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Kyriazopoulou E, Hasin-Brumshtein Y, Midic U, Poulakou G, Milionis H, Metallidis S, Astriti M, Fragkou A, Rapti A, Taddei E, Kalomenidis I, Chrysos G, Angheben A, Kainis I, Alexiou Z, Castelli F, Serino FS, Bakakos P, Nicastri E, Tzavara V, Ioannou S, Dagna L, Dimakou K, Tzatzagou G, Chini M, Bassetti M, Kotsis V, Tsoukalas DG, Selmi C, Konstantinou A, Samarkos M, Doumas M, Masgala A, Pagkratis K, Argyraki A, Akinosoglou K, Symbardi S, Netea MG, Panagopoulos P, Dalekos GN, Liesenfeld O, Sweeney TE, Khatri P, Giamarellos-Bourboulis EJ. Transitions of blood immune endotypes and improved outcome by anakinra in COVID-19 pneumonia: an analysis of the SAVE-MORE randomized controlled trial. Crit Care 2024; 28:73. [PMID: 38475786 PMCID: PMC10935809 DOI: 10.1186/s13054-024-04852-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: 01/11/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Endotype classification may guide immunomodulatory management of patients with bacterial and viral sepsis. We aimed to identify immune endotypes and transitions associated with response to anakinra (human interleukin 1 receptor antagonist) in participants in the SAVE-MORE trial. METHODS Adult patients hospitalized with radiological findings of PCR-confirmed severe pneumonia caused by SARS-CoV-2 and plasma-soluble urokinase plasminogen activator receptor levels of ≥ 6 ng/ml in the SAVE-MORE trial (NCT04680949) were characterized at baseline and days 4 and 7 of treatment using a previously defined 33-messenger RNA classifier to assign an immunological endotype in blood. Endpoints were changes in endotypes and progression to severe respiratory failure (SRF) associated with anakinra treatment. RESULTS At baseline, 23.2% of 393 patients were designated as inflammopathic, 41.1% as adaptive, and 35.7% as coagulopathic. Only 23.9% were designated as the same endotype at days 4 and 7 compared to baseline, while all other patients transitioned between endotypes. Anakinra-treated patients were more likely to remain in the adaptive endotype during 7-day treatment (24.4% vs. 9.9%; p < 0.001). Anakinra also protected patients with coagulopathic endotype at day 7 against SRF compared to placebo (27.8% vs. 55.9%; p = 0.013). CONCLUSION We identify an association between endotypes defined using blood transcriptome and anakinra therapy for COVID-19 pneumonia, with anakinra-treated patients shifting toward endotypes associated with a better outcome, mainly the adaptive endotype. Trial registration ClinicalTrials.gov, NCT04680949, December 23, 2020.
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Affiliation(s)
- Evdoxia Kyriazopoulou
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Garyfallia Poulakou
- 3rd Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Haralampos Milionis
- 1st Department of Internal Medicine, Medical School, University of Ioannina, Ioannina, Greece
| | - Simeon Metallidis
- 1st Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Myrto Astriti
- 1st Department of Internal Medicine, G. Gennimatas General Hospital of Athens, Athens, Greece
| | | | - Aggeliki Rapti
- 2nd Department of Pulmonary Medicine, Sotiria General Hospital of Chest Diseases, Athens, Greece
| | - Eleonora Taddei
- Dipartimento Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Gemelli IRCCS, Rome, Italy
| | - Ioannis Kalomenidis
- 1st Department of Critical Care and Pulmonary Medicine, Medical School, National and Kapodistrian University of Athens, Evangelismos General Hospital, Athens, Greece
| | - Georgios Chrysos
- 2nd Department of Internal Medicine, Tzaneio General Hospital of Piraeus, Athens, Greece
| | - Andrea Angheben
- Department of Infectious - Tropical Diseases and Microbiology, IRCSS Sacro Cuore Hospital, Negrar, Verona, Italy
| | - Ilias Kainis
- 10th Department of Pulmonary Medicine, Sotiria General Hospital of Chest Diseases of Athens, Athens, Greece
| | - Zoi Alexiou
- 2nd Department of Internal Medicine, Thriasio General Hospital of Eleusis, Athens, Greece
| | - Francesco Castelli
- Spedali Civili, Brescia ASST Spedali Civili Hospital, University of Brescia, Brescia, Italy
| | | | - Petros Bakakos
- 1st Department of Chest Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Emanuele Nicastri
- Department of Internal Medicine, Spallanzani Institute of Rome, Rome, Italy
| | - Vasiliki Tzavara
- 1st Department of Internal Medicine, Korgialeneion-Benakeion General Hospital, Athens, Greece
| | - Sofia Ioannou
- Department of Therapeutics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Lorenzo Dagna
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases (UnIRAR), IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milan, Italy
| | - Katerina Dimakou
- 5th Department of Pulmonary Medicine, Sotiria General Hospital of Chest Diseases, Athens, Athens, Greece
| | - Glykeria Tzatzagou
- 1st Department of Internal Medicine, Papageorgiou General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Maria Chini
- 3rd Department of Internal Medicine and Infectious Diseases Unit, Korgialeneion-Benakeion General Hospital, Athens, Greece
| | - Matteo Bassetti
- Infectious Diseases Clinic, Ospedale Policlinico San Martino IRCCS and Department of Health Sciences, University of Genova, Genova, Italy
| | - Vasileios Kotsis
- 3rd Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dionysios G Tsoukalas
- 4th Department of Pulmonary Medicine, Sotiria General Hospital of Chest Diseases, Athens, Greece
| | - Carlo Selmi
- Department of Biomedical Sciences, Humanitas University and IRCCS Humanitas Research Hospital, Milan, Italy
| | - Alexandra Konstantinou
- 1st Department of Internal Medicine, Asklepieio General Hospital of Voula, Voula, Greece
| | - Michael Samarkos
- 1st Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Michael Doumas
- 2nd Department of Propedeutic Medicine, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aikaterini Masgala
- 2nd Department of Internal Medicine, Konstantopouleio General Hospital, Athens, Greece
| | | | - Aikaterini Argyraki
- Department of Internal Medicine, Sotiria General Hospital of Chest Diseases, Athens, Greece
| | | | - Styliani Symbardi
- 1st Department of Internal Medicine, Thriasio General Hospital of Eleusis, Athens, Greece
| | - Mihai G Netea
- Department of Internal Medicine and Center for Infectious Diseases, Radboud University, Nijmegen, The Netherlands
- Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Periklis Panagopoulos
- 2nd Department of Internal Medicine, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - George N Dalekos
- Department of Medicine and Research Laboratory of Internal Medicine, National Expertise Center of Greece in Autoimmune Liver Diseases, European Reference Network on Hepatological Diseases (ERN RARE-LIVER), General University Hospital of Larissa, Larissa, Greece
| | | | | | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Evangelos J Giamarellos-Bourboulis
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
- 4th Department of Internal Medicine, ATTIKON University Hospital, 1 Rimini Street, 124 62, Athens, Greece.
