brain Health Imaging Institute, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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6
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Anderson EC, DiPalazzo J, Lucas FL, Hall MJ, Antov A, Helbig P, Bourne J, Graham L, Gaitor L, Lu-Emerson C, Bradford LS, Inhorn R, Sinclair SJ, Brooks PL, Thomas CA, Rasmussen K, Han PKJ, Liu ET, Rueter J. Genome-matched treatments and patient outcomes in the Maine Cancer Genomics Initiative (MCGI). NPJ Precis Oncol 2024; 8:67. [PMID: 38461318 PMCID: PMC10924947 DOI: 10.1038/s41698-024-00547-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 02/16/2024] [Indexed: 03/11/2024] Open
Abstract
Genomic tumor testing (GTT) is an emerging technology aimed at identifying variants in tumors that can be targeted with genomically matched drugs. Due to limited resources, rural patients receiving care in community oncology settings may be less likely to benefit from GTT. We analyzed GTT results and observational clinical outcomes data from patients enrolled in the Maine Cancer Genomics Initiative (MCGI), which provided access to GTTs; clinician educational resources; and genomic tumor boards in community practices in a predominantly rural state. 1603 adult cancer patients completed enrollment; 1258 had at least one potentially actionable variant identified. 206 (16.4%) patients received a total of 240 genome matched treatments, of those treatments, 64% were FDA-approved in the tumor type, 27% FDA-approved in a different tumor type and 9% were given on a clinical trial. Using Inverse Probability of Treatment Weighting to adjust for baseline characteristics, a Cox proportional hazards model demonstrated that patients who received genome matched treatment were 31% less likely to die within 1 year compared to those who did not receive genome matched treatment (HR: 0.69; 95% CI: 0.52-0.90; p-value: 0.006). Overall, GTT through this initiative resulted in levels of genome matched treatment that were similar to other initiatives, however, clinical trials represented a smaller share of treatments than previously reported, and "off-label" treatments represented a greater share. Although this was an observational study, we found evidence for a potential 1-year survival benefit for patients who received genome matched treatments. These findings suggest that when disseminated and implemented with a supportive infrastructure, GTT may benefit cancer patients in rural community oncology settings, with further work remaining on providing genome-matched clinical trials.
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Affiliation(s)
- Eric C Anderson
- Center for Interdisciplinary Population and Health Research, MaineHealth Institute for Research, Portland, ME, USA
- Tufts University School of Medicine, Boston, MA, USA
| | - John DiPalazzo
- Center for Interdisciplinary Population and Health Research, MaineHealth Institute for Research, Portland, ME, USA
| | - F Lee Lucas
- Center for Interdisciplinary Population and Health Research, MaineHealth Institute for Research, Portland, ME, USA
| | | | | | | | | | | | | | | | - Leslie S Bradford
- Maine Medical Partners Women's Health, Gynecologic Oncology, Scarborough, ME, USA
| | - Roger Inhorn
- PenBay Medical Center Oncology, Rockport, ME, USA
| | | | | | | | | | - Paul K J Han
- Center for Interdisciplinary Population and Health Research, MaineHealth Institute for Research, Portland, ME, USA
- National Cancer Institute, Bethesda, MD, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
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7
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Cheng X, An J, Lou J, Gu Q, Ding W, Droby GN, Wang Y, Wang C, Gao Y, Anand JR, Shelton A, Satterlee AB, Mann B, Hsiao YC, Liu CW, Lu K, Hingtgen S, Wang J, Liu Z, Miller CR, Wu D, Vaziri C, Yang Y. Trans-lesion synthesis and mismatch repair pathway crosstalk defines chemoresistance and hypermutation mechanisms in glioblastoma. Nat Commun 2024; 15:1957. [PMID: 38438348 PMCID: PMC10912752 DOI: 10.1038/s41467-024-45979-5] [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: 12/11/2022] [Accepted: 02/08/2024] [Indexed: 03/06/2024] Open
Abstract
Almost all Glioblastoma (GBM) are either intrinsically resistant to the chemotherapeutical drug temozolomide (TMZ) or acquire therapy-induced mutations that cause chemoresistance and recurrence. The genome maintenance mechanisms responsible for GBM chemoresistance and hypermutation are unknown. We show that the E3 ubiquitin ligase RAD18 (a proximal regulator of TLS) is activated in a Mismatch repair (MMR)-dependent manner in TMZ-treated GBM cells, promoting post-replicative gap-filling and survival. An unbiased CRISPR screen provides an aerial map of RAD18-interacting DNA damage response (DDR) pathways deployed by GBM to tolerate TMZ genotoxicity. Analysis of mutation signatures from TMZ-treated GBM reveals a role for RAD18 in error-free bypass of O6mG (the most toxic TMZ-induced lesion), and error-prone bypass of other TMZ-induced lesions. Our analyses of recurrent GBM patient samples establishes a correlation between low RAD18 expression and hypermutation. Taken together we define molecular underpinnings for the hallmark tumorigenic phenotypes of TMZ-treated GBM.
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Affiliation(s)
- Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - Jitong Lou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Eli Lilly and Company, Indianapolis, IN, 46285, USA
| | - Qisheng Gu
- Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- Department of Immunology, Université Paris Cité, Paris, France
| | - Weimin Ding
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Oncology Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Gaith Nabil Droby
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yilin Wang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Chenghao Wang
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jay Ramanlal Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Abigail Shelton
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Andrew Benson Satterlee
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Breanna Mann
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Shawn Hingtgen
- Eshelman School of Pharmacy, Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jiguang Wang
- Division of Life Science, Department of Chemical and Biological Engineering, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Hong Kong Center for Neurodegenerative Diseases, InnoHK, Hong Kong SAR, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, China
| | - C Ryan Miller
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Division of Oral and Craniofacial Health Science, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
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8
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Thirunavukkarasu S, Taylor R, Khunti K, Tapp RJ, Raben A, Zhu R, Kapoor N, Narayan KMV, Ali MK, Shaw JE. Low-calorie diets for people with isolated impaired fasting glucose. Commun Med (Lond) 2024; 4:35. [PMID: 38429400 PMCID: PMC10907622 DOI: 10.1038/s43856-024-00466-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/22/2024] [Indexed: 03/03/2024] Open
Abstract
Thirunavukkarasu et al. discuss how standard lifestyle interventions prove ineffective in preventing type 2 diabetes in individuals with isolated impaired fasting glucose, a highly prevalent prediabetes phenotype globally. They propose low-calorie diets as a promising strategy for diabetes prevention in this high-risk population.
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Affiliation(s)
- Sathish Thirunavukkarasu
- Department of Family and Preventive Medicine, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Roy Taylor
- Translational and Clinical Research Institute, Magnetic Resonance Centre, Campus for Ageing and Vitality, Newcastle University, Newcastle upon Tyne, UK
| | - Kamlesh Khunti
- Diabetes Research Centre, University of Leicester, Leicester, UK
| | - Robyn J Tapp
- Centre for Intelligent Health Care, Coventry University, Coventry, UK
| | - Anne Raben
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Ruixin Zhu
- Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Nitin Kapoor
- Department of Endocrinology, Diabetes and Metabolism, Christian Medical College, Vellore, India
| | - K M Venkat Narayan
- Emory Global Diabetes Research Center, Woodruff Health Sciences Center, Emory University, Atlanta, GA, USA
| | - Mohammed K Ali
- Department of Family and Preventive Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Jonathan E Shaw
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
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9
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Churchill RA, Pecoraro TYC, Tooley AA, Houghton OM, Mashayekhi A, Dalvin LA. Multimodal imaging risk factors predictive of small choroidal melanocytic lesion growth to melanoma: An educational study and pictorial guide. Eye (Lond) 2024; 38:798-805. [PMID: 37880451 PMCID: PMC10920886 DOI: 10.1038/s41433-023-02782-8] [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: 01/26/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Risk factors for small choroidal melanocytic lesion growth to melanoma have been redefined using multimodal imaging. We explored provider ability to recognize risk factors for small choroidal melanocytic lesion growth to melanoma before and after image-based education and with and without multimodal imaging. METHODS Providers were invited to participate in a survey assessing ability to identify risk factors for small choroidal melanocytic lesion growth to melanoma using either fundus imaging or multimodal imaging. Risk factors included thickness >2 mm on ultrasonography, subretinal fluid on optical coherence tomography, presence of orange pigment by autofluorescence, acoustic hollowness by ultrasonography, and diameter >5 mm by fundus imaging. Performance was assessed before and after reviewing an educational PowerPoint providing pictorial examples of risk factors. Comparison between groups was conducted using two-tailed Fisher's exact test. RESULTS Thirty and 26 providers completed the pre-education and post-education assessments, respectively. Post-education participants were more accurate within ±1 risk factor for lesions with zero risk factors (77% vs. 100%, p = 0.01) or two risk factors (79% vs. 91%, p = 0.03). Following education, participants presented with multimodal imaging more often correctly identified lesions with four (12% vs. 42%, p = 0.03) or five (4% vs. 39%, p = 0.004) risk factors, demonstrated lower mean level of concern for lesions with zero risk factors (2.0 vs. 1.4, p < 0.001), and expressed higher level of concern for lesions with 5 risk factors (2.4 vs. 3.6, p < 0.001). CONCLUSION Use of multimodal imaging may be more beneficial than education itself to improve accuracy of risk factor identification for small choroidal melanocytic lesions.
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Affiliation(s)
| | | | - Andrea A Tooley
- Department of Ophthalmology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Lauren A Dalvin
- Department of Ophthalmology, Mayo Clinic, Rochester, MN, USA.
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10
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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11
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van Rheede JJ, Alagapan S, Denison TJ, Riva-Posse P, Rozell CJ, Mayberg HS, Waters AC, Sharott A. Cortical signatures of sleep are altered following effective deep brain stimulation for depression. Transl Psychiatry 2024; 14:103. [PMID: 38378677 PMCID: PMC10879134 DOI: 10.1038/s41398-024-02816-z] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Deep brain stimulation (DBS) of the subcallosal cingulate cortex (SCC) is an experimental therapy for treatment-resistant depression (TRD). Chronic SCC DBS leads to long-term changes in the electrophysiological dynamics measured from local field potential (LFP) during wakefulness, but it is unclear how it impacts sleep-related brain activity. This is a crucial gap in knowledge, given the link between depression and sleep disturbances, and an emerging interest in the interaction between DBS, sleep, and circadian rhythms. We therefore sought to characterize changes in electrophysiological markers of sleep associated with DBS treatment for depression. We analyzed key electrophysiological signatures of sleep-slow-wave activity (SWA, 0.5-4.5 Hz) and sleep spindles-in LFPs recorded from the SCC of 9 patients who responded to DBS for TRD. This allowed us to compare the electrophysiological changes before and after 24 weeks of therapeutically effective SCC DBS. SWA power was highly correlated between hemispheres, consistent with a global sleep state. Furthermore, SWA occurred earlier in the night after chronic DBS and had a more prominent peak. While we found no evidence for changes to slow-wave power or stability, we found an increase in the density of sleep spindles. Our results represent a first-of-its-kind report on long-term electrophysiological markers of sleep recorded from the SCC in patients with TRD, and provides evidence of earlier NREM sleep and increased sleep spindle activity following clinically effective DBS treatment. Future work is needed to establish the causal relationship between long-term DBS and the neural mechanisms underlying sleep.
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Affiliation(s)
- Joram J van Rheede
- MRC Brain Network Dynamics Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
| | - Sankaraleengam Alagapan
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Timothy J Denison
- MRC Brain Network Dynamics Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Institute for Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Patricio Riva-Posse
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher J Rozell
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Helen S Mayberg
- Nash Family Center for Advanced Circuit Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Allison C Waters
- Nash Family Center for Advanced Circuit Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Sharott
- MRC Brain Network Dynamics Unit, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
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12
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Wang HY, Li L, Nelson CS, Barfield R, Valencia S, Chan C, Muramatsu H, Lin PJC, Pardi N, An Z, Weissman D, Permar SR. Multivalent cytomegalovirus glycoprotein B nucleoside modified mRNA vaccines did not demonstrate a greater antibody breadth. NPJ Vaccines 2024; 9:38. [PMID: 38378950 PMCID: PMC10879498 DOI: 10.1038/s41541-024-00821-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
Human cytomegalovirus (HCMV) remains the most common congenital infection and infectious complication in immunocompromised patients. The most successful HCMV vaccine to date, an HCMV glycoprotein B (gB) subunit vaccine adjuvanted with MF59, achieved 50% efficacy against primary HCMV infection. A previous study demonstrated that gB/MF59 vaccinees were less frequently infected with HCMV gB genotype strains most similar to the vaccine strain than strains encoding genetically distinct gB genotypes, suggesting strain-specific immunity accounted for the limited efficacy. To determine whether vaccination with multiple HCMV gB genotypes could increase the breadth of anti-HCMV gB humoral and cellular responses, we immunized 18 female rabbits with monovalent (gB-1), bivalent (gB-1+gB-3), or pentavalent (gB-1+gB-2+gB-3+gB-4+gB-5) gB lipid nanoparticle-encapsulated nucleoside-modified RNA (mRNA-LNP) vaccines. The multivalent vaccine groups did not demonstrate a higher magnitude or breadth of the IgG response to the gB ectodomain or cell-associated gB compared to that of the monovalent vaccine. Also, the multivalent vaccines did not show an increase in the breadth of neutralization activity and antibody-dependent cellular phagocytosis against HCMV strains encoding distinct gB genotypes. Interestingly, peripheral blood mononuclear cell-derived gB-2-specific T-cell responses elicited by multivalent vaccines were of a higher magnitude compared to that of monovalent vaccinated animals against a vaccine-mismatched gB genotype at peak immunogenicity. Yet, no statistical differences were observed in T cell response against gB-3 and gB-5 variable regions among the three vaccine groups. Our data suggests that the inclusion of multivalent gB antigens is not an effective strategy to increase the breadth of anti-HCMV gB antibody and T cell responses. Understanding how to increase the HCMV vaccine protection breadth will be essential to improve the vaccine efficacy.