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Shojaei M, Chen UI, Midic U, Thair S, Teoh S, McLean A, Sweeney TE, Thompson M, Liesenfeld O, Khatri P, Tang B. Multisite validation of a host response signature for predicting likelihood of bacterial and viral infections in patients with suspected influenza. Eur J Clin Invest 2023; 53:e13957. [PMID: 36692131 DOI: 10.1111/eci.13957] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/08/2022] [Accepted: 01/05/2023] [Indexed: 01/25/2023]
Abstract
BACKGROUND Indiscriminate use of antimicrobials and antimicrobial resistance is a public health threat. IMX-BVN-1, a 29-host mRNA classifier, provides two separate scores that predict likelihoods of bacterial and viral infections in patients with suspected acute infections. We validated the performance of IMX-BVN-1 in adults attending acute health care settings with suspected influenza. METHOD We amplified 29-host response genes in RNA extracted from blood by NanoString nCounter. IMX-BVN-1 calculated two scores to predict probabilities of bacterial and viral infections. Results were compared against the infection status (no infection; highly probable/possible infection; confirmed infection) determined by clinical adjudication. RESULTS Amongst 602 adult patients (74.9% ED, 16.9% ICU, 8.1% outpatients), 7.6% showed in-hospital mortality and 15.5% immunosuppression. Median IMX-BVN-1 bacterial and viral scores were higher in patients with confirmed bacterial (0.27) and viral (0.62) infections than in those without bacterial (0.08) or viral (0.21) infection, respectively. The AUROC distinguishing bacterial from nonbacterial illness was 0.81 and 0.87 when distinguishing viral from nonviral illness. The bacterial top quartile's positive likelihood ratio (LR) was 4.38 with a rule-in specificity of 88%; the bacterial bottom quartile's negative LR was 0.13 with a rule-out sensitivity of 96%. Similarly, the viral top quartile showed an infinite LR with rule-in specificity of 100%; the viral bottom quartile had a LR of 0.22 and a rule-out sensitivity of 85%. CONCLUSION IMX-BVN-1 showed high accuracy for differentiating bacterial and viral infections from noninfectious illness in patients with suspected influenza. Clinical utility of IMX-BVN will be validated following integration into a point of care system.
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Affiliation(s)
- Maryam Shojaei
- Department of Medicine, Sydney Medical School Nepean, Nepean Hospital, University of Sydney, Penrith, New South Wales, Australia.,Department of Intensive Care Medicine, Nepean Hospital, Penrith, New South Wales, Australia.,Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Uan-I Chen
- Inflammatix, Inc., Sunnyvale, California, USA
| | - Uros Midic
- Inflammatix, Inc., Sunnyvale, California, USA
| | | | - Sally Teoh
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, New South Wales, Australia
| | - Anthony McLean
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, New South Wales, Australia
| | | | | | | | | | - Benjamin Tang
- Department of Intensive Care Medicine, Nepean Hospital, Penrith, New South Wales, Australia.,Centre for Immunology and Allergy Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
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Brakenridge SC, Chen UI, Loftus T, Ungaro R, Dirain M, Kerr A, Zhong L, Bacher R, Starostik P, Ghita G, Midic U, Darden D, Fenner B, Wacker J, Efron PA, Liesenfeld O, Sweeney TE, Moldawer LL. Evaluation of a Multivalent Transcriptomic Metric for Diagnosing Surgical Sepsis and Estimating Mortality Among Critically Ill Patients. JAMA Netw Open 2022; 5:e2221520. [PMID: 35819783 PMCID: PMC9277492 DOI: 10.1001/jamanetworkopen.2022.21520] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/19/2022] [Indexed: 02/02/2023] Open
Abstract
Importance Rapid and accurate discrimination of sepsis and its potential severity currently require multiple assays with slow processing times that are often inconclusive in discerning sepsis from sterile inflammation. Objective To analyze a whole-blood, multivalent, host-messenger RNA expression metric for estimating the likelihood of bacterial infection and 30-day mortality and compare performance of the metric with that of other diagnostic and prognostic biomarkers and clinical parameters. Design, Setting, and Participants This prospective diagnostic and prognostic study was performed in the surgical intensive care unit (ICU) of a single, academic health science center. The analysis included 200 critically ill adult patients admitted with suspected sepsis (cohort A) or those at high risk for developing sepsis (cohort B) between July 1, 2020, and July 30, 2021. Exposures Whole-blood sample measurements of a custom 29-messenger RNA transcriptomic metric classifier for likelihood of bacterial infection (IMX-BVN-3) or 30-day mortality (severity) (IMX-SEV-3) in a clinical-diagnostic laboratory setting using an analysis platform (510[k]-cleared nCounter FLEX; NanoString, Inc), compared with measurement of procalcitonin and interleukin 6 (IL-6) plasma levels, and maximum 24-hour sequential organ failure assessment (SOFA) scores. Main Outcomes and Measures Estimated sepsis and 30-day mortality performance. Results Among the 200 patients included (124 men [62.0%] and 76 women [38.0%]; median age, 62.5 [IQR, 47.0-72.0] years), the IMX-BVN-3 bacterial infection classifier had an area under the receiver operating characteristics curve (AUROC) of 0.84 (95% CI, 0.77-0.90) for discriminating bacterial infection at ICU admission, similar to procalcitonin (0.85 [95% CI, 0.79-0.90]; P = .79) and significantly better than IL-6 (0.67 [95% CI, 0.58-0.75]; P < .001). For estimating 30-day mortality, the IMX-SEV-3 metric had an AUROC of 0.81 (95% CI, 0.66-0.95), which was significantly better than IL-6 levels (0.57 [95% CI, 0.37-0.77]; P = .006), marginally better than procalcitonin levels (0.65 [95% CI, 0.50-0.79]; P = .06), and similar to the SOFA score (0.76 [95% CI, 0.62-0.91]; P = .48). Combining IMX-BVN-3 and IMX-SEV-3 with procalcitonin or IL-6 levels or SOFA scores did not significantly improve performance. Among patients with sepsis, IMX-BVN-3 scores decreased over time, reflecting the resolution of sepsis. In 11 individuals at high risk (cohort B) who subsequently developed sepsis during their hospital course, IMX-BVN-3 bacterial infection scores did not decline over time and peaked on the day of documented infection. Conclusions and Relevance In this diagnostic and prognostic study, a novel, multivalent, transcriptomic metric accurately estimated the presence of bacterial infection and risk for 30-day mortality in patients admitted to a surgical ICU. The performance of this single transcriptomic metric was equivalent to or better than multiple alternative diagnostic and prognostic metrics when measured at admission and provided additional information when measured over time.
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Affiliation(s)
- Scott C. Brakenridge
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
- Division of Burn, Trauma & Critical Care Surgery, Department of Surgery, University of Washington, Seattle
| | - Uan-I Chen
- Inflammatix, Inc, Burlingame, California
| | - Tyler Loftus
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | - Ricardo Ungaro
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | - Marvin Dirain
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | - Austin Kerr
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | - Luer Zhong
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | - Rhonda Bacher
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | - Petr Starostik
- Molecular Pathology Laboratory at Rocky Point, Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville
- Clinical and Diagnostic Laboratories, Health Science Center, UF (University of Florida) Health Shands Hospital, Gainesville
| | - Gabriella Ghita
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | - Uros Midic
- Inflammatix, Inc, Burlingame, California
| | - Dijoia Darden
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | - Brittany Fenner
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | | | - Philip A. Efron
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
| | | | | | - Lyle L. Moldawer
- Sepsis and Critical Illness Research Center, Department of Surgery, University of Florida College of Medicine, Gainesville
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Mayhew MB, Tran E, Choi K, Midic U, Luethy R, Damaraju N, Buturovic L. Optimization of Genomic Classifiers for Clinical Deployment: Evaluation of Bayesian Optimization to Select Predictive Models of Acute Infection and In-Hospital Mortality. Pac Symp Biocomput 2021; 26:208-219. [PMID: 33691018] [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] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Acute infection, if not rapidly and accurately detected, can lead to sepsis, organ failure and even death. Current detection of acute infection as well as assessment of a patient's severity of illness are imperfect. Characterization of a patient's immune response by quantifying expression levels of specific genes from blood represents a potentially more timely and precise means of accomplishing both tasks. Machine learning methods provide a platform to leverage this host response for development of deployment-ready classification models. Prioritization of promising classifiers is dependent, in part, on hyperparameter optimization for which a number of approaches including grid search, random sampling and Bayesian optimization have been shown to be effective. We compare HO approaches for the development of diagnostic classifiers of acute infection and in-hospital mortality from gene expression of 29 diagnostic markers. We take a deployment-centered approach to our comprehensive analysis, accounting for heterogeneity in our multi-study patient cohort with our choices of dataset partitioning and hyperparameter optimization objective as well as assessing selected classifiers in external (as well as internal) validation. We find that classifiers selected by Bayesian optimization for in-hospital mortality can outperform those selected by grid search or random sampling. However, in contrast to previous research: 1) Bayesian optimization is not more efficient in selecting classifiers in all instances compared to grid search or random sampling-based methods and 2) we note marginal gains in classifier performance in only specific circumstances when using a common variant of Bayesian optimization (i.e. automatic relevance determination). Our analysis highlights the need for further practical, deployment-centered benchmarking of HO approaches in the healthcare context.
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Buturovic L, Khatri P, Tang B, Lai K, Kuan WS, Gillett M, Santram R, Shojaei M, Almansa R, Nieto J, Muñoz S, Herrero C, Antonakos N, Degree M, Koufargyris P, Kontogiorgi M, Damoraki G, Liesenfeld O, Wacker J, Midic U, Luethy R, Rawling DC, Remmel M, Coyle S, Giamarellos EJ, Sweeney T. 630. A 5-mRNA host response whole-blood classifier trained using patients with non-COVID-19 viral infections accurately predicts severity of COVID-19. Open Forum Infect Dis 2020. [PMCID: PMC7777045 DOI: 10.1093/ofid/ofaa439.824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background While major progress has been made to establish diagnostic tools for the diagnosis of SARS-CoV-2 infection, determining the severity of COVID-19 remains an unmet medical need. With limited hospital resources, gauging severity would allow for some patients to safely recover in home quarantine while ensuring sicker patients get needed care. We discovered a 5 host mRNA-based classifier for the severity of influenza and other acute viral infections and validated the classifier in COVID-19 patients from Greece. Methods We used training data (N=705) from 21 retrospective clinical studies of influenza and other viral illnesses. Five host mRNAs from a preselected panel were applied to train a logistic regression classifier for predicting 30-day mortality in influenza and other viral illnesses. We then applied this classifier, with fixed weights, to an independent cohort of subjects with confirmed COVID-19 from Athens, Greece (N=71) using NanoString nCounter. Finally, we developed a proof-of-concept rapid, isothermal qRT-LAMP assay for the 5-mRNA host signature using the QuantStudio 6 qPCR platform. Results In 71 patients with COVID-19, the 5 mRNA classifier had an AUROC of 0.88 (95% CI 0.80-0.97) for identifying patients with severe respiratory failure and/or 30-day mortality (Figure 1). Applying a preset cutoff based on training data, the 5-mRNA classifier had 100% sensitivity and 46% specificity for identifying mortality, and 88% sensitivity and 68% specificity for identifying severe respiratory failure. Finally, our proof-of-concept qRT-LAMP assay showed high correlation with the reference NanoString 5-mRNA classifier (r=0.95). Figure 1. Validation of the 5-mRNA classifier in the COVID-19 cohort. (A) Expression of the 5 genes used in the logistic regression model in patients with (red) and without (blue) mortality. (B) The 5-mRNA classifier accurately distinguishes non-severe and severe patients with COVID-19 as well as those at risk of death. ![]()
Conclusion Our 5-mRNA classifier demonstrated very high accuracy for the prediction of COVID-19 severity and could assist in the rapid, point-of-impact assessment of patients with confirmed COVID-19 to determine level of care thereby improving patient management and healthcare burden. Disclosures ljubomir Buturovic, PhD, Inflammatix Inc. (Employee, Shareholder) Purvesh Khatri, PhD, Inflammatix Inc. (Shareholder) Oliver Liesenfeld, MD, Inflammatix Inc. (Employee, Shareholder) James Wacker, n/a, Inflammatix Inc. (Employee, Shareholder) Uros Midic, PhD, Inflammatix Inc. (Employee, Shareholder) Roland Luethy, PhD, Inflammatix Inc. (Employee, Shareholder) David C. Rawling, PhD, Inflammatix Inc. (Employee, Shareholder) Timothy Sweeney, MD, Inflammatix, Inc. (Employee)
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Affiliation(s)
| | | | | | - Kevin Lai
- Westmead Hospital, Sydney, New South Wales, Australia
| | - Win Sen Kuan
- National University Hospital Singapore, singapore, Not Applicable, Singapore
| | - Mark Gillett
- Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Rahul Santram
- St Vincent Hospital, Sydney, New South Wales, Australia
| | - Maryam Shojaei
- WESTMEAD INSTITUTE FOR MEDICAL RESEARCH, Sydney, New South Wales, Australia
| | | | - Jose Nieto
- Servicio de Urgencias de Atención Primaria, Salamanca, Castilla y Leon, Spain
| | - Sonsoles Muñoz