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Affiliation(s)
- Hsuan-Yuan Wang
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, 10065, USA
- Duke University Medical Center, Duke Human Vaccine Institute, Durham, NC, 27710, USA
| | - Leike Li
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Takeda Pharmaceutical, San Diego, CA, 92121, USA
| | - Cody S Nelson
- Division of Allergy and Clinical Immunology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Richard Barfield
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
- Center for Human Systems Immunology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Sarah Valencia
- Duke University Medical Center, Duke Human Vaccine Institute, Durham, NC, 27710, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, 27710, USA
- Center for Human Systems Immunology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Hiromi Muramatsu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Paulo J C Lin
- Acuitas Therapeutics, Vancouver, BC, V6T 1Z3, Canada
| | - Norbert Pardi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Drew Weissman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sallie R Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, 10065, USA.
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13
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Erazo D, Grant L, Ghisbain G, Marini G, Colón-González FJ, Wint W, Rizzoli A, Van Bortel W, Vogels CBF, Grubaugh ND, Mengel M, Frieler K, Thiery W, Dellicour S. Contribution of climate change to the spatial expansion of West Nile virus in Europe. Nat Commun 2024; 15:1196. [PMID: 38331945 PMCID: PMC10853512 DOI: 10.1038/s41467-024-45290-3] [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: 06/27/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
West Nile virus (WNV) is an emerging mosquito-borne pathogen in Europe where it represents a new public health threat. While climate change has been cited as a potential driver of its spatial expansion on the continent, a formal evaluation of this causal relationship is lacking. Here, we investigate the extent to which WNV spatial expansion in Europe can be attributed to climate change while accounting for other direct human influences such as land-use and human population changes. To this end, we trained ecological niche models to predict the risk of local WNV circulation leading to human cases to then unravel the isolated effect of climate change by comparing factual simulations to a counterfactual based on the same environmental changes but a counterfactual climate where long-term trends have been removed. Our findings demonstrate a notable increase in the area ecologically suitable for WNV circulation during the period 1901-2019, whereas this area remains largely unchanged in a no-climate-change counterfactual. We show that the drastic increase in the human population at risk of exposure is partly due to historical changes in population density, but that climate change has also been a critical driver behind the heightened risk of WNV circulation in Europe.
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Affiliation(s)
- Diana Erazo
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.
| | - Luke Grant
- Department of Water and Climate, Vrije Universiteit Brussel, Brussels, Belgium
| | - Guillaume Ghisbain
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Laboratory of Zoology, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Giovanni Marini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | | | - William Wint
- Environmental Research Group Oxford Ltd, Department of Biology, Mansfield Road, Oxford, OX1 3SZ, UK
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy
| | - Wim Van Bortel
- Unit Entomology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Outbreak Research team, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Matthias Mengel
- Department Transformation Pathways, Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
| | - Katja Frieler
- Department Transformation Pathways, Potsdam Institute for Climate Impact Research (PIK), Potsdam, Germany
| | - Wim Thiery
- Department of Water and Climate, Vrije Universiteit Brussel, Brussels, Belgium
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.
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14
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Sun Q, Rowland BT, Chen J, Mikhaylova AV, Avery C, Peters U, Lundin J, Matise T, Buyske S, Tao R, Mathias RA, Reiner AP, Auer PL, Cox NJ, Kooperberg C, Thornton TA, Raffield LM, Li Y. Improving polygenic risk prediction in admixed populations by explicitly modeling ancestral-differential effects via GAUDI. Nat Commun 2024; 15:1016. [PMID: 38310129 PMCID: PMC10838303 DOI: 10.1038/s41467-024-45135-z] [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: 10/07/2022] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
Polygenic risk scores (PRS) have shown successes in clinics, but most PRS methods focus only on participants with distinct primary continental ancestry without accommodating recently-admixed individuals with mosaic continental ancestry backgrounds for different segments of their genomes. Here, we develop GAUDI, a novel penalized-regression-based method specifically designed for admixed individuals. GAUDI explicitly models ancestry-differential effects while borrowing information across segments with shared ancestry in admixed genomes. We demonstrate marked advantages of GAUDI over other methods through comprehensive simulation and real data analyses for traits with associated variants exhibiting ancestral-differential effects. Leveraging data from the Women's Health Initiative study, we show that GAUDI improves PRS prediction of white blood cell count and C-reactive protein in African Americans by > 64% compared to alternative methods, and even outperforms PRS-CSx with large European GWAS for some scenarios. We believe GAUDI will be a valuable tool to mitigate disparities in PRS performance in admixed individuals.
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Affiliation(s)
- Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bryce T Rowland
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Anna V Mikhaylova
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Christy Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Jessica Lundin
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Tara Matise
- Department of Genetics, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Steve Buyske
- Department of Statistics, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ran Tao
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Timothy A Thornton
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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15
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Yang J, Huggins AA, Sun D, Baird CL, Haswell CC, Frijling JL, Olff M, van Zuiden M, Koch SBJ, Nawijn L, Veltman DJ, Suarez-Jimenez B, Zhu X, Neria Y, Hudson AR, Mueller SC, Baker JT, Lebois LAM, Kaufman ML, Qi R, Lu GM, Říha P, Rektor I, Dennis EL, Ching CRK, Thomopoulos SI, Salminen LE, Jahanshad N, Thompson PM, Stein DJ, Koopowitz SM, Ipser JC, Seedat S, du Plessis S, van den Heuvel LL, Wang L, Zhu Y, Li G, Sierk A, Manthey A, Walter H, Daniels JK, Schmahl C, Herzog JI, Liberzon I, King A, Angstadt M, Davenport ND, Sponheim SR, Disner SG, Straube T, Hofmann D, Grupe DW, Nitschke JB, Davidson RJ, Larson CL, deRoon-Cassini TA, Blackford JU, Olatunji BO, Gordon EM, May G, Nelson SM, Abdallah CG, Levy I, Harpaz-Rotem I, Krystal JH, Morey RA, Sotiras A. Examining the association between posttraumatic stress disorder and disruptions in cortical networks identified using data-driven methods. Neuropsychopharmacology 2024; 49:609-619. [PMID: 38017161 PMCID: PMC10789873 DOI: 10.1038/s41386-023-01763-5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 11/30/2023]
Abstract
Posttraumatic stress disorder (PTSD) is associated with lower cortical thickness (CT) in prefrontal, cingulate, and insular cortices in diverse trauma-affected samples. However, some studies have failed to detect differences between PTSD patients and healthy controls or reported that PTSD is associated with greater CT. Using data-driven dimensionality reduction, we sought to conduct a well-powered study to identify vulnerable networks without regard to neuroanatomic boundaries. Moreover, this approach enabled us to avoid the excessive burden of multiple comparison correction that plagues vertex-wise methods. We derived structural covariance networks (SCNs) by applying non-negative matrix factorization (NMF) to CT data from 961 PTSD patients and 1124 trauma-exposed controls without PTSD. We used regression analyses to investigate associations between CT within SCNs and PTSD diagnosis (with and without accounting for the potential confounding effect of trauma type) and symptom severity in the full sample. We performed additional regression analyses in subsets of the data to examine associations between SCNs and comorbid depression, childhood trauma severity, and alcohol abuse. NMF identified 20 unbiased SCNs, which aligned closely with functionally defined brain networks. PTSD diagnosis was most strongly associated with diminished CT in SCNs that encompassed the bilateral superior frontal cortex, motor cortex, insular cortex, orbitofrontal cortex, medial occipital cortex, anterior cingulate cortex, and posterior cingulate cortex. CT in these networks was significantly negatively correlated with PTSD symptom severity. Collectively, these findings suggest that PTSD diagnosis is associated with widespread reductions in CT, particularly within prefrontal regulatory regions and broader emotion and sensory processing cortical regions.
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Affiliation(s)
- Jin Yang
- Department of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ashley A Huggins
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- Mid-Atlantic Mental Illness Research Education and Clinical Center, Durham VA Medical Center, Durham, NC, USA
| | - Delin Sun
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- Mid-Atlantic Mental Illness Research Education and Clinical Center, Durham VA Medical Center, Durham, NC, USA
- Department of Psychology, The Education University of Hong Kong, Hong Kong, China
| | - C Lexi Baird
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- Mid-Atlantic Mental Illness Research Education and Clinical Center, Durham VA Medical Center, Durham, NC, USA
| | - Courtney C Haswell
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- Mid-Atlantic Mental Illness Research Education and Clinical Center, Durham VA Medical Center, Durham, NC, USA
| | - Jessie L Frijling
- Department of Psychiatry, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Miranda Olff
- Department of Psychiatry, Amsterdam University Medical Center, Amsterdam, The Netherlands
- ARQ National Psychotrauma Centre, Diemen, The Netherlands
| | - Mirjam van Zuiden
- Department of Psychiatry, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Saskia B J Koch
- Department of Psychiatry, Amsterdam University Medical Center, Amsterdam, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Laura Nawijn
- Department of Psychiatry, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Dick J Veltman
- Department of Psychiatry, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Benjamin Suarez-Jimenez
- Del Monte Institute for Neuroscience, University of Rochester Medical Center, Rochester, NY, USA
| | - Xi Zhu
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
| | - Yuval Neria
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
| | - Anna R Hudson
- Department of Experimental Clinical and Health Psychology, Ghent University, Ghent, Belgium
| | - Sven C Mueller
- Department of Experimental Clinical and Health Psychology, Ghent University, Ghent, Belgium
| | - Justin T Baker
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Institute for Technology in Psychiatry, McLean Hospital, Harvard University, Belmont, MA, USA
| | - Lauren A M Lebois
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Depression and Anxiety Disorders, McLean Hospital, Belmont, MA, USA
| | - Milissa L Kaufman
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Women's Mental Health, McLean Hospital, Belmont, MA, USA
| | - Rongfeng Qi
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Jiangsu, China
| | - Guang Ming Lu
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, Jiangsu, China
| | - Pavel Říha
- First Department of Neurology, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Multimodal and Functional Neuroimaging Research Group, Masaryk University, Brno, Czech Republic
| | - Ivan Rektor
- CEITEC-Central European Institute of Technology, Multimodal and Functional Neuroimaging Research Group, Masaryk University, Brno, Czech Republic
| | - Emily L Dennis
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
- George E. Wahlen Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Christopher R K Ching
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Sophia I Thomopoulos
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Lauren E Salminen
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Neda Jahanshad
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Dan J Stein
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Sheri M Koopowitz
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Jonathan C Ipser
- Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Soraya Seedat
- Department of Psychiatry, Stellenbosch University, Cape Town, South Africa
| | - Stefan du Plessis
- Department of Psychiatry, Stellenbosch University, Cape Town, South Africa
| | | | - Li Wang
- Laboratory for Traumatic Stress Studies, Chinese Academy of Sciences Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Zhu
- Laboratory for Traumatic Stress Studies, Chinese Academy of Sciences Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Gen Li
- Laboratory for Traumatic Stress Studies, Chinese Academy of Sciences Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Anika Sierk
- University Medical Centre Charité, Berlin, Germany
| | | | | | - Judith K Daniels
- Department of Clinical Psychology, University of Groningen, Groningen, The Netherlands
| | - Christian Schmahl
- Department of Psychosomatic Medicine and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Julia I Herzog
- Department of Psychosomatic Medicine and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Israel Liberzon
- Department of Psychiatry and Behavioral Science, Texas A&M University, College Station, TX, USA
| | - Anthony King
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Mike Angstadt
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas D Davenport
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Scott R Sponheim
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Seth G Disner
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Thomas Straube
- Institute of Medical Psychology and Systems Neuroscience, University of Münster, Münster, Germany
| | - David Hofmann
- Institute of Medical Psychology and Systems Neuroscience, University of Münster, Münster, Germany
| | - Daniel W Grupe
- Center for Healthy Minds, University of Wisconsin-Madison, Madison, WI, USA
| | - Jack B Nitschke
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI, USA
| | - Richard J Davidson
- Center for Healthy Minds, University of Wisconsin-Madison, Madison, WI, USA
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Psychology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christine L Larson
- Department of Psychology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Terri A deRoon-Cassini
- Division of Trauma and Acute Care Surgery, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, USA
- Comprehensive Injury Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jennifer U Blackford
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bunmi O Olatunji
- Department of Psychology, Vanderbilt University, Nashville, TN, USA
| | - Evan M Gordon
- Department of Radiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Geoffrey May
- Veterans Integrated Service Network-17 Center of Excellence for Research on Returning War Veterans, Waco, TX, USA
- Department of Psychology and Neuroscience, Baylor University, Waco, TX, USA
- Center for Vital Longevity, School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, USA
- Department of Psychiatry and Behavioral Science, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Steven M Nelson
- Veterans Integrated Service Network-17 Center of Excellence for Research on Returning War Veterans, Waco, TX, USA
- Department of Psychology and Neuroscience, Baylor University, Waco, TX, USA
- Center for Vital Longevity, School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, USA
- Department of Psychiatry and Behavioral Science, Texas A&M University Health Science Center, Bryan, TX, USA
| | - Chadi G Abdallah
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychiatry of Behavioral Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Ifat Levy
- Department of Comparative Medicine, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale University, New Haven, CT, USA
- Department of Psychology, Yale University, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
- Division of Clinical Neuroscience, National Center for PTSD, West Haven, CT, USA
| | - Ilan Harpaz-Rotem
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Department of Psychology, Yale University, New Haven, CT, USA
- Division of Clinical Neuroscience, National Center for PTSD, West Haven, CT, USA
| | - John H Krystal
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Division of Clinical Neuroscience, National Center for PTSD, West Haven, CT, USA
| | - Rajendra A Morey
- Duke-UNC Brain Imaging and Analysis Center, Duke University, Durham, NC, USA.