- Servicio de Urgencias de Atención Primaria, Salamanca, Castilla y Leon, Spain
| | - Carmen Herrero
- Servicio de Urgencias de Atención Primaria, Salamanca, Castilla y Leon, Spain
| | | | | | - Panayiotis Koufargyris
- National and Kapodistrian University of Athens, Medical School, Greece, Athens, Attiki, Greece
| | - Marina Kontogiorgi
- 14. 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece, Athens, Attiki, Greece
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Schall PZ, Ruebel ML, Midic U, VandeVoort CA, Latham KE. Temporal patterns of gene regulation and upstream regulators contributing to major developmental transitions during Rhesus macaque preimplantation development. Mol Hum Reprod 2020; 25:111-123. [PMID: 30698740 DOI: 10.1093/molehr/gaz001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/11/2018] [Accepted: 01/24/2019] [Indexed: 02/07/2023] Open
Abstract
The preimplantation period of life in mammals encompasses a tremendous amount of restructuring and remodeling of the embryonic genome and reprogramming of gene expression. These vast changes support metabolic activation and cellular processes that drive early cleavage divisions and enable the creation of the earliest primitive cell lineages. A major question in mammalian embryology is how such vast, sweeping changes in gene expression are orchestrated, so that changes in gene expression are exactly appropriate to meet the developmental needs of the embryo over time. Using the rhesus macaque as an experimentally tractable model species closely related to the human, we combined high quality RNA-seq libraries, in-depth sequencing and advanced systems analysis to discover the underlying mechanisms that drive major changes in gene regulation during preimplantation development. We identified the major changes in mRNA population and the biological pathways and processes impacted by those changes. Most importantly, we identified 24 key upstream regulators that are themselves modulated during development and that are associated with the regulation of over 1000 downstream genes. Through their roles in extensive gene networks, these 24 upstream regulators are situated to either drive major changes in target gene expression or modify the cellular environment in which other genes function, thereby directing major developmental transitions in the preimplantation embryo. The data presented here highlight some of the specific molecular features that likely drive preimplantation development in a nonhuman primate species and provides an extensive database for novel hypothesis-driven studies.
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Affiliation(s)
- Peter Z Schall
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA.,Comparative Medicine and Integrative Biology Program, Michigan State University, East Lansing, MI, USA
| | - Meghan L Ruebel
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Uros Midic
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, CA, USA
| | - Keith E Latham
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
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7
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Mayhew MB, Buturovic L, Luethy R, Midic U, Moore AR, Roque JA, Shaller BD, Asuni T, Rawling D, Remmel M, Choi K, Wacker J, Khatri P, Rogers AJ, Sweeney TE. A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections. Nat Commun 2020; 11:1177. [PMID: 32132525 PMCID: PMC7055276 DOI: 10.1038/s41467-020-14975-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Improved identification of bacterial and viral infections would reduce morbidity from sepsis, reduce antibiotic overuse, and lower healthcare costs. Here, we develop a generalizable host-gene-expression-based classifier for acute bacterial and viral infections. We use training data (N = 1069) from 18 retrospective transcriptomic studies. Using only 29 preselected host mRNAs, we train a neural-network classifier with a bacterial-vs-other area under the receiver-operating characteristic curve (AUROC) 0.92 (95% CI 0.90–0.93) and a viral-vs-other AUROC 0.92 (95% CI 0.90–0.93). We then apply this classifier, inflammatix-bacterial-viral-noninfected-version 1 (IMX-BVN-1), without retraining, to an independent cohort (N = 163). In this cohort, IMX-BVN-1 AUROCs are: bacterial-vs.-other 0.86 (95% CI 0.77–0.93), and viral-vs.-other 0.85 (95% CI 0.76–0.93). In patients enrolled within 36 h of hospital admission (N = 70), IMX-BVN-1 AUROCs are: bacterial-vs.-other 0.92 (95% CI 0.83–0.99), and viral-vs.-other 0.91 (95% CI 0.82–0.98). With further study, IMX-BVN-1 could provide a tool for assessing patients with suspected infection and sepsis at hospital admission. Diagnosing acute infections based on transcriptional host response shows promise, but generalizability is wanting. Here, the authors use a co-normalization framework to train a classifier to diagnose acute infections and apply it to independent data on a targeted diagnostic platform.
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Affiliation(s)
- Michael B Mayhew
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | | | - Roland Luethy
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Uros Midic
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Andrew R Moore
- Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Jonasel A Roque
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Brian D Shaller
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Tola Asuni
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - David Rawling
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Melissa Remmel
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Kirindi Choi
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - James Wacker
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infections, Stanford University, Palo Alto, CA, 94305, USA.,Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Angela J Rogers
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Timothy E Sweeney
- Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA.
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8
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Severance AL, Midic U, Latham KE. Genotypic divergence in mouse oocyte transcriptomes: possible pathways to hybrid vigor impacting fertility and embryogenesis. Physiol Genomics 2019; 52:96-109. [PMID: 31869285 DOI: 10.1152/physiolgenomics.00078.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
What causes hybrid vigor phenotypes in mammalian oocytes and preimplantation embryos? Answering this question should provide new insight into determinants of oocyte and embryo quality and infertility. Hybrid vigor could arise through a variety of mechanisms, many of which must operate through posttranscriptional mechanisms affecting oocyte mRNA accumulation, stability, translation, and degradation. The differential regulation of such mRNAs may impact essential pathways and functions within the oocyte. We conducted in-depth transcriptome comparisons of immature and mature oocytes of C57BL/6J and DBA/2J inbred strains and C57BL/6J × DBA/2J F1 (BDF1) hybrid oocytes with RNA sequencing, combined with novel computational methods of analysis. We observed extensive differences in mRNA expression and regulation between parental inbred strains and between inbred and hybrid genotypes, including mRNAs encoding proposed markers of oocyte quality. Unique BDF1 oocyte characteristics arise through a combination of additive dominance and incomplete dominance features in the transcriptome, with a lesser degree of transgressive mRNA expression. Special features of the BDF1 transcriptome most prominently relate to histone expression, mitochondrial function, and oxidative phosphorylation. The study reveals the major underlying mechanisms that contribute to superior properties of hybrid oocytes in a mouse model.
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Affiliation(s)
- Ashley L Severance
- Genetics Graduate Program, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Uros Midic
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan.,Department of Animal Science, Michigan State University, East Lansing, Michigan
| | - Keith E Latham
- Genetics Graduate Program, Michigan State University, East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan.,Department of Animal Science, Michigan State University, East Lansing, Michigan.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing, Michigan
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9
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Schultz BJ, Sweeney T, DeBaun MR, Remmel M, Midic U, Khatri P, Gardner MJ. Pilot study of a novel serum mRNA gene panel for diagnosis of acute septic arthritis. World J Orthop 2019; 10:424-433. [PMID: 31908991 PMCID: PMC6937427 DOI: 10.5312/wjo.v10.i12.424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/30/2019] [Accepted: 10/18/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Septic arthritis is an orthopedic emergency requiring immediate surgical intervention. Current diagnostic standard of care is an invasive joint aspiration. Aspirations provide information about the inflammatory cells in the sample within a few hours, but there is often ambiguity about whether the source is infectious (e.g. bacterial) or non-infectious (e.g. gout). Cultures can take days to result, so decisions about surgery are often made with incomplete data. Novel diagnostics are thus needed. The “Sepsis MetaScore” (SMS) is an 11-mRNA host immune blood signature that can distinguish between infectious and non-infectious acute inflammation. It has been validated in multiple cohorts across heterogeneous clinical settings.
AIM To study whether the SMS holds diagnostic validity in determining the etiology of acute arthritis.
METHODS We conducted a blinded, prospective, non-interventional clinical study of the SMS. All patients undergoing work-up for a septic primary joint were enrolled. Patients proceeded through the normal standard-of-care pathway, including joint aspiration and inflammatory labs [white blood cell (WBC), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP)]. Venous blood was also drawn into PAX gene RNA-stabilizing tubes and mRNAs were measured using Nano String nCounter™. SMS was calculated blinded to clinical results.
RESULTS A total of 20 samples were included, of which 11 were infected based on aspiration or intra-operative cultures. The SMS had an area under the ROC curve (AUROC) of 0.87 for separating infectious from non-infectious conditions. For comparison, the AUROCs for ESR = 0.58, CRP = 0.6, and WBC = 0.59. At 100% sensitivity for infection, the specificity of the SMS was 40%, meaning nearly half of non-septic patients could have been ruled out for further intervention.
CONCLUSION In this pilot study, SMS showed a high level of diagnostic accuracy in predicting septic joints compared to other diagnostic biomarkers. This quick blood test could be an important tool for early, accurate identification of acute septic joints and need for emergent surgery, improving clinical care and healthcare spending.
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Affiliation(s)
- Blake J Schultz
- Department of Orthopedic Surgery, Stanford University, Redwood City, CA 94063, United States
| | - Timothy Sweeney
- Inflammatix, Inc, 863 Mitten Road, Suite 104, Burlingame, CA 94010, United States
| | - Malcolm R DeBaun
- Department of Orthopedic Surgery, Stanford University, Redwood City, CA 94063, United States
| | - Melissa Remmel
- Inflammatix, Inc, 863 Mitten Road, Suite 104, Burlingame, CA 94010, United States
| | - Uros Midic
- Inflammatix, Inc, 863 Mitten Road, Suite 104, Burlingame, CA 94010, United States
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infections, Center for Biomedical Research, Department of Medicine, Stanford University, Stanford, Redwood City, CA 94305, United States
| | - Michael J Gardner
- Department of Orthopedic Surgery, Stanford University, Redwood City, CA 94063, United States
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10
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Schultz B, Sweeney TE, Remmel M, Midic U, Liesenfeld O, DeBaun M, Gardner M. 649. Prospective Validation of an 11-mRNA Host Immune Signature as a Novel Blood Test for Acute Septic Arthritis. Open Forum Infect Dis 2019. [PMCID: PMC6811011 DOI: 10.1093/ofid/ofz360.717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
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11
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Midic U, Vincent KA, Wang K, Lokken A, Severance AL, Ralston A, Knott JG, Latham KE. Novel key roles for structural maintenance of chromosome flexible domain containing 1 (Smchd1) during preimplantation mouse development. Mol Reprod Dev 2019; 85:635-648. [PMID: 29900695 DOI: 10.1002/mrd.23001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 04/24/2018] [Accepted: 06/08/2018] [Indexed: 12/16/2022]
Abstract
Structural maintenance of chromosome flexible domain containing 1 (Smchd1) is a chromatin regulatory gene for which mutations are associated with facioscapulohumeral muscular dystrophy and arhinia. The contribution of oocyte- and zygote-expressed SMCHD1 to early development was examined in mice ( Mus musculus) using a small interfering RNA knockdown approach. Smchd1 knockdown compromised long-term embryo viability, with reduced embryo nuclear volumes at the morula stage, reduced blastocyst cell number, formation and hatching, and reduced viability to term. RNA sequencing analysis of Smchd1 knockdown morulae revealed aberrant increases in expression of a small number of trophectoderm (TE)-related genes and reduced expression of cell proliferation genes, including S-phase kinase-associated protein 2 ( Skp2). Smchd1 expression was elevated in embryos deficient for Caudal-type homeobox transcription factor 2 ( Cdx2, a key regulator of TE specification), indicating that Smchd1 is normally repressed by CDX2. These results indicate that Smchd1 plays an important role in the preimplantation embryo, regulating early gene expression and contributing to long-term embryo viability. These results extend the known functions of SMCHD1 to the preimplantation period and highlight important function for maternally expressed Smchd1 messenger RNA and protein.