- Mid-Atlantic Mental Illness Research Education and Clinical Center, Durham VA Medical Center, Durham, NC, USA.
| | - Aristeidis Sotiras
- Department of Radiology, Washington University in St. Louis, St. Louis, MO, USA
- Institute for Informatics, Data Science & Biostatistics, Washington University in St. Louis, St. Louis, MO, USA
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16
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Hariharan S, Whitfield BT, Pirozzi CJ, Waitkus MS, Brown MC, Bowie ML, Irvin DM, Roso K, Fuller R, Hostettler J, Dharmaiah S, Gibson EA, Briley A, Mangoli A, Fraley C, Shobande M, Stevenson K, Zhang G, Malgulwar PB, Roberts H, Roskoski M, Spasojevic I, Keir ST, He Y, Castro MG, Huse JT, Ashley DM. Interplay between ATRX and IDH1 mutations governs innate immune responses in diffuse gliomas. Nat Commun 2024; 15:730. [PMID: 38272925 PMCID: PMC10810843 DOI: 10.1038/s41467-024-44932-w] [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: 04/24/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Stimulating the innate immune system has been explored as a therapeutic option for the treatment of gliomas. Inactivating mutations in ATRX, defining molecular alterations in IDH-mutant astrocytomas, have been implicated in dysfunctional immune signaling. However, little is known about the interplay between ATRX loss and IDH mutation on innate immunity. To explore this, we generated ATRX-deficient glioma models in the presence and absence of the IDH1R132H mutation. ATRX-deficient glioma cells are sensitive to dsRNA-based innate immune agonism and exhibit impaired lethality and increased T-cell infiltration in vivo. However, the presence of IDH1R132H dampens baseline expression of key innate immune genes and cytokines in a manner restored by genetic and pharmacological IDH1R132H inhibition. IDH1R132H co-expression does not interfere with the ATRX deficiency-mediated sensitivity to dsRNA. Thus, ATRX loss primes cells for recognition of dsRNA, while IDH1R132H reversibly masks this priming. This work reveals innate immunity as a therapeutic vulnerability of astrocytomas.
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Affiliation(s)
- Seethalakshmi Hariharan
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Benjamin T Whitfield
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher J Pirozzi
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Matthew S Waitkus
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Michael C Brown
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Michelle L Bowie
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - David M Irvin
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristen Roso
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Rebecca Fuller
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Janell Hostettler
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Sharvari Dharmaiah
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emiley A Gibson
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Aaron Briley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Avani Mangoli
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Casey Fraley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Mariah Shobande
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Kevin Stevenson
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Gao Zhang
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Prit Benny Malgulwar
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hannah Roberts
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Martin Roskoski
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Ivan Spasojevic
- PK/PD Core Laboratory, Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
- Department of Medicine - Oncology, Duke University Medical Center, Durham, NC, USA
| | - Stephen T Keir
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Yiping He
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Jason T Huse
- Departments of Pathology and Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - David M Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, USA.
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA.
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17
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Kanatani S, Stiffler D, Bousema T, Yenokyan G, Sinnis P. Revisiting the Plasmodium sporozoite inoculum and elucidating the efficiency with which malaria parasites progress through the mosquito. Nat Commun 2024; 15:748. [PMID: 38272943 PMCID: PMC10811227 DOI: 10.1038/s41467-024-44962-4] [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: 10/30/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Malaria is initiated when infected anopheline mosquitoes inoculate sporozoites as they probe for blood. It is thought that all infected mosquitoes are equivalent in terms of their infectious potential, with parasite burden having no role in transmission success. In this study, using mosquitoes harboring the entire range of salivary gland sporozoite loads observed in the field, we demonstrate a strong and highly significant correlation between mosquito parasite burden and inoculum size. We then link the inoculum data to oocyst counts, the most commonly-used metric to assess mosquito infection in the field, and determine the efficiency with which oocyst sporozoites enter mosquito salivary glands. Taken together our data support the conclusion that mosquitoes with higher parasite burdens are more likely to initiate infection and contribute to onward transmission. Overall these data may account for some of the unexplained heterogeneity in transmission and enable more precise benchmarks for transmission-blocking interventions.
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Affiliation(s)
- Sachie Kanatani
- Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Johns Hopkins Malaria Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Deborah Stiffler
- Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Johns Hopkins Malaria Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Teun Bousema
- Department of Medical Microbiology & Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gayane Yenokyan
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Photini Sinnis
- Department of Molecular Microbiology & Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Johns Hopkins Malaria Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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18
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Lenze E, Torous J, Arean P. Digital and precision clinical trials: innovations for testing mental health medications, devices, and psychosocial treatments. Neuropsychopharmacology 2024; 49:205-214. [PMID: 37550438 PMCID: PMC10700595 DOI: 10.1038/s41386-023-01664-7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Abstract
Mental health treatment advances - including neuropsychiatric medications and devices, psychotherapies, and cognitive treatments - lag behind other fields of clinical medicine such as cardiovascular care. One reason for this gap is the traditional techniques used in mental health clinical trials, which slow the pace of progress, produce inequities in care, and undermine precision medicine goals. Newer techniques and methodologies, which we term digital and precision trials, offer solutions. These techniques consist of (1) decentralized (i.e., fully-remote) trials which improve the speed and quality of clinical trials and increase equity of access to research, (2) precision measurement which improves success rate and is essential for precision medicine, and (3) digital interventions, which offer increased reach of, and equity of access to, evidence-based treatments. These techniques and their rationales are described in detail, along with challenges and solutions for their utilization. We conclude with a vignette of a depression clinical trial using these techniques.
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Affiliation(s)
- Eric Lenze
- Departments of Psychiatry and Anesthesiology, Washington University School of Medicine, St Louis, MO, USA.
| | - John Torous
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Patricia Arean
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
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19
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Eisenlohr-Moul T, Swales DA, Rubinow DR, Schiff L, Schiller CE. Temporal dynamics of neurobehavioral hormone sensitivity in a scaled-down experimental model of early pregnancy and parturition. Neuropsychopharmacology 2024; 49:414-421. [PMID: 37524753 PMCID: PMC10724266 DOI: 10.1038/s41386-023-01687-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/02/2023]
Abstract
The hormonal changes of pregnancy and parturition can trigger robust changes in affective state, particularly among patients with a history of postpartum depression. However, more work is needed to elucidate the temporal dynamics of symptom emergence. The current study explored how quickly hormone-sensitive (HS+) individuals can be differentiated from hormone-insensitive (HS-) controls in the context of a tightly controlled experimental hormone manipulation, and which symptoms demonstrate the most rapid, consistent, and largest response during this protocol. Participants were female, non-pregnant, and euthymic, with a history of DSM-5 major depressive episode with peripartum onset (n = 15) or parous healthy controls with no psychiatric history (n = 15). Perinatal hormonal changes were simulated by inducing hypogonadism, adding back estradiol (E2) and progesterone (P4) to reach first-trimester levels for 8 weeks, and then subsequently withdrawing both hormones. Those reporting a 30% or greater increase during addback or withdrawal on select subscales of the Inventory of Depression and Anxiety Symptoms (IDAS) were identified as HS+. Participants provided daily ratings of symptoms throughout the study via the Daily Record of Severity of Problems. Results indicated that HS+ participants could be differentiated from HS- participants early in the hormone protocol, with many symptoms showing significantly greater change from baseline within the first week of addback. Notably, the most rapid symptom increases were observed for Anger/Irritability, Mood Swings, Overwhelm, Lethargy, Increased Appetite, Joint and Muscle Pain, and Breast Tenderness, reaching 50% of peak group contrast within the first week of hormone addback. The largest group effects were observed for Anger/Irritability, followed by Fatigue and Anxiety, and the most consistent group effects were observed for Anger/Irritability, Interpersonal Conflict, Overwhelm, and Hopelessness. Findings support the role of reproductive hormones in the onset of perinatal affective disorders. The rapid emergence of anger and irritability in HS+ participants suggests that these symptoms may be early indicators of perinatal hormone sensitivity.
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Affiliation(s)
- Tory Eisenlohr-Moul
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, 60612, USA.
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Danielle A Swales
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - David R Rubinow
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Lauren Schiff
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Crystal E Schiller
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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20
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Gadaleta M, Harrington P, Barnhill E, Hytopoulos E, Turakhia MP, Steinhubl SR, Quer G. Prediction of atrial fibrillation from at-home single-lead ECG signals without arrhythmias. NPJ Digit Med 2023; 6:229. [PMID: 38087028 PMCID: PMC10716265 DOI: 10.1038/s41746-023-00966-w] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024] Open
Abstract
Early identification of atrial fibrillation (AF) can reduce the risk of stroke, heart failure, and other serious cardiovascular outcomes. However, paroxysmal AF may not be detected even after a two-week continuous monitoring period. We developed a model to quantify the risk of near-term AF in a two-week period, based on AF-free ECG intervals of up to 24 h from 459,889 patch-based ambulatory single-lead ECG (modified lead II) recordings of up to 14 days. A deep learning model was used to integrate ECG morphology data with demographic and heart rhythm features toward AF prediction. Observing a 1-day AF-free ECG recording, the model with deep learning features produced the most accurate prediction of near-term AF with an area under the curve AUC = 0.80 (95% confidence interval, CI = 0.79-0.81), significantly improving discrimination compared to demographic metrics alone (AUC 0.67; CI = 0.66-0.68). Our model was able to predict incident AF over a two-week time frame with high discrimination, based on AF-free single-lead ECG recordings of various lengths. Application of the model may enable a digital strategy for improving diagnostic capture of AF by risk stratifying individuals with AF-negative ambulatory monitoring for prolonged or recurrent monitoring, potentially leading to more rapid initiation of treatment.
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Affiliation(s)
| | | | | | | | - Mintu P Turakhia
- iRhythm Technologies, San Francisco, CA, USA
- Stanford University School of Medicine, Stanford, CA, USA
| | - Steven R Steinhubl
- Scripps Research Translational Institute, La Jolla, CA, USA
- Purdue University, Weldon School of Biomedical Engineering, West Lafayette, IN, USA
| | - Giorgio Quer
- Scripps Research Translational Institute, La Jolla, CA, USA.
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21
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Puklin LS, Li F, Cartmel B, Zhao J, Sanft T, Lisevick A, Winer EP, Lustberg M, Spiegelman D, Sharifi M, Irwin ML, Ferrucci LM. Post-diagnosis weight trajectories and mortality among women with breast cancer. NPJ Breast Cancer 2023; 9:98. [PMID: 38042922 PMCID: PMC10693588 DOI: 10.1038/s41523-023-00603-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/16/2023] [Indexed: 12/04/2023] Open
Abstract
Weight gain after breast cancer diagnosis is associated with adverse health outcomes. Yet, few studies have characterized post-diagnosis weight change in the modern treatment era or populations most at risk for weight changes. Among women diagnosed with stages I-III breast cancer in the Smilow Care Network (2013-2019; N = 5441), we abstracted demographic and clinical characteristics from electronic health records and survival data from tumor registries. We assessed if baseline characteristics modified weight trajectories with nonlinear multilevel mixed-effect models. We evaluated body mass index (BMI) at diagnosis and weight change 1-year post-diagnosis in relation to all-cause and breast cancer-specific mortality with Cox proportional hazard models. Women had 34.4 ± 25.5 weight measurements over 3.2 ± 1.8 years of follow-up. Weight gain was associated with ER/PR-, HER2+ tumors, BMI ≤ 18.5 kg/m2, and age ≤ 45 years (+4.90 kg (standard error [SE] = 0.59), +3.24 kg (SE = 0.34), and +1.75 kg (SE = 0.10), respectively). Weight loss was associated with BMI ≥ 35 kg/m2 and age ≥ 70 years (-4.50 kg (SE = 0.08) and -4.34 kg (SE = 0.08), respectively). Large weight loss (≥10%), moderate weight loss (5-10%), and moderate weight gain (5-10%) 1-year after diagnosis were associated with higher all-cause mortality (hazard ratio [HR] = 2.93, 95% confidence interval [CI] = 2.28-3.75, HR = 1.32, 95% CI = 1.02-1.70 and HR = 1.39, 95% CI = 1.04-1.85, respectively). BMI ≥ 35 kg/m2 or BMI ≤ 18.5 kg/m2 at diagnosis were also associated with higher all-cause mortality. Weight change after a breast cancer diagnosis differed by demographic and clinical characteristics highlighting subgroups at-risk for weight change during a 5-year period post-diagnosis. Monitoring and interventions for weight management early in clinical care are important.