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Affiliation(s)
- Uros Midic
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Kailey A Vincent
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Kai Wang
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Alyson Lokken
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Ashley L Severance
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Amy Ralston
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Jason G Knott
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
| | - Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan
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12
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Ruebel ML, Schall PZ, Midic U, Vincent KA, Goheen B, VandeVoort CA, Latham KE. Transcriptome analysis of rhesus monkey failed-to-mature oocytes: deficiencies in transcriptional regulation and cytoplasmic maturation of the oocyte mRNA population. Mol Hum Reprod 2019; 24:478-494. [PMID: 30085220 DOI: 10.1093/molehr/gay032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
STUDY QUESTION Which different pathways and functions are altered in rhesus monkey oocytes that fail to mature after an ovulatory stimulus? SUMMARY ANSWER Failed to mature (FTM) oocytes complete a large portion of the transition in transcriptome composition associated with normal maturation, but also manifest numerous differences that indicate incomplete transcriptional repression and cytoplasmic maturation affecting multiple processes. WHAT IS KNOWN ALREADY Oocyte maturation defects contribute to unexplained female infertility. Failure of some oocytes to undergo germinal vesicle breakdown or progress to second meiotic metaphase in response to an ovulatory stimulus can limit the number of high quality oocytes available for ART. STUDY DESIGN, SIZE, DURATION The transcriptome of rhesus monkey oocytes that failed to mature (FTM; n = 11, 5 donors) in response to an ovulatory stimulus in vivo was compared to those of normal germinal vesicle stage (GV, n = 7, 2 donors) and metaphase II stage (MII, n = 7, 5 donors) oocytes by RNA-sequencing (RNAseq). PARTICIPANTS/MATERIALS, SETTING, METHODS Female rhesus monkeys of normal breeding age (6-12 years old) and with regular menstrual cycles were used. Animals underwent a controlled ovarian stimulation protocol for the collection of oocytes by ultrasound-guided needle aspiration of follicles. MAIN RESULTS AND THE ROLE OF CHANCE We obtained a high quality RNAseq dataset consisting of n = 7, n = 7, and n = 11 libraries for normal GV, normal MII and FTM oocytes, respectively. Total reads acquired were an average of 34 million for each GV sample, 41 million for each FTM sample and 59 million for each MII oocyte sample. Approximately 44% of the total reads were exonic reads that successfully aligned to the rhesus monkey genome as unique non-rRNA gene transcript sequences, providing high depth of coverage. Approximately 44% of the mRNAs that undergo changes in abundance during normal maturation display partial modulations to intermediate abundances, and 9.2% fail to diverge significantly from GV stage oocytes. Additionally, a small group of mRNAs are grossly mis-regulated in the FTM oocyte. Differential expression was seen for mRNAs associated with mitochondrial functions, fatty acid beta oxidation, lipid accumulation, meiosis, zona pellucida formation, Hippo pathway signaling, and maternal mRNA regulation. A deficiency DNA methyltransferase one mRNA expression indicates a potential defect in transcriptional silencing. LARGE SCALE DATA All RNAseq data are published in the Gene Expression Omnibus Database (GSE112536). LIMITATIONS, REASONS FOR CAUTION These results do not establish cause of maturation failure but reveal novel correlates of incompetence to mature. Transcriptome studies likely do not capture all post-transcriptional or post-translational events that inhibit maturation, but do reveal mRNA expression changes that lie downstream of such events or that are related to effects on upstream regulators. The use of an animal model allows the study of oocyte maturation failure independent of covariates and confounders, such as pre-existing conditions of the female, which is a significant concern in human studies. Depending on the legislation, it may not be possible to collect and study oocytes from healthy women; and using surplus oocytes from patients undergoing ART may introduce confounders that vary from case to case. FTM oocytes were at various stages of meiotic progression, so correlates of specific times of arrest are not revealed. All the FTM oocytes failed to respond appropriately to an ovulatory stimulus in vivo. Therefore, this analysis informs us about common transcriptome features associated with meiotic incompetence. WIDER IMPLICATIONS OF THE FINDINGS These results reveal that some diagnostic markers of oocyte quality may not reflect developmental competence because even meiotically incompetent oocytes display many normal gene expression features. The results also reveal potential mechanisms by which maternal and environmental factors may impact transcriptional repression and cytoplasmic maturation, and prevent oocyte maturation. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by grants from the National Institutes of Health Office of Research Infrastructure Programs Division of Comparative Medicine Grants R24 [OD012221 to K.E.L., OD011107/RR00169 (California National Primate Research Center), and OD010967/RR025880 to C.A.V.]; the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the National Institutes of Health under the award number T32HD087166; MSU AgBioResearch, Michigan State University. Authors have nothing to disclose.
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Affiliation(s)
- Meghan L Ruebel
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Peter Z Schall
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Uros Midic
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Kailey A Vincent
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Benjamin Goheen
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, CA, USA
| | - Keith E Latham
- Department of Animal Science and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, USA
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13
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Abstract
To account for sex as a biological variable, it is sometimes necessary to identify the sex of an embryo or embryonic cell that was used to generate libraries for RNA sequencing, without the sex being known a priori. The preferred approach for this would take advantage of the mRNA data, rather than relying on other methods that require separation and analysis of genomic DNA or diversion of limiting RNA for other assays. We describe here a method that has been optimized for this purpose in samples of rhesus monkey and mouse embryos. This method is broadly applicable to any species for which a sufficiently well characterized genome and knowledge of polymorphisms are available, and for embryos that are transcriptionally active and expressing their genome.
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Affiliation(s)
- Uros Midic
- Department of Animal Science, Michigan State University , East Lansing, Michigan
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California , Davis, California
| | - Keith E Latham
- Department of Animal Science, Michigan State University , East Lansing, Michigan.,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University , East Lansing, Michigan.,Reproductive and Developmental Sciences Program, Michigan State University , East Lansing, Michigan
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14
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Midic U, Goheen B, Vincent KA, VandeVoort CA, Latham KE. Changes in gene expression following long-term in vitro exposure of Macaca mulatta trophoblast stem cells to biologically relevant levels of endocrine disruptors. Reprod Toxicol 2018; 77:154-165. [PMID: 29505797 PMCID: PMC5898618 DOI: 10.1016/j.reprotox.2018.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 09/22/2017] [Revised: 02/20/2018] [Accepted: 02/27/2018] [Indexed: 12/11/2022]
Abstract
Trophoblast stem cells (TSCs) are crucial for embryo implantation and placentation. Environmental toxicants that compromise TSC function could impact fetal viability, pregnancy, and progeny health. Understanding the effects of low, chronic EDC exposures on TSCs and pregnancy is a priority in developmental toxicology. Differences in early implantation between primates and other mammals make a nonhuman primate model ideal. We examined effects of chronic low-level exposure to atrazine, tributyltin, bisphenol A, bis(2-ethylhexyl) phthalate, and perfluorooctanoic acid on rhesus monkey TSCs in vitro by RNA sequencing. Pathway analysis of affected genes revealed negative effects on cytokine signaling related to anti-viral response, most strongly for atrazine and tributyltin, but shared with the other three EDCs. Other affected processes included metabolism, DNA repair, and cell migration. Low-level chronic exposure of primate TSCs to EDCs may thus compromise trophoblast development in vivo, inhibit responses to infection, and negatively affect embryo implantation and pregnancy.