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Affiliation(s)
- Leah S Puklin
- Yale School of Public Health, Yale University, New Haven, CT, 06510, USA.
| | - Fangyong Li
- Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Brenda Cartmel
- Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
- Yale Cancer Center, New Haven, CT, 06510, USA
| | - Julian Zhao
- Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Tara Sanft
- Yale Cancer Center, New Haven, CT, 06510, USA
- Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
| | - Alexa Lisevick
- Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
- Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Eric P Winer
- Yale Cancer Center, New Haven, CT, 06510, USA
- Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
| | - Maryam Lustberg
- Yale Cancer Center, New Haven, CT, 06510, USA
- Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
| | - Donna Spiegelman
- Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
- Yale Cancer Center, New Haven, CT, 06510, USA
| | - Mona Sharifi
- Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
- Yale University School of Medicine, 333 Cedar St., New Haven, CT, 06520, USA
| | - Melinda L Irwin
- Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
- Yale Cancer Center, New Haven, CT, 06510, USA
| | - Leah M Ferrucci
- Yale School of Public Health, Yale University, New Haven, CT, 06510, USA
- Yale Cancer Center, New Haven, CT, 06510, USA
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22
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Oniani D, Hilsman J, Peng Y, Poropatich RK, Pamplin JC, Legault GL, Wang Y. Adopting and expanding ethical principles for generative artificial intelligence from military to healthcare. NPJ Digit Med 2023; 6:225. [PMID: 38042910 PMCID: PMC10693640 DOI: 10.1038/s41746-023-00965-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/15/2023] [Indexed: 12/04/2023] Open
Abstract
In 2020, the U.S. Department of Defense officially disclosed a set of ethical principles to guide the use of Artificial Intelligence (AI) technologies on future battlefields. Despite stark differences, there are core similarities between the military and medical service. Warriors on battlefields often face life-altering circumstances that require quick decision-making. Medical providers experience similar challenges in a rapidly changing healthcare environment, such as in the emergency department or during surgery treating a life-threatening condition. Generative AI, an emerging technology designed to efficiently generate valuable information, holds great promise. As computing power becomes more accessible and the abundance of health data, such as electronic health records, electrocardiograms, and medical images, increases, it is inevitable that healthcare will be revolutionized by this technology. Recently, generative AI has garnered a lot of attention in the medical research community, leading to debates about its application in the healthcare sector, mainly due to concerns about transparency and related issues. Meanwhile, questions around the potential exacerbation of health disparities due to modeling biases have raised notable ethical concerns regarding the use of this technology in healthcare. However, the ethical principles for generative AI in healthcare have been understudied. As a result, there are no clear solutions to address ethical concerns, and decision-makers often neglect to consider the significance of ethical principles before implementing generative AI in clinical practice. In an attempt to address these issues, we explore ethical principles from the military perspective and propose the "GREAT PLEA" ethical principles, namely Governability, Reliability, Equity, Accountability, Traceability, Privacy, Lawfulness, Empathy, and Eutonomy, for generative AI in healthcare. Furthermore, we introduce a framework for adopting and expanding these ethical principles in a practical way that has been useful in the military and can be applied to healthcare for generative AI, based on contrasting their ethical concerns and risks. Ultimately, we aim to proactively address the ethical dilemmas and challenges posed by the integration of generative AI into healthcare practice.
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Affiliation(s)
- David Oniani
- Department of Health Information Management, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jordan Hilsman
- Department of Health Information Management, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yifan Peng
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Ronald K Poropatich
- Division of Pulmonary, Allergy, Critical Care & Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Military Medicine Research, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jeremy C Pamplin
- Telemedicine & Advanced Technology Research Center, US Army, Fort Detrick, Frederick, MD, USA
| | - Gary L Legault
- Department of Surgery, Uniformed Services University, Bethesda, MD, USA
- Virtual Medical Center, Brooke Army Medical Center, San Antonio, TX, USA
| | - Yanshan Wang
- Department of Health Information Management, University of Pittsburgh, Pittsburgh, PA, USA.
- Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA.
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA.
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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23
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Hicks MR, Saleh KK, Clock B, Gibbs DE, Yang M, Younesi S, Gane L, Gutierrez-Garcia V, Xi H, Pyle AD. Regenerating human skeletal muscle forms an emerging niche in vivo to support PAX7 cells. Nat Cell Biol 2023; 25:1758-1773. [PMID: 37919520 PMCID: PMC10709143 DOI: 10.1038/s41556-023-01271-0] [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] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 09/26/2023] [Indexed: 11/04/2023]
Abstract
Skeletal muscle stem and progenitor cells including those derived from human pluripotent stem cells (hPSCs) offer an avenue towards personalized therapies and readily fuse to form human-mouse myofibres in vivo. However, skeletal muscle progenitor cells (SMPCs) inefficiently colonize chimeric stem cell niches and instead associate with human myofibres resembling foetal niches. We hypothesized competition with mouse satellite cells (SCs) prevented SMPC engraftment into the SC niche and thus generated an SC ablation mouse compatible with human engraftment. Single-nucleus RNA sequencing of SC-ablated mice identified the absence of a transient myofibre subtype during regeneration expressing Actc1. Similarly, ACTC1+ human myofibres supporting PAX7+ SMPCs increased in SC-ablated mice, and after re-injury we found SMPCs could now repopulate into chimeric niches. To demonstrate ACTC1+ myofibres are essential to supporting PAX7 SMPCs, we generated caspase-inducible ACTC1 depletion human pluripotent stem cells, and upon SMPC engraftment we found a 90% reduction in ACTC1+ myofibres and a 100-fold decrease in PAX7 cell numbers compared with non-induced controls. We used spatial RNA sequencing to identify key factors driving emerging human niche formation between ACTC1+ myofibres and PAX7+ SMPCs in vivo. This revealed that transient regenerating human myofibres are essential for emerging niche formation in vivo to support PAX7 SMPCs.
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Affiliation(s)
- Michael R Hicks
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA.
- Physiology and Biophysics, University of California, Irvine, CA, USA.
| | - Kholoud K Saleh
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Molecular, Cellular & Integrative Physiology Program, University of California, Los Angeles, CA, USA
| | - Ben Clock
- Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Devin E Gibbs
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Mandee Yang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Shahab Younesi
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Lily Gane
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | | | - Haibin Xi
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - April D Pyle
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
- Jonnson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
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24
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Min Y, Wang X, İş Ö, Patel TA, Gao J, Reddy JS, Quicksall ZS, Nguyen T, Lin S, Tutor-New FQ, Chalk JL, Mitchell AO, Crook JE, Nelson PT, Van Eldik LJ, Golde TE, Carrasquillo MM, Dickson DW, Zhang K, Allen M, Ertekin-Taner N. Cross species systems biology discovers glial DDR2, STOM, and KANK2 as therapeutic targets in progressive supranuclear palsy. Nat Commun 2023; 14:6801. [PMID: 37919278 PMCID: PMC10622416 DOI: 10.1038/s41467-023-42626-3] [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: 12/07/2022] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Progressive supranuclear palsy (PSP) is a neurodegenerative parkinsonian disorder characterized by cell-type-specific tau lesions in neurons and glia. Prior work uncovered transcriptome changes in human PSP brains, although their cell-specificity is unknown. Further, systematic data integration and experimental validation platforms to prioritize brain transcriptional perturbations as therapeutic targets in PSP are currently lacking. In this study, we combine bulk tissue (n = 408) and single nucleus RNAseq (n = 34) data from PSP and control brains with transcriptome data from a mouse tauopathy and experimental validations in Drosophila tau models for systematic discovery of high-confidence expression changes in PSP with therapeutic potential. We discover, replicate, and annotate thousands of differentially expressed genes in PSP, many of which reside in glia-enriched co-expression modules and cells. We prioritize DDR2, STOM, and KANK2 as promising therapeutic targets in PSP with striking cross-species validations. We share our findings and data via our interactive application tool PSP RNAseq Atlas ( https://rtools.mayo.edu/PSP_RNAseq_Atlas/ ). Our findings reveal robust glial transcriptome changes in PSP, provide a cross-species systems biology approach, and a tool for therapeutic target discoveries in PSP with potential application in other neurodegenerative diseases.
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Affiliation(s)
- Yuhao Min
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Özkan İş
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Tulsi A Patel
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Junli Gao
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Joseph S Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Zachary S Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - Thuy Nguyen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Shu Lin
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Jessica L Chalk
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Julia E Crook
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, MN, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY, USA
| | - Linda J Van Eldik
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, University of Kentucky, Lexington, KY, USA
| | - Todd E Golde
- Department of Pharmacology and Chemical Biology, Department of Neurology, Emory Center for Neurodegenerative Disease, Emory University, Atlanta, GA, USA
| | | | | | - Ke Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
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25
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Green CE, Tyson JE, Heyne RJ, Hintz SR, Vohr BR, Bann CM, Das A, Bell EF, Debsareea SB, Stephens E, Gantz MG, Petrie Huitema CM, Johnson KJ, Watterberg KL, Mosquera R, Peralta-Carcelen M, Wilson-Costello DE, Colaizy TT, Maitre NL, Merhar SL, Adams-Chapman I, Fuller J, Hartley-McAndrew ME, Malcolm WF, Winter S, Duncan AF, Myer GJ, Kicklighter SD, Wyckoff MH, DeMauro SB, Hibbs AM, Stoll BJ, Carlo WA, Van Meurs KP, Rysavy MA, Patel RM, Sánchez PJ, Laptook AR, Cotten CM, D'Angio CT, Walsh MC. Use of term reference infants in assessing the developmental outcome of extremely preterm infants: lessons learned in a multicenter study. J Perinatol 2023; 43:1398-1405. [PMID: 37542155 PMCID: PMC10615749 DOI: 10.1038/s41372-023-01729-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 07/27/2022] [Revised: 03/17/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023]
Abstract
OBJECTIVE Extremely preterm (EP) impairment rates are likely underestimated using the Bayley III norm-based thresholds scores and may be better assessed relative to concurrent healthy term reference (TR) infants born in the same hospital. STUDY DESIGN Blinded, certified examiners in the Neonatal Research Network (NRN) evaluated EP survivors and a sample of healthy TR infants recruited near the 2-year assessment age. RESULTS We assessed 1452 EP infants and 183 TR infants. TR-based thresholds showed higher overall EP impairment than Bayley norm-based thresholds (O.R. = 1.86; [95% CI 1.56-2.23], especially for severe impairment (36% vs. 24%; p ≤ 0.001). Difficulty recruiting TR patients at 2 years extended the study by 14 months and affected their demographics. CONCLUSION Impairment rates among EP infants appear to be substantially underestimated from Bayley III norms. These rates may be best assessed by comparison with healthy term infants followed with minimal attrition from birth in the same centers. CLINICALTRIALS GOV ID Term Reference (under the Generic Database Study): NCT00063063.
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Affiliation(s)
- Charles E Green
- Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Jon E Tyson
- Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Roy J Heyne
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Susan R Hintz
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine and Lucile Packard Children's Hospital, Palo Alto, CA, USA
| | - Betty R Vohr
- Department of Pediatrics, Women & Infants Hospital, Brown University, Providence, RI, USA
| | - Carla M Bann
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, Greensboro, NC, USA
| | - Abhik Das
- Social, Statistical and Environmental Sciences Unit, RTI International, Rockville, MD, USA
| | - Edward F Bell
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Sana Boral Debsareea
- Center for Clinical Research and Evidence-Based Medicine, University of Texas Houston McGovern Medical School, Houston, TX, USA
| | - Emily Stephens
- Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Marie G Gantz
- Social, Statistical and Environmental Sciences Unit, RTI International, Research Triangle Park, Greensboro, NC, USA
| | | | - Karen J Johnson
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | | | | | | | - Deanne E Wilson-Costello
- Department of Pediatrics, Rainbow Babies & Children's Hospital, Case Western Reserve University, Cleveland, OH, USA
| | - Tarah T Colaizy
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Nathalie L Maitre
- Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Stephanie L Merhar
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ira Adams-Chapman
- Emory University School of Medicine, Department of Pediatrics, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Janell Fuller
- Department of Pediatrics, University of New Mexico, Albuquerque, NM, USA
| | | | | | - Sarah Winter
- Department of Pediatrics, Division of Neonatology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrea F Duncan
- Department of Pediatrics, Pennsylvania Hospital, Philadelphia, PA, USA
| | - Gary J Myer
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | | | - Myra H Wyckoff
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sara B DeMauro
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Anna Maria Hibbs
- Department of Pediatrics, Rainbow Babies & Children's Hospital, Case Western Reserve University, Cleveland, OH, USA
| | - Barbara J Stoll
- Department of Pediatrics, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Waldemar A Carlo
- Division of Neonatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Krisa P Van Meurs
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine and Lucile Packard Children's Hospital, Palo Alto, CA, USA
| | - Matthew A Rysavy
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Ravi M Patel
- Emory University School of Medicine, Department of Pediatrics, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Pablo J Sánchez
- Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Abbot R Laptook
- Department of Pediatrics, Women & Infants Hospital, Brown University, Providence, RI, USA
| | | | - Carl T D'Angio
- Department of Pediatrics, Wake Medical Center, Raleigh, NC, USA
| | - Michele C Walsh
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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26
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Sidana S, Hosoya H, Jensen A, Liu L, Goyal A, Hovanky V, Sahaf B, Bharadwaj S, Latchford T, Arai S, Leahy S, Mei M, Budde LE, Muffly LS, Frank MJ, Dahiya S, Htut M, Miklos D, Janakiram M. Bendamustine vs. fludarabine/cyclophosphamide lymphodepletion prior to BCMA CAR-T cell therapy in multiple myeloma. Blood Cancer J 2023; 13:158. [PMID: 37833271 PMCID: PMC10576036 DOI: 10.1038/s41408-023-00929-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/15/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Affiliation(s)
- Surbhi Sidana
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA.
| | - Hitomi Hosoya
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexandria Jensen
- Quantitative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Anmol Goyal
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Vanna Hovanky
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Bita Sahaf
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Correlative Science Unit, Stanford University, Stanford, CA, USA
| | - Sushma Bharadwaj
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Theresa Latchford
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Sally Arai
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | | | - Lori S Muffly
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew J Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Saurabh Dahiya
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Myo Htut
- City of Hope Cancer Center, Duarte, CA, USA
| | - David Miklos
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
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27
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Timberline S, Bhatt A, Sunderji S, Tancredi DJ, Lakshminrusimha S, Siefkes H. Novel scoring tool of hypoxemic respiratory failure and pulmonary hypertension for defining severity of persistent pulmonary hypertension of newborn. J Perinatol 2023; 43:1281-1287. [PMID: 37626160 PMCID: PMC10541330 DOI: 10.1038/s41372-023-01762-w] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/02/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
OBJECTIVE To obtain preliminary validity data for a hypoxemic respiratory failure/pulmonary hypertension (HRF/PH) score for classifying persistent pulmonary hypertension of the newborn (PPHN). STUDY DESIGN Retrospective chart review of 100 consecutive neonates admitted to a Children's hospital from 2016-2021 with PPHN, gestational age ≥34 weeks, and echocardiograms in the first week. We assessed the correlation between HRF/PH score and short-term outcomes using linear and logistic regressions. RESULTS HRF/PH scores ranged 2-12 (mean 8.5), and were classified mild (0-5), moderate (6-10), and severe (11-15), with 6%, 77% and 17% infants in respective categories. HRF/PH score category correlated with invasive ventilation, nitric oxide, high frequency ventilation, vasoactive infusions, extracorporeal life support and death. HRF/PH score category did not correlate with duration of support or length of stay. CONCLUSION The HRF/PH score offers a promising representation of disease severity for PPHN. The tool requires further validation in prospective studies and evaluation for long-term outcomes.
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Affiliation(s)
- Sage Timberline
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Avni Bhatt
- School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Sherzana Sunderji
- Department of Pediatrics, University of California, Davis, Sacramento, CA, USA
| | - Daniel J Tancredi
- Department of Pediatrics, University of California, Davis, Sacramento, CA, USA
| | | | - Heather Siefkes
- Department of Pediatrics, University of California, Davis, Sacramento, CA, USA.
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28
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Sircar A, Singh S, Xu-Monette ZY, Coyle KM, Hilton LK, Chavdoula E, Ranganathan P, Jain N, Hanel W, Tsichlis P, Alinari L, Peterson BR, Tao J, Muthusamy N, Baiocchi R, Epperla N, Young KH, Morin R, Sehgal L. Exploiting the fibroblast growth factor receptor-1 vulnerability to therapeutically restrict the MYC-EZH2-CDKN1C axis-driven proliferation in Mantle cell lymphoma. Leukemia 2023; 37:2094-2106. [PMID: 37598282 PMCID: PMC10539170 DOI: 10.1038/s41375-023-02006-8] [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: 02/10/2023] [Accepted: 08/08/2023] [Indexed: 08/21/2023]
Abstract
Mantle cell lymphoma (MCL) is a lethal hematological malignancy with a median survival of 4 years. Its lethality is mainly attributed to a limited understanding of clinical tumor progression and resistance to current therapeutic regimes. Intrinsic, prolonged drug treatment and tumor-microenvironment (TME) facilitated factors impart pro-tumorigenic and drug-insensitivity properties to MCL cells. Hence, elucidating neoteric pharmacotherapeutic molecular targets involved in MCL progression utilizing a global "unified" analysis for improved disease prevention is an earnest need. Using integrated transcriptomic analyses in MCL patients, we identified a Fibroblast Growth Factor Receptor-1 (FGFR1), and analyses of MCL patient samples showed that high FGFR1 expression was associated with shorter overall survival in MCL patient cohorts. Functional studies using pharmacological intervention and loss of function identify a novel MYC-EZH2-CDKN1C axis-driven proliferation in MCL. Further, pharmacological targeting with erdafitinib, a selective small molecule targeting FGFRs, induced cell-cycle arrest and cell death in-vitro, inhibited tumor progression, and improved overall survival in-vivo. We performed extensive pre-clinical assessments in multiple in-vivo model systems to confirm the therapeutic potential of erdafitinib in MCL and demonstrated FGFR1 as a viable therapeutic target in MCL.
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Affiliation(s)
- Anuvrat Sircar
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Satishkumar Singh
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Zijun Y Xu-Monette
- Division of Hematopathology, Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Krysta Mila Coyle
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Laura K Hilton
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Evangelia Chavdoula
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Parvathi Ranganathan
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Neeraj Jain
- Division of Cancer Biology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Walter Hanel
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Philip Tsichlis
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Lapo Alinari
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Blake R Peterson
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Jianguo Tao
- Division of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Natarajan Muthusamy
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Robert Baiocchi
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Narendranath Epperla
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Ken H Young
- Division of Hematopathology, Department of Pathology, Duke University Medical Center, Durham, NC, USA
- Duke Cancer Institute, Durham, NC, USA
| | - Ryan Morin
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, BC, Canada
| | - Lalit Sehgal
- Division of Hematology, College of Medicine, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA.
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29
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Fowler A, Van Rompay KKA, Sampson M, Leo J, Watanabe JK, Usachenko JL, Immareddy R, Lovato DM, Schiller JT, Remaley AT, Chackerian B. A virus-like particle-based bivalent PCSK9 vaccine lowers LDL-cholesterol levels in non-human primates. NPJ Vaccines 2023; 8:142. [PMID: 37770440 PMCID: PMC10539315 DOI: 10.1038/s41541-023-00743-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023] Open
Abstract
Elevated low-density lipoprotein cholesterol (LDL-C) is an important risk factor in the development of atherosclerotic cardiovascular disease (ASCVD). Inhibitors of proprotein convertase subtilisin/kexin type 9 (PCSK9), a negative regulator of LDL-C metabolism, have emerged as promising approaches for reducing elevated LDL-C levels. Here, we evaluated the cholesterol-lowering efficacy of virus-like particle (VLP) based vaccines that target epitopes found within the LDL receptor (LDL-R) binding domain of PCSK9. In both mice and non-human primates, a bivalent VLP vaccine targeting two distinct epitopes on PCSK9 elicited strong and durable antibody responses and lowered cholesterol levels. In macaques, a VLP vaccine targeting a single PCSK9 epitope was only effective at lowering LDL-C levels in combination with statins, whereas immunization with the bivalent vaccine lowered LDL-C without requiring statin co-administration. These data highlight the efficacy of an alternative, vaccine-based approach for lowering LDL-C.
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Affiliation(s)
- Alexandra Fowler
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Maureen Sampson
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Javier Leo
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Jennifer K Watanabe
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Jodie L Usachenko
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Ramya Immareddy
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Debbie M Lovato
- Clinical and Translational Research Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - John T Schiller
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Alan T Remaley
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bryce Chackerian
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, USA.
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Houghton DC, Spratt HM, Keyser-Marcus L, Bjork JM, Neigh GN, Cunningham KA, Ramey T, Moeller FG. Behavioral and neurocognitive factors distinguishing post-traumatic stress comorbidity in substance use disorders. Transl Psychiatry 2023; 13:296. [PMID: 37709748 PMCID: PMC10502088 DOI: 10.1038/s41398-023-02591-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 08/08/2023] [Accepted: 08/25/2023] [Indexed: 09/16/2023] Open
Abstract
Significant trauma histories and post-traumatic stress disorder (PTSD) are common in persons with substance use disorders (SUD) and often associate with increased SUD severity and poorer response to SUD treatment. As such, this sub-population has been associated with unique risk factors and treatment needs. Understanding the distinct etiological profile of persons with co-occurring SUD and PTSD is therefore crucial for advancing our knowledge of underlying mechanisms and the development of precision treatments. To this end, we employed supervised machine learning algorithms to interrogate the responses of 160 participants with SUD on the multidimensional NIDA Phenotyping Assessment Battery. Significant PTSD symptomatology was correctly predicted in 75% of participants (sensitivity: 80%; specificity: 72.22%) using a classification-based model based on anxiety and depressive symptoms, perseverative thinking styles, and interoceptive awareness. A regression-based machine learning model also utilized similar predictors, but failed to accurately predict severity of PTSD symptoms. These data indicate that even in a population already characterized by elevated negative affect (individuals with SUD), especially severe negative affect was predictive of PTSD symptomatology. In a follow-up analysis of a subset of 102 participants who also completed neurocognitive tasks, comorbidity status was correctly predicted in 86.67% of participants (sensitivity: 91.67%; specificity: 66.67%) based on depressive symptoms and fear-related attentional bias. However, a regression-based analysis did not identify fear-related attentional bias as a splitting factor, but instead split and categorized the sample based on indices of aggression, metacognition, distress tolerance, and interoceptive awareness. These data indicate that within a population of individuals with SUD, aberrations in tolerating and regulating aversive internal experiences may also characterize those with significant trauma histories, akin to findings in persons with anxiety without SUD. The results also highlight the need for further research on PTSD-SUD comorbidity that includes additional comparison groups (i.e., persons with only PTSD), captures additional comorbid diagnoses that may influence the PTSD-SUD relationship, examines additional types of SUDs (e.g., alcohol use disorder), and differentiates between subtypes of PTSD.
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Affiliation(s)
- David C Houghton
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Psychiatry and Behavioral Sciences, University of Texas Medical Branch, Galveston, TX, USA.
| | - Heidi M Spratt
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch, Galveston, TX, USA
- Department of Biostatistics and Data Science, University of Texas Medical Branch, Galveston, TX, USA
| | - Lori Keyser-Marcus
- Institute for Drug and Alcohol Studies, Virginia Commonwealth University, Richmond, VA, USA
| | - James M Bjork
- Institute for Drug and Alcohol Studies, Virginia Commonwealth University, Richmond, VA, USA
| | - Gretchen N Neigh
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA, USA
| | - Kathryn A Cunningham
- Center for Addiction Sciences and Therapeutics, University of Texas Medical Branch, Galveston, TX, USA
- Department of Psychiatry and Behavioral Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA
| | - Tatiana Ramey
- Division of Therapeutics and Medical Consequences, National Institute of Drug Abuse, National Institutes of Health, Rockville, MD, USA
| | - F Gerard Moeller
- Institute for Drug and Alcohol Studies, Virginia Commonwealth University, Richmond, VA, USA
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31
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Jose A, Elwing JM, Kawut SM, Pauciulo MW, Sherman KE, Nichols WC, Fallon MB, McCormack FX. Human liver single nuclear RNA sequencing implicates BMPR2, GDF15, arginine, and estrogen in portopulmonary hypertension. Commun Biol 2023; 6:826. [PMID: 37558836 PMCID: PMC10412637 DOI: 10.1038/s42003-023-05193-3] [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: 03/27/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
Portopulmonary hypertension (PoPH) is a type of pulmonary vascular disease due to portal hypertension that exhibits high morbidity and mortality. The mechanisms driving disease are unknown, and transcriptional characteristics unique to the PoPH liver remain unexplored. Here, we apply single nuclear RNA sequencing to compare cirrhotic livers from patients with and without PoPH. We identify characteristics unique to PoPH in cells surrounding the central hepatic vein, including increased growth differentiation factor signaling, enrichment of the arginine biosynthesis pathway, and differential expression of the bone morphogenic protein type II receptor and estrogen receptor type I genes. These results provide insight into the transcriptomic characteristics of the PoPH liver and mechanisms by which PoPH cellular dysfunction might contribute to pulmonary vascular remodeling.
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Affiliation(s)
- Arun Jose
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Jean M Elwing
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Steven M Kawut
- Department of Medicine, Perelman School at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael W Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kenneth E Sherman
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - William C Nichols
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Francis X McCormack
- Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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32
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Schmidt DR, Gramatikov IMT, Sheen A, Williams CL, Hurwitz M, Dodge LE, Holupka E, Kiger WS, Cornwall-Brady MR, Huang W, Mak HH, Cormier KS, Condon C, Dane Wittrup K, Yilmaz ÖH, Stevenson MA, Down JD, Floyd SR, Roper J, Vander Heiden MG. Ablative radiotherapy improves survival but does not cure autochthonous mouse models of prostate and colorectal cancer. Commun Med (Lond) 2023; 3:108. [PMID: 37558833 PMCID: PMC10412558 DOI: 10.1038/s43856-023-00336-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/24/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Genetically engineered mouse models (GEMMs) of cancer are powerful tools to study mechanisms of disease progression and therapy response, yet little is known about how these models respond to multimodality therapy used in patients. Radiation therapy (RT) is frequently used to treat localized cancers with curative intent, delay progression of oligometastases, and palliate symptoms of metastatic disease. METHODS Here we report the development, testing, and validation of a platform to immobilize and target tumors in mice with stereotactic ablative RT (SART). Xenograft and autochthonous tumor models were treated with hypofractionated ablative doses of radiotherapy. RESULTS We demonstrate that hypofractionated regimens used in clinical practice can be effectively delivered in mouse models. SART alters tumor stroma and the immune environment, improves survival in GEMMs of primary prostate and colorectal cancer, and synergizes with androgen deprivation in prostate cancer. Complete pathologic responses were achieved in xenograft models, but not in GEMMs. CONCLUSIONS While SART is capable of fully ablating xenografts, it is unable to completely eradicate disease in GEMMs, arguing that resistance to potentially curative therapy can be modeled in GEMMs.
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Affiliation(s)
- Daniel R Schmidt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Iva Monique T Gramatikov
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Allison Sheen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher L Williams
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Boston, MA, USA
| | - Martina Hurwitz
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Laura E Dodge
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward Holupka
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - W S Kiger
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Milton R Cornwall-Brady
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wei Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Howard H Mak
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathleen S Cormier
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Charlene Condon
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - K Dane Wittrup
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ömer H Yilmaz
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, USA
| | - Mary Ann Stevenson
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Julian D Down
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott R Floyd
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC, USA
| | - Jatin Roper
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Division of Gastroenterology, and Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Dana-Farber Cancer Institute, Boston, MA, USA.