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Affiliation(s)
- Uros Midic
- Department of Animal Science, Department of Obstetrics, Gynecology and Reproductive Biology, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, United States
| | - Benjamin Goheen
- Department of Animal Science, Department of Obstetrics, Gynecology and Reproductive Biology, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, United States
| | - Kailey A Vincent
- Department of Animal Science, Department of Obstetrics, Gynecology and Reproductive Biology, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, United States
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, CA 95616, United States
| | - Keith E Latham
- Department of Animal Science, Department of Obstetrics, Gynecology and Reproductive Biology, Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, United States.
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15
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Midic U, Hung PH, Vincent KA, Goheen B, Schupp PG, Chen DD, Bauer DE, VandeVoort CA, Latham KE. Quantitative assessment of timing, efficiency, specificity and genetic mosaicism of CRISPR/Cas9-mediated gene editing of hemoglobin beta gene in rhesus monkey embryos. Hum Mol Genet 2018; 26:2678-2689. [PMID: 28444193 DOI: 10.1093/hmg/ddx154] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 02/15/2017] [Accepted: 04/19/2017] [Indexed: 12/26/2022] Open
Abstract
Gene editing technologies offer new options for developing novel biomedical research models and for gene and stem cell based therapies. However, applications in many species demand high efficiencies, specificity, and a thorough understanding of likely editing outcomes. To date, overall efficiencies, rates of off-targeting and degree of genetic mosaicism have not been well-characterized for most species, limiting our ability to optimize methods. As a model gene for measuring these parameters of the CRISPR/Cas9 application in a primate species (rhesus monkey), we selected the β-hemoglobin gene (HBB), which also has high relevance to the potential application of gene editing and stem-cell technologies for treating human disease. Our data demonstrate an ability to achieve a high efficiency of gene editing in rhesus monkey zygotes, with no detected off-target effects at selected off-target loci. Considerable genetic mosaicism and variation in the fraction of embryonic cells bearing targeted alleles are observed, and the timing of editing events is revealed using a new model. The uses of Cas9-WT protein combined with optimized concentrations of sgRNAs are two likely areas for further refinement to enhance efficiency while limiting unfavorable outcomes that can be exceedingly costly for application of gene editing in primate species.
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Affiliation(s)
- Uros Midic
- Department of Animal Science, and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
| | - Pei-Hsuan Hung
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, Davis, CA 95616, USA
| | - Kailey A Vincent
- Department of Animal Science, and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
| | - Benjamin Goheen
- Department of Animal Science, and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
| | - Patrick G Schupp
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Diane D Chen
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School and Harvard Stem Cell Institute, Harvard University, Boston, MA, USA
| | - Catherine A VandeVoort
- California National Primate Research Center and Department of Obstetrics and Gynecology, University of California, Davis, Davis, CA 95616, USA
| | - Keith E Latham
- Department of Animal Science, and Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
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Ding D, Liu J, Dong K, Midic U, Hess RA, Xie H, Demireva EY, Chen C. PNLDC1 is essential for piRNA 3' end trimming and transposon silencing during spermatogenesis in mice. Nat Commun 2017; 8:819. [PMID: 29018194 PMCID: PMC5635004 DOI: 10.1038/s41467-017-00854-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 07/28/2017] [Indexed: 12/04/2022] Open
Abstract
Piwi-interacting RNAs are small regulatory RNAs with key roles in transposon silencing and regulation of gametogenesis. The production of mature piwi-interacting RNAs requires a critical step of trimming piwi-interacting RNA intermediates to achieve optimally sized piwi-interacting RNAs. The poly(A)-specific ribonuclease family deadenylase PNLDC1 is implicated in piwi-interacting RNA trimming in silkworms. The physiological function of PNLDC1 in mammals remains unknown. Using Pnldc1-deficient mice, here we show that PNLDC1 is required for piwi-interacting RNA biogenesis, transposon silencing, and spermatogenesis. Pnldc1 mutation in mice inhibits piwi-interacting RNA trimming and causes accumulation of untrimmed piwi-interacting RNA intermediates with 3′ end extension, leading to severe reduction of mature piwi-interacting RNAs in the testis. Pnldc1 mutant mice exhibit disrupted LINE1 retrotransposon silencing and defect in spermiogenesis. Together, these results define PNLDC1 as a mammalian piwi-interacting RNA biogenesis factor that protects the germline genome and ensures normal sperm production in mice. piRNAs are regulatory RNAs that play a critical role in transposon silencing and gametogenesis. Here, the authors provide evidence that mammalian PNLDC1 is a regulator of piRNA biogenesis, transposon silencing and spermatogenesis, protecting the germline genome in mice.
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Affiliation(s)
- Deqiang Ding
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiali Liu
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.,State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Kunzhe Dong
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Uros Midic
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Rex A Hess
- Department of Comparative Biosciences, University of Illinois, Urbana, IL, 61801, USA
| | - Huirong Xie
- Transgenic and Genome Editing Facility, Michigan State University, East Lansing, MI, 48824, USA
| | - Elena Y Demireva
- Transgenic and Genome Editing Facility, Michigan State University, East Lansing, MI, 48824, USA
| | - Chen Chen
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA. .,Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, Grand Rapids, MI, 49503, USA.
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17
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VandeVoort CA, Mtango NR, Midic U, Latham KE. Disruptions in follicle cell functions in the ovaries of rhesus monkeys during summer. Physiol Genomics 2015; 47:102-12. [PMID: 25586978 DOI: 10.1152/physiolgenomics.00092.2014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 01/13/2015] [Indexed: 11/22/2022] Open
Abstract
Oocytes isolated from female rhesus monkeys following standard ovarian stimulation protocols during the summer months displayed a reduced capacity to mature compared with stimulation during the normal breeding season. Because the gene expression profiles of oocyte-associated cumulus cells and mural granulosa cells (CCs and GCs) are indicative of altered oocyte quality and can provide insight into intrafollicular processes that may be disrupted during oogenesis, we performed array-based transcriptome comparisons of CCs and GCs from summer and normal breeding season stimulation cycles. Summer CCs and GCs both display deficiencies in expression of mRNAs related to cell proliferation, angiogenesis, and endocrine signaling, as well as reduced expression of glycogen phosphorylase. Additionally, CCs display deficiencies in expression of mRNAs related to stress response. These results provide the first insight into the specific molecular pathways and processes that are disrupted in the follicles of rhesus macaque females during the summer season. Some of the changes seen in summer GCs and CCs have been reported in humans and in other model mammalian species. This suggests that the seasonal effects seen in the rhesus monkey may help us to understand better the mechanisms that contribute to reduced oocyte quality and fertility in humans.