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33
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Diamond EL, Francis JH, Lacouture ME, Rotemberg V, Yabe M, Petrova-Drus K, Ulaner GA, Reddy R, Abdel-Wahab O, Durham BH. CSF1R inhibition for histiocytic neoplasm with CBL mutations refractory to MEK1/2 inhibition. Leukemia 2023; 37:1737-1740. [PMID: 37355734 PMCID: PMC10400417 DOI: 10.1038/s41375-023-01947-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/02/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Affiliation(s)
- Eli L Diamond
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jasmine H Francis
- Ophthalmic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mario E Lacouture
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Veronica Rotemberg
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariko Yabe
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gary A Ulaner
- Department of Molecular Imaging and Therapy, Hoag Family Cancer Institute, Irvine, CA, USA
| | - Ryan Reddy
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin H Durham
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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34
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Reeves DB, Gaebler C, Oliveira TY, Peluso MJ, Schiffer JT, Cohn LB, Deeks SG, Nussenzweig MC. Impact of misclassified defective proviruses on HIV reservoir measurements. Nat Commun 2023; 14:4186. [PMID: 37443365 PMCID: PMC10345136 DOI: 10.1038/s41467-023-39837-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 10/17/2022] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Most proviruses persisting in people living with HIV (PWH) on antiretroviral therapy (ART) are defective. However, rarer intact proviruses almost always reinitiate viral rebound if ART stops. Therefore, assessing therapies to prevent viral rebound hinges on specifically quantifying intact proviruses. We evaluated the same samples from 10 male PWH on ART using the two-probe intact proviral DNA assay (IPDA) and near full length (nfl) Q4PCR. Both assays admitted similar ratios of intact to total HIV DNA, but IPDA found ~40-fold more intact proviruses. Neither assay suggested defective proviruses decay over 10 years. However, the mean intact half-lives were different: 108 months for IPDA and 65 months for Q4PCR. To reconcile this difference, we modeled additional longitudinal IPDA data and showed that decelerating intact decay could arise from very long-lived intact proviruses and/or misclassified defective proviruses: slowly decaying defective proviruses that are intact in IPDA probe locations (estimated up to 5%, in agreement with sequence library based predictions). The model also demonstrates how misclassification can lead to underestimated efficacy of therapies that exclusively reduce intact proviruses. We conclude that sensitive multi-probe assays combined with specific nfl-verified assays would be optimal to document absolute and changing levels of intact HIV proviruses.
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Affiliation(s)
- Daniel B Reeves
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Laboratory of Translational Immunology of Viral Infections, Department of Infectious Diseases, Charité -Universitätsmedizin, Berlin, Germany
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Lillian B Cohn
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, UCSF, San Francisco, CA, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
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35
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Pineda R, Kellner P, Guth R, Gronemeyer A, Smith J. NICU sensory experiences associated with positive outcomes: an integrative review of evidence from 2015-2020. J Perinatol 2023; 43:837-848. [PMID: 37029165 PMCID: PMC10325947 DOI: 10.1038/s41372-023-01655-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 12/01/2022] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/09/2023]
Abstract
To inform changes to the Supporting and Enhancing NICU Sensory Experiences (SENSE) program, studies investigating sensory-based interventions in the NICU with preterm infants born ≤32 weeks were identified. Studies published between October 2015 to December 2020, and with outcomes related to infant development or parent well-being, were included in this integrative review. The systematic search used databases including MEDLINE, Cumulative Index to Nursing and Allied Health Literature, the Cochrane Library, and Google Scholar. Fifty-seven articles (15 tactile, 9 auditory, 5 visual, 1 gustatory/olfactory, 5 kinesthetic, and 22 multimodal) were identified. The majority of the sensory interventions that were identified within the articles were reported in a previous integrative review (1995-2015) and already included in the SENSE program. New evidence has led to refinements of the SENSE program, notably the addition of position changes across postmenstrual age (PMA) and visual tracking starting at 34 weeks PMA.
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Affiliation(s)
- Roberta Pineda
- Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA.
- Keck School of Medicine, Department of Pediatrics, Los Angeles, CA, USA.
- Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO, USA.
| | - Polly Kellner
- Chan Division of Occupational Science and Occupational Therapy, University of Southern California, Los Angeles, CA, USA
| | - Rebecca Guth
- Center for Clinical Excellence, BJC HealthCare, St. Louis, MO, USA
| | | | - Joan Smith
- Department of Quality, Safety, and Practice Excellence, St. Louis Children's Hospital, St. Louis, MO, USA
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36
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Gonzalez-Reiche AS, Alshammary H, Schaefer S, Patel G, Polanco J, Carreño JM, Amoako AA, Rooker A, Cognigni C, Floda D, van de Guchte A, Khalil Z, Farrugia K, Assad N, Zhang J, Alburquerque B, Sominsky LA, Gleason C, Srivastava K, Sebra R, Ramirez JD, Banu R, Shrestha P, Krammer F, Paniz-Mondolfi A, Sordillo EM, Simon V, van Bakel H. Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants. Nat Commun 2023; 14:3235. [PMID: 37270625 PMCID: PMC10239218 DOI: 10.1038/s41467-023-38867-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [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: 10/07/2022] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, direct evidence of subsequent transmission and continued stepwise adaptation is lacking. Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins. Our findings demonstrate not only that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome but also that patients with persistent infections can transmit these viral variants. Thus, there is, an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients.
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Affiliation(s)
- Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Schaefer
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gopi Patel
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jose Polanco
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Angela A Amoako
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aria Rooker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christian Cognigni
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel Floda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nima Assad
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jian Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bremy Alburquerque
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Levy A Sominsky
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan David Ramirez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Amadori L, Calcagno C, Fernandez DM, Koplev S, Fernandez N, Kaur R, Mury P, Khan NS, Sajja S, Shamailova R, Cyr Y, Jeon M, Hill CA, Chong PS, Naidu S, Sakurai K, Ghotbi AA, Soler R, Eberhardt N, Rahman A, Faries P, Moore KJ, Fayad ZA, Ma’ayan A, Giannarelli C. Systems immunology-based drug repurposing framework to target inflammation in atherosclerosis. Nat Cardiovasc Res 2023; 2:550-571. [PMID: 37771373 PMCID: PMC10538622 DOI: 10.1038/s44161-023-00278-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/28/2023] [Indexed: 09/30/2023]
Abstract
The development of new immunotherapies to treat the inflammatory mechanisms that sustain atherosclerotic cardiovascular disease (ASCVD) is urgently needed. Herein, we present a path to drug repurposing to identify immunotherapies for ASCVD. The integration of time-of-flight mass cytometry and RNA sequencing identified unique inflammatory signatures in peripheral blood mononuclear cells stimulated with ASCVD plasma. By comparing these inflammatory signatures to large-scale gene expression data from the LINCS L1000 dataset, we identified drugs that could reverse this inflammatory response. Ex vivo screens, using human samples, showed that saracatinib-a phase 2a-ready SRC and ABL inhibitor-reversed the inflammatory responses induced by ASCVD plasma. In Apoe-/- mice, saracatinib reduced atherosclerosis progression by reprogramming reparative macrophages. In a rabbit model of advanced atherosclerosis, saracatinib reduced plaque inflammation measured by [18F] fluorodeoxyglucose positron emission tomography-magnetic resonance imaging. Here we show a systems immunology-driven drug repurposing with a preclinical validation strategy to aid the development of cardiovascular immunotherapies.
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Affiliation(s)
- Letizia Amadori
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
- The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Claudia Calcagno
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Dawn M. Fernandez
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Simon Koplev
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nicolas Fernandez
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ravneet Kaur
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Pauline Mury
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Nayaab S Khan
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Swathy Sajja
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Roza Shamailova
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Yannick Cyr
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Minji Jeon
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Christopher A. Hill
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Peik Sean Chong
- The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Sonum Naidu
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Ken Sakurai
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Adam Ali Ghotbi
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Raphael Soler
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Natalia Eberhardt
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Adeeb Rahman
- The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Peter Faries
- Department of Surgery, Vascular Division, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Kathryn J. Moore
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
| | - Zahi A. Fayad
- BioMedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Diagnostic, Molecular and Interventional Radiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Avi Ma’ayan
- Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Chiara Giannarelli
- Department of Medicine, Division of Cardiology, NYU Cardiovascular Research Center, New York, NY USA
- Department of Medicine, Division of Cardiology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Pathology; NYU Grossman School of Medicine, NYU Langone Health, New York, NY USA
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38
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Fineberg SK, Choi EY, Shapiro-Thompson R, Dhaliwal K, Neustadter E, Sakheim M, Null K, Trujillo-Diaz D, Rondeau J, Pittaro GF, Peters JR, Corlett PR, Krystal JH. A pilot randomized controlled trial of ketamine in Borderline Personality Disorder. Neuropsychopharmacology 2023; 48:991-999. [PMID: 36804489 PMCID: PMC10209175 DOI: 10.1038/s41386-023-01540-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/13/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 02/19/2023]
Abstract
This study is the first randomized controlled trial to test the effects of ketamine in Borderline Personality Disorder (BPD). BPD remains undertreated in the community and no medication has FDA approval for this indication. People with BPD experience chronic mood disturbances with depressed mood, suicidal ideation, and severe social difficulties. In this double-blind, randomized controlled pilot study, we tested the effects of one infusion of ketamine (0.5 mg/kg, n = 10) or the psychoactive comparator drug midazolam (0.04 mg/kg, n = 12) in adults with BPD. Infusions were well tolerated in both groups. Dissociative symptoms during infusion were more intense with ketamine than midazolam (t(12.3) = 3.61, p = 0.01), but they resolved by 40 min after infusion in both groups. Post-infusion adverse events were at the expected low levels in both groups. For our primary outcome measure of suicidal ideation and our secondary outcome measure of depression, we found numerical reduction but not significant group or group x timepoint difference (p > 0.05). For our secondary outcome measures of anxiety and BPD symptoms, we did not observe group or group x timepoint differences. There was a group x timepoint effect for socio-occupational functioning (F(1,20.12) = 5.16, p = 0.03, at Day 14, ketamine group showed more improvement than midazolam group). An exploratory analysis revealed that improvement in socio-occupational functioning was correlated with improvement in depression in the ketamine group (r(8) = 0.65, p = 0.04) but not midazolam group (r(9) = 0.41, p = 0.216). This pilot study provides the first randomized controlled evidence of the effects of antidepressant-dosed ketamine in people with BPD. Our results provide reason for optimism that antidepressant-dosed ketamine will be well-tolerated in larger studies and may provide clinical benefit for mood symptoms and related impairments in people with BPD.
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Affiliation(s)
- Sarah K Fineberg
- Yale School of Medicine Department of Psychiatry, New Haven, CT, USA.
| | - Esther Y Choi
- Yale School of Medicine Department of Psychiatry, New Haven, CT, USA
| | - Rosa Shapiro-Thompson
- Yale School of Medicine Department of Psychiatry, New Haven, CT, USA
- Goucher College Post-Baccalaureate Premedical Program, Baltimore, MA, USA
| | | | - Eli Neustadter
- Yale School of Medicine Department of Psychiatry, New Haven, CT, USA
| | | | - Kaylee Null
- University of California Los Angeles Department of Psychology, Los Angeles, CA, USA
| | - Daniel Trujillo-Diaz
- Alpert Medical School of Brown University Department of Psychiatry and Human Behavior, Providence, RI, USA
| | | | | | - Jessica R Peters
- Alpert Medical School of Brown University Department of Psychiatry and Human Behavior, Providence, RI, USA
| | - Philip R Corlett
- Yale School of Medicine Department of Psychiatry, New Haven, CT, USA
| | - John H Krystal
- Yale School of Medicine Department of Psychiatry, New Haven, CT, USA
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39
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Cho H, Ren Z, Divaris K, Roach J, Lin BM, Liu C, Azcarate-Peril MA, Simancas-Pallares MA, Shrestha P, Orlenko A, Ginnis J, North KE, Zandona AGF, Ribeiro AA, Wu D, Koo H. Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries. Nat Commun 2023; 14:2919. [PMID: 37217495 PMCID: PMC10202936 DOI: 10.1038/s41467-023-38346-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 06/11/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.
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Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhi Ren
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeffrey Roach
- UNC Information Technology Services and Research Computing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chuwen Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miguel A Simancas-Pallares
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Poojan Shrestha
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Orlenko
- Artificial Intelligence Innovation Lab, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeannie Ginnis
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hyun Koo
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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40
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Brannock MD, Chew RF, Preiss AJ, Hadley EC, Redfield S, McMurry JA, Leese PJ, Girvin AT, Crosskey M, Zhou AG, Moffitt RA, Funk MJ, Pfaff ER, Haendel MA, Chute CG. Long COVID risk and pre-COVID vaccination in an EHR-based cohort study from the RECOVER program. Nat Commun 2023; 14:2914. [PMID: 37217471 PMCID: PMC10201472 DOI: 10.1038/s41467-023-38388-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [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: 11/04/2022] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Long COVID, or complications arising from COVID-19 weeks after infection, has become a central concern for public health experts. The United States National Institutes of Health founded the RECOVER initiative to better understand long COVID. We used electronic health records available through the National COVID Cohort Collaborative to characterize the association between SARS-CoV-2 vaccination and long COVID diagnosis. Among patients with a COVID-19 infection between August 1, 2021 and January 31, 2022, we defined two cohorts using distinct definitions of long COVID-a clinical diagnosis (n = 47,404) or a previously described computational phenotype (n = 198,514)-to compare unvaccinated individuals to those with a complete vaccine series prior to infection. Evidence of long COVID was monitored through June or July of 2022, depending on patients' data availability. We found that vaccination was consistently associated with lower odds and rates of long COVID clinical diagnosis and high-confidence computationally derived diagnosis after adjusting for sex, demographics, and medical history.
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Affiliation(s)
| | | | | | | | | | - Julie A McMurry
- University of Colorado Anschutz Medical Campus, Denver, CO, USA
| | - Peter J Leese
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Andrea G Zhou
- iTHRIV, University of Virginia, Charlottesville, VA, USA
| | - Richard A Moffitt
- Department of Biomedical Informatics, Stony Brook University, Stony Brook, NY, USA
- Departments of Biomedical Informatics and Hematology and Medical Ontology, Emory University, Atlanta, GA, USA
| | | | - Emily R Pfaff
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD, USA
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41
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Callahan TJ, Stefanski AL, Wyrwa JM, Zeng C, Ostropolets A, Banda JM, Baumgartner WA, Boyce RD, Casiraghi E, Coleman BD, Collins JH, Deakyne Davies SJ, Feinstein JA, Lin AY, Martin B, Matentzoglu NA, Meeker D, Reese J, Sinclair J, Taneja SB, Trinkley KE, Vasilevsky NA, Williams AE, Zhang XA, Denny JC, Ryan PB, Hripcsak G, Bennett TD, Haendel MA, Robinson PN, Hunter LE, Kahn MG. Ontologizing health systems data at scale: making translational discovery a reality. NPJ Digit Med 2023; 6:89. [PMID: 37208468 PMCID: PMC10196319 DOI: 10.1038/s41746-023-00830-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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
Common data models solve many challenges of standardizing electronic health record (EHR) data but are unable to semantically integrate all of the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping.
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Affiliation(s)
- Tiffany J Callahan
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Adrianne L Stefanski
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Jordan M Wyrwa
- Department of Physical Medicine and Rehabilitation, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Chenjie Zeng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anna Ostropolets
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Juan M Banda
- Department of Computer Science, Georgia State University, Atlanta, GA, 30303, USA
| | - William A Baumgartner
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Richard D Boyce
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15260, USA
| | - Elena Casiraghi
- Computer Science, Università degli Studi di Milano, Milan, Italy
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Ben D Coleman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Janine H Collins
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Sara J Deakyne Davies
- Department of Research Informatics & Data Science, Analytics Resource Center, Children's Hospital Colorado, Aurora, CO, 80045, USA
| | - James A Feinstein
- Adult and Child Center for Health Outcomes Research and Delivery Science (ACCORDS), University of Colorado Anschutz School of Medicine, Aurora, CO, 80045, USA
| | - Asiyah Y Lin
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Blake Martin
- Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | | | | | - Justin Reese
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Sanya B Taneja
- Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Katy E Trinkley
- Department of Family Medicine, University of Colorado Anschutz School of Medicine, Aurora, CO, 80045, USA
| | - Nicole A Vasilevsky
- Translational and Integrative Sciences Lab, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Andrew E Williams
- Tufts Institute for Clinical Research and Health Policy Studies, Tufts University, Boston, MA, 02155, USA
| | - Xingmin A Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Joshua C Denny
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Patrick B Ryan
- Janssen Research and Development, Raritan, NJ, 08869, USA
| | - George Hripcsak
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Tellen D Bennett
- Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Melissa A Haendel
- Departments of Biomedical Informatics and Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Lawrence E Hunter
- Computational Bioscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael G Kahn
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
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42
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Marino S, Akel N, Li S, Cregor M, Jones M, Perez B, Troncoso G, Meeks J, Stewart S, Sato AY, Nookaew I, Bellido T. Reversal of the diabetic bone signature with anabolic therapies in mice. Bone Res 2023; 11:19. [PMID: 37076478 PMCID: PMC10115794 DOI: 10.1038/s41413-023-00261-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/01/2023] [Accepted: 03/22/2023] [Indexed: 04/21/2023] Open
Abstract
The mechanisms underlying the bone disease induced by diabetes are complex and not fully understood; and antiresorptive agents, the current standard of care, do not restore the weakened bone architecture. Herein, we reveal the diabetic bone signature in mice at the tissue, cell, and transcriptome levels and demonstrate that three FDA-approved bone-anabolic agents correct it. Diabetes decreased bone mineral density (BMD) and bone formation, damaged microarchitecture, increased porosity of cortical bone, and compromised bone strength. Teriparatide (PTH), abaloparatide (ABL), and romosozumab/anti-sclerostin antibody (Scl-Ab) all restored BMD and corrected the deteriorated bone architecture. Mechanistically, PTH and more potently ABL induced similar responses at the tissue and gene signature levels, increasing both formation and resorption with positive balance towards bone gain. In contrast, Scl-Ab increased formation but decreased resorption. All agents restored bone architecture, corrected cortical porosity, and improved mechanical properties of diabetic bone; and ABL and Scl-Ab increased toughness, a fracture resistance index. Remarkably, all agents increased bone strength over the healthy controls even in the presence of severe hyperglycemia. These findings demonstrate the therapeutic value of bone anabolic agents to treat diabetes-induced bone disease and suggest the need for revisiting the approaches for the treatment of bone fragility in diabetes.
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Affiliation(s)
- Silvia Marino
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Central Arkansas Veterans Healthcare System, John L. McClellan Little Rock, Little Rock, AR, USA
| | - Nisreen Akel
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Central Arkansas Veterans Healthcare System, John L. McClellan Little Rock, Little Rock, AR, USA
| | - Shenyang Li
- Central Arkansas Veterans Healthcare System, John L. McClellan Little Rock, Little Rock, AR, USA
| | - Meloney Cregor
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Central Arkansas Veterans Healthcare System, John L. McClellan Little Rock, Little Rock, AR, USA
| | - Meghan Jones
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Betiana Perez
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gaston Troncoso
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jomeeka Meeks
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Scott Stewart
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Amy Y Sato
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Central Arkansas Veterans Healthcare System, John L. McClellan Little Rock, Little Rock, AR, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Teresita Bellido
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Central Arkansas Veterans Healthcare System, John L. McClellan Little Rock, Little Rock, AR, USA.
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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43
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Stecklein SR, Kimler BF, Yoder R, Schwensen K, Staley JM, Khan QJ, O'Dea AP, Nye LE, Elia M, Heldstab J, Home T, Hyter S, Isakova K, Pathak HB, Godwin AK, Sharma P. ctDNA and residual cancer burden are prognostic in triple-negative breast cancer patients with residual disease. NPJ Breast Cancer 2023; 9:10. [PMID: 36878909 PMCID: PMC9988835 DOI: 10.1038/s41523-023-00512-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Triple-negative breast cancer (TNBC) patients with residual disease (RD) after neoadjuvant systemic therapy (NAST) are at high risk for recurrence. Biomarkers to risk-stratify patients with RD could help individualize adjuvant therapy and inform future adjuvant therapy trials. We aim to investigate the impact of circulating tumor DNA (ctDNA) status and residual cancer burden (RCB) class on outcomes in TNBC patients with RD. We analyze end-of-treatment ctDNA status in 80 TNBC patients with residual disease who are enrolled in a prospective multisite registry. Among 80 patients, 33% are ctDNA positive (ctDNA+) and RCB class distribution is RCB-I = 26%, RCB-II = 49%, RCB-III = 18% and 7% unknown. ctDNA status is associated with RCB status, with 14%, 31%, and 57% of patients within RCB-I, -II, and -III classes demonstrating ctDNA+ status (P = 0.028). ctDNA+ status is associated with inferior 3-year EFS (48% vs. 82%, P < 0.001) and OS (50% vs. 86%, P = 0.002). ctDNA+ status predicts inferior 3-year EFS among RCB-II patients (65% vs. 87%, P = 0.044) and shows a trend for inferior EFS among RCB-III patients (13% vs. 40%, P = 0.081). On multivariate analysis accounting for T stage and nodal status, RCB class and ctDNA status independently predict EFS (HR = 5.16, P = 0.016 for RCB class; HR = 3.71, P = 0.020 for ctDNA status). End-of-treatment ctDNA is detectable in one-third of TNBC patients with residual disease after NAST. ctDNA status and RCB are independently prognostic in this setting.
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Affiliation(s)
- Shane R Stecklein
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, USA
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Bruce F Kimler
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Rachel Yoder
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kelsey Schwensen
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Joshua M Staley
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Qamar J Khan
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Anne P O'Dea
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Lauren E Nye
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Manana Elia
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jaimie Heldstab
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Trisha Home
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Stephen Hyter
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Kamilla Isakova
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Harsh B Pathak
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA
| | - Priyanka Sharma
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, USA.
- Division of Medical Oncology, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA.
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Tallman JE, Wallis CJD, Huang LC, Zhao Z, Penson DF, Koyama T, Conwill R, Goodman M, Hamilton AS, Wu XC, Paddock LE, Stroup A, Cooperberg MR, Hashibe M, O'Neil BB, Kaplan SH, Greenfield S, Barocas DA, Hoffman KE. Association between adherence to radiation therapy quality metrics and patient reported outcomes in prostate cancer. Prostate Cancer Prostatic Dis 2023; 26:80-87. [PMID: 35217831 DOI: 10.1038/s41391-022-00518-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND Prior studies have shown significant variability in the quality of prostate cancer care in the US with questionable associations between quality measures and patient reported outcomes. We evaluated the impact of compliance with nationally recognized radiation therapy (RT) quality measures on patient-reported health-related quality of life (HRQOL) outcomes in the Comparative Effectiveness Analysis of Surgery and Radiation (CEASAR) cohort. METHODS CEASAR is a population-based, prospective cohort study of men with localized prostate cancer from which we identified 649 who received primary RT and completed HRQOL surveys for inclusion. Eight quality measures were identified based on national guidelines. We analyzed the impact of compliance with these measures on HRQOL assessed by the 26-item Expanded Prostate Index Composite at pre-specified intervals up to 5 years after treatment. Multivariable analysis was performed controlling for demographic and clinicopathologic features. RESULTS Among eligible participants, 566 (87%) patients received external beam radiation therapy and 83 (13%) received brachytherapy. Median age was 69 years (interquartile range: 64-73), 33% had low-, 43% intermediate-, and 23% high-risk disease. 28% received care non-compliant with at least one measure. In multivariable analyses, while some statistically significant associations were identified, there were no clinically significant associations between compliance with evaluated RT quality measures and patient reported urinary irritative, urinary incontinence, bowel, sexual or hormonal function. CONCLUSIONS Compliance with RT quality measures was not meaningfully associated with patient-reported outcomes after prostate cancer treatment. Further work is needed to identify patient-centered quality measures of prostate cancer care.
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Affiliation(s)
- Jacob E Tallman
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | | | - Li-Ching Huang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zhiguo Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David F Penson
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Tatsuki Koyama
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ralph Conwill
- Office of Patient and Community Education, Patient Advocacy Program, Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael Goodman
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Ann S Hamilton
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Xiao-Cheng Wu
- Department of Epidemiology, Louisiana State University New Orleans School of Public Health, New Orleans, LA, USA
| | - Lisa E Paddock
- Department of Epidemiology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Antoinette Stroup
- Department of Epidemiology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | | | - Mia Hashibe
- Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Brock B O'Neil
- Department of Urology, University of Utah Health, Salt Lake City, UT, USA
| | - Sherrie H Kaplan
- Department of Medicine, University of California Irvine, Irvine, CA, USA
| | - Sheldon Greenfield
- Department of Medicine, University of California Irvine, Irvine, CA, USA
| | - Daniel A Barocas
- Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Karen E Hoffman
- Department of Radiation Oncology, University of Texas M. D. Anderson Center, Houston, TX, USA
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Foltz SM, Greene CS, Taroni JN. Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously. Commun Biol 2023; 6:222. [PMID: 36841852 PMCID: PMC9968332 DOI: 10.1038/s42003-023-04588-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/13/2023] [Indexed: 02/27/2023] Open
Abstract
Large compendia of gene expression data have proven valuable for the discovery of novel biological relationships. Historically, most available RNA assays were run on microarray, while RNA-seq is now the platform of choice for many new experiments. The data structure and distributions between the platforms differ, making it challenging to combine them directly. Here we perform supervised and unsupervised machine learning evaluations to assess which existing normalization methods are best suited for combining microarray and RNA-seq data. We find that quantile and Training Distribution Matching normalization allow for supervised and unsupervised model training on microarray and RNA-seq data simultaneously. Nonparanormal normalization and z-scores are also appropriate for some applications, including pathway analysis with Pathway-Level Information Extractor (PLIER). We demonstrate that it is possible to perform effective cross-platform normalization using existing methods to combine microarray and RNA-seq data for machine learning applications.
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Affiliation(s)
- Steven M Foltz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Wynnewood, PA, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Center for Health AI, University of Colorado School of Medicine, Aurora, CO, USA.
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.
| | - Jaclyn N Taroni
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Wynnewood, PA, USA.
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Tsueng G, Cano MAA, Bento J, Czech C, Kang M, Pache L, Rasmussen LV, Savidge TC, Starren J, Wu Q, Xin J, Yeaman MR, Zhou X, Su AI, Wu C, Brown L, Shabman RS, Hughes LD. Developing a standardized but extendable framework to increase the findability of infectious disease datasets. Sci Data 2023; 10:99. [PMID: 36823157 PMCID: PMC9950378 DOI: 10.1038/s41597-023-01968-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/13/2023] [Indexed: 02/25/2023] Open
Abstract
Biomedical datasets are increasing in size, stored in many repositories, and face challenges in FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices to promote transparency, encourage reproducibility, and accelerate research advances through data reuse. To improve FAIRness of our datasets and computational tools, we evaluated metadata standards across established biomedical data repositories. The vast majority do not adhere to a single standard, such as Schema.org, which is widely-adopted by generalist repositories. Consequently, datasets in these repositories are not findable in aggregation projects like Google Dataset Search. We alleviated this gap by creating a reusable metadata schema based on Schema.org and catalogued nearly 400 datasets and computational tools we collected. The approach is easily reusable to create schemas interoperable with community standards, but customized to a particular context. Our approach enabled data discovery, increased the reusability of datasets from a large research consortium, and accelerated research. Lastly, we discuss ongoing challenges with FAIRness beyond discoverability.
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Affiliation(s)
- Ginger Tsueng
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Marco A Alvarado Cano
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - José Bento
- Department of Computer Science, Boston College, 245 Beacon St, Chestnut Hill, MA, 02467, USA
| | - Candice Czech
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Mengjia Kang
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Lars Pache
- Infectious and Inflammatory Disease Center, Immunity and Pathogenesis Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Luke V Rasmussen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Tor C Savidge
- Texas Children's Microbiome Center & Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin Starren
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Qinglong Wu
- Texas Children's Microbiome Center & Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiwen Xin
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael R Yeaman
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Divisions of Molecular Medicine and Infectious Diseases, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
- Lundquist Institute for Infection & Immunity at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Xinghua Zhou
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andrew I Su
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chunlei Wu
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Scripps Research Translational Institute, La Jolla, CA, 92037, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Liliana Brown
- Office of Genomics and Advanced Technologies, National Institute of Allergy and Infectious Diseases, Rockville, MD, 20852, USA
| | - Reed S Shabman
- Office of Genomics and Advanced Technologies, National Institute of Allergy and Infectious Diseases, Rockville, MD, 20852, USA
| | - Laura D Hughes
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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Vaid A, Argulian E, Lerakis S, Beaulieu-Jones BK, Krittanawong C, Klang E, Lampert J, Reddy VY, Narula J, Nadkarni GN, Glicksberg BS. Multi-center retrospective cohort study applying deep learning to electrocardiograms to identify left heart valvular dysfunction. Commun Med (Lond) 2023; 3:24. [PMID: 36788316 PMCID: PMC9929085 DOI: 10.1038/s43856-023-00240-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/09/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Aortic Stenosis and Mitral Regurgitation are common valvular conditions representing a hidden burden of disease within the population. The aim of this study was to develop and validate deep learning-based screening and diagnostic tools that can help guide clinical decision making. METHODS In this multi-center retrospective cohort study, we acquired Transthoracic Echocardiogram reports from five Mount Sinai hospitals within New York City representing a demographically diverse cohort of patients. We developed a Natural Language Processing pipeline to extract ground-truth labels about valvular status and paired these to Electrocardiograms (ECGs). We developed and externally validated deep learning models capable of detecting valvular disease, in addition to considering scenarios of clinical deployment. RESULTS We use 617,338 ECGs paired to transthoracic echocardiograms from 123,096 patients to develop a deep learning model for detection of Mitral Regurgitation. Area Under Receiver Operating Characteristic curve (AUROC) is 0.88 (95% CI:0.88-0.89) in internal testing, and 0.81 (95% CI:0.80-0.82) in external validation. To develop a model for detection of Aortic Stenosis, we use 617,338 Echo-ECG pairs for 128,628 patients. AUROC is 0.89 (95% CI: 0.88-0.89) in internal testing, going to 0.86 (95% CI: 0.85-0.87) in external validation. The model's performance increases leading up to the time of the diagnostic echo, and it performs well in validation against requirement of Transcatheter Aortic Valve Replacement procedures. CONCLUSIONS Deep learning based tools can increase the amount of information extracted from ubiquitous investigations such as the ECG. Such tools are inexpensive, can help in earlier disease detection, and potentially improve prognosis.
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Affiliation(s)
- Akhil Vaid
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edgar Argulian
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cardiology, Mount Sinai Morningside Hospital, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stamatios Lerakis
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cardiology, Mount Sinai Morningside Hospital, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brett K Beaulieu-Jones
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Section of Biomedical Data Science, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Eyal Klang
- Sheba Medical Center, Department of Diagnostic Imaging, Tel Hashomer, Israel
- Sackler Medical School, Tel Aviv University, Tel Aviv, 52621, Israel
| | - Joshua Lampert
- Helmsley Electrophysiology Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vivek Y Reddy
- Helmsley Electrophysiology Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jagat Narula
- Mount Sinai Heart, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Cardiology, Mount Sinai Morningside Hospital, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Zena and Michael A. Wiener Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Division of Data Driven and Digital Medicine (D3M), The Department of Medicine, Icahn School of Medicine at Mount Siniai, New York, NY, USA
| | - Benjamin S Glicksberg
- The Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Young IC, Massud I, Cottrell ML, Shrivastava R, Maturavongsadit P, Prasher A, Wong-Sam A, Dinh C, Edwards T, Mrotz V, Mitchell J, Seixas JN, Pallerla A, Thorson A, Schauer A, Sykes C, De la Cruz G, Montgomery SA, Kashuba ADM, Heneine W, Dobard CW, Kovarova M, Garcia JV, García-Lerma JG, Benhabbour SR. Ultra-long-acting in-situ forming implants with cabotegravir protect female macaques against rectal SHIV infection. Nat Commun 2023; 14:708. [PMID: 36759645 PMCID: PMC9911691 DOI: 10.1038/s41467-023-36330-5] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Ultra-long-acting delivery platforms for HIV pre-exposure prophylaxis (PrEP) may increase adherence and maximize public health benefit. We report on an injectable, biodegradable, and removable in-situ forming implant (ISFI) that is administered subcutaneously and can release the integrase inhibitor cabotegravir (CAB) above protective benchmarks for more than 6 months. CAB ISFIs are well-tolerated in female mice and female macaques showing no signs of toxicity or chronic inflammation. In macaques, median plasma CAB concentrations exceed established PrEP protection benchmarks within 3 weeks and confer complete protection against repeated rectal SHIV challenges. Implant removal via a small incision in 2 macaques at week 12 results in a 7- to 48-fold decrease in plasma CAB levels within 72 hours. Modeling to translate CAB ISFI dosing suggests that a 3 mL injection would exceed protective benchmarks in humans for over 5 months post administration. Our results support the clinical advancement of CAB ISFIs for ultra-long-acting PrEP in humans.
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Affiliation(s)
- Isabella C Young
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ivana Massud
- Laboratory Branch, Division of HIV Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mackenzie L Cottrell
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Roopali Shrivastava
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Panita Maturavongsadit
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alka Prasher
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andres Wong-Sam
- Laboratory Branch, Division of HIV Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chuong Dinh
- Laboratory Branch, Division of HIV Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tiancheng Edwards
- Laboratory Branch, Division of HIV Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Victoria Mrotz
- Comparative Medicine Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infection Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - James Mitchell
- Laboratory Branch, Division of HIV Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Josilene Nascimento Seixas
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infection Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Aryani Pallerla
- Department of Psychology and Neuroscience, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison Thorson
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Schauer
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Craig Sykes
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriela De la Cruz
- Pathology Services Core, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Stephanie A Montgomery
- Pathology Services Core, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Angela D M Kashuba
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Walid Heneine
- Laboratory Branch, Division of HIV Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Charles W Dobard
- Laboratory Branch, Division of HIV Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Martina Kovarova
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, Division of Infectious Diseases, Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Gerardo García-Lerma
- Laboratory Branch, Division of HIV Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - S Rahima Benhabbour
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Villéger R, Chulkina M, Mifflin RC, Markov NS, Trieu J, Sinha M, Johnson P, Saada JI, Adegboyega PA, Luxon BA, Beswick EJ, Powell DW, Pinchuk IV. Loss of alcohol dehydrogenase 1B in cancer-associated fibroblasts: contribution to the increase of tumor-promoting IL-6 in colon cancer. Br J Cancer 2023; 128:537-548. [PMID: 36482184 PMCID: PMC9938173 DOI: 10.1038/s41416-022-02066-0] [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: 04/15/2022] [Revised: 10/24/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Increases in IL-6 by cancer-associated fibroblasts (CAFs) contribute to colon cancer progression, but the mechanisms involved in the increase of this tumor-promoting cytokine are unknown. The aim of this study was to identify novel targets involved in the dysregulation of IL-6 expression by CAFs in colon cancer. METHODS Colonic normal (N), hyperplastic, tubular adenoma, adenocarcinoma tissues, and tissue-derived myo-/fibroblasts (MFs) were used in these studies. RESULTS Transcriptomic analysis demonstrated a striking decrease in alcohol dehydrogenase 1B (ADH1B) expression, a gene potentially involved in IL-6 dysregulation in CAFs. ADH1B expression was downregulated in approximately 50% of studied tubular adenomas and all T1-4 colon tumors, but not in hyperplastic polyps. ADH1B metabolizes alcohols, including retinol (RO), and is involved in the generation of all-trans retinoic acid (atRA). LPS-induced IL-6 production was inhibited by either RO or its byproduct atRA in N-MFs, but only atRA was effective in CAFs. Silencing ADH1B in N-MFs significantly upregulated LPS-induced IL-6 similar to those observed in CAFs and lead to the loss of RO inhibitory effect on inducible IL-6 expression. CONCLUSION Our data identify ADH1B as a novel potential mesenchymal tumor suppressor, which plays a critical role in ADH1B/retinoid-mediated regulation of tumor-promoting IL-6.
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Affiliation(s)
- Romain Villéger
- Laboratoire Ecologie and Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, Poitiers, France
| | - Marina Chulkina
- Department of Medicine at PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Randy C Mifflin
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, UTMB, Galveston, TX, 77555, USA
| | - Nikolay S Markov
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Judy Trieu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, UTMB, Galveston, TX, 77555, USA
| | - Mala Sinha
- Institute for Translational Sciences, UTMB, Galveston, TX, 77555, USA
| | - Paul Johnson
- Department of Surgery, UTMB, Galveston, TX, 77555, USA
| | - Jamal I Saada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, UTMB, Galveston, TX, 77555, USA
| | - Patrick A Adegboyega
- Department of Pathology, St. Louis University School of Medicine, St. Louis, MO, 63106, USA
| | - Bruce A Luxon
- Institute for Translational Sciences, UTMB, Galveston, TX, 77555, USA
| | - Ellen J Beswick
- Division of Gastroenterology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, 84132, USA
| | - Don W Powell
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, UTMB, Galveston, TX, 77555, USA
- Division of Gastroenterology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, 84132, USA
- Department of Neuroscience and Cell Biology, UTMB, Galveston, TX, 77555, USA
| | - Irina V Pinchuk
- Department of Medicine at PennState Health Milton S. Hershey Medical Center, Hershey, PA, USA.
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Rapanelli M, Wang W, Hurley E, Feltri ML, Pittenger C, Frick LR, Yan Z. Cholinergic neurons in the basal forebrain are involved in behavioral abnormalities associated with Cul3 deficiency: Role of prefrontal cortex projections in cognitive deficits. Transl Psychiatry 2023; 13:22. [PMID: 36693858 PMCID: PMC9873627 DOI: 10.1038/s41398-023-02306-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/02/2023] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
Loss-of-function mutations of the gene Cul3 have been identified as a risk factor for autism-spectrum disorder (ASD), but the pathogenic mechanisms are not well understood. Conditional Cul3 ablation in cholinergic neurons of mice (ChatCRECul3F/+) recapitulated ASD-like social and sensory gating phenotypes and caused significant cognitive impairments, with diminished activity of cholinergic neurons in the basal forebrain (BF). Chemogenetic inhibition of BF cholinergic neurons in healthy mice induced similar social and cognitive deficits. Conversely, chemogenetic stimulation of BF cholinergic neurons in ChatCRECul3F/+ mice reversed abnormalities in sensory gating and cognition. Cortical hypofunction was also found after ChAT-specific Cul3 ablation and stimulation of cholinergic projections from the BF to the prefrontal cortex (PFC) mitigated cognitive deficits. Overall, we demonstrate that cholinergic dysfunction due to Cul3 deficiency is involved in ASD-like behavioral abnormalities, and that BF cholinergic neurons are particularly critical for cognitive component through their projections to the PFC.
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Affiliation(s)
- Maximiliano Rapanelli
- Department of Physiology and Biophysics, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
| | - Wei Wang
- Department of Physiology and Biophysics, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
| | - Edward Hurley
- Department of Neurology, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
- Institute for Myelin and Glia Exploration, University at Buffalo, The State University of New York, Buffalo, USA
| | - Maria Laura Feltri
- Department of Neurology, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
- Institute for Myelin and Glia Exploration, University at Buffalo, The State University of New York, Buffalo, USA
- Department of Biochemistry, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
- Neuroscience Graduate Program. Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA
| | - Christopher Pittenger
- Departments of Psychiatry and Psychology, Yale Child Study Center, and Interdepartmental Neuroscience Program, Yale University School of Medicine, Buffalo, USA
| | - Luciana Romina Frick
- Department of Neurology, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
- Neuroscience Graduate Program. Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
- Department of Medicine, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
- Clinical and Translational Research Center, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
| | - Zhen Yan
- Department of Physiology and Biophysics, Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
- Neuroscience Graduate Program. Jacobs School of Medicine, University at Buffalo, The State University of New York, Buffalo, USA.
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