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Affiliation(s)
- Catherine A VandeVoort
- California National Primate Research Center, University of California, Davis, California; Department of Obstetrics and Gynecology, University of California, Davis, California
| | - Namdori R Mtango
- The Fels Institute for Cancer Research & Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania; and
| | - Uros Midic
- Department of Animal Science, Reproductive and Developmental Science Program and Department of Obstetrics and Gynecology, Michigan State University, East Lansing, Michigan
| | - Keith E Latham
- Department of Animal Science, Reproductive and Developmental Science Program and Department of Obstetrics and Gynecology, Michigan State University, East Lansing, Michigan
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18
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Chaffin CL, Latham KE, Mtango NR, Midic U, VandeVoort CA. Dietary sugar in healthy female primates perturbs oocyte maturation and in vitro preimplantation embryo development. Endocrinology 2014; 155:2688-95. [PMID: 24731100 PMCID: PMC4060180 DOI: 10.1210/en.2014-1104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The consumption of refined sugars continues to pose a significant health risk. However, nearly nothing is known about the effects of sugar intake by healthy women on the oocyte or embryo. Using rhesus monkeys, we show that low-dose sucrose intake over a 6-month period has an impact on the oocyte with subsequent effects on the early embryo. The ability of oocytes to resume meiosis was significantly impaired, although the differentiation of the somatic component of the ovarian follicle into progesterone-producing cells was not altered. Although the small subset of oocytes that did mature were able to be fertilized in vitro and develop into preimplantation blastocysts, there were >1100 changes in blastocyst gene expression. Because sucrose treatment ended before fertilization, the effects of sugar intake by healthy primates are concluded to be epigenetic modifications to the immature oocyte that are manifest in the preimplantation embryo.
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Affiliation(s)
- Charles L Chaffin
- Department of Obstetrics, Gynecology, and Reproductive Sciences (C.L.C.), University of Maryland School of Medicine, Baltimore, Maryland 21210; Department of Animal Science (K.E.L., U.M.), Michigan State University, East Lansing, Michigan 48824; The Fels Institute for Cancer Research and Molecular Biology and Department of Biochemistry (N.R.M.), Temple University School of Medicine, Philadelphia, Pennsylvania 19140; and California National Primate Research Center and Department of Obstetrics and Gynecology (C.A.V.), University of California, Davis, California 95616
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Hao L, Midic U, Garriga J, Latham KE. Contribution of CBX4 to cumulus oophorus cell phenotype in mice and attendant effects in cumulus cell cloned embryos. Physiol Genomics 2013; 46:66-80. [PMID: 24280258 DOI: 10.1152/physiolgenomics.00071.2013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cumulus oophorus cells play an essential role in oocyte development. They are also widely employed as donor cells for cloning by somatic cell nuclear transfer. Our previous studies revealed that Cbx4 mRNA was overexpressed in cloned two-cell embryos. These data indicated that CBX4 may regulate normal cumulus cell differentiation and that its overexpression in clones could contribute to aberrant gene regulation. We used siRNA-mediated knockdown of Cbx4 to assess its role in determining cumulus cell phenotype and compared the effects of this knockdown to published data for aberrant gene regulation in cloned embryos. We observed widespread effects on the expression of genes related to diverse processes in cultured cumulus cells, including cell assembly/proliferation and DNA replication/repair, endocrine function, carbohydrate and lipid metabolism, inflammation, and cell morphology, with apparent effects of CBX4 in promoting cumulus cell proliferation and survival and inhibiting differentiation. Overall, the data implicate CBX4 as a key component in the pathway integrating endocrine signals, intraovarian paracrine factors, and oocyte-derived factors in the control of cumulus cell functions. We also observed altered expression of 25 cumulus cell markers of oocyte quality, indicating an important role of CBX4 in production of high quality oocytes. Finally, we found that about one-quarter of the genes showing aberrant transcription in cloned embryos are sensitive to Cbx4 knockdown in cumulus cells, consistent with a role for aberrant Cbx4 regulation in elaborating abnormal cloned embryo characteristics.
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Affiliation(s)
- Lanping Hao
- The Fels Institute for Cancer Research, Temple University School of Medicine, Philadelphia, Pennsylvania; and
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Tallarida RJ, Midic U, Lamarre NS, Obradovic Z. A search for interaction among combinations of drugs of abuse and the use of isobolographic analysis. J Clin Pharm Ther 2013; 38:190-5. [PMID: 23550787 DOI: 10.1111/jcpt.12055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 02/18/2013] [Indexed: 11/29/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE Individuals who abuse drugs usually use more than one substance. Toxic consequences of single and multi-drug use are well documented in the Treatment Episodes Data Set that lists drug combinations that result in hospital admissions. Using this list as a guide, we focused our attention on combinations that result in the most hospital admissions and searched the PubMed database with the objective of determining the number of such publications and, in particular, those that used the term synergism in their titles or abstracts. COMMENT Using the search criteria produced an extensive list of published articles. However, a further intersection of the search terms with the term isobole revealed a surprisingly small number of literature reports. WHAT IS NEW AND CONCLUSION Because the method of isoboles is the most common quantitative method for distinguishing between drug synergism and simple additivity, the small number of investigations that actually employed this quantification suggests that the term synergism is not properly documented in describing the toxicity among abused substances. The possible reasons for this lack of quantification may be related to a misunderstanding of the modelling equations. To help rectify this possible hurdle to understanding and clinical utility, the theory and modelling are discussed here.
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Affiliation(s)
- R J Tallarida
- Department of Pharmacology and Center for Substance Abuse Research, Temple University School of Medicine, Philadelphia, PA, USA.
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Abstract
Background Intrinsically disordered proteins (IDPs) and regions (IDRs) perform a variety of crucial biological functions despite lacking stable tertiary structure under physiological conditions in vitro. State-of-the-art sequence-based predictors of intrinsic disorder are achieving per-residue accuracies over 80%. In a genome-wide study of intrinsic disorder in human genome we observed a big difference in predicted disorder content between confirmed and putative human proteins. We investigated a hypothesis that this discrepancy is not correct, and that it is due to incorrectly annotated parts of the putative protein sequences that exhibit some similarities to confirmed IDRs, which lead to high predicted disorder content. Methods To test this hypothesis we trained a predictor to discriminate sequences of real proteins from synthetic sequences that mimic errors of gene finding algorithms. We developed a procedure to create synthetic peptide sequences by translation of non-coding regions of genomic sequences and translation of coding regions with incorrect codon alignment. Results Application of the developed predictor to putative human protein sequences showed that they contain a substantial fraction of incorrectly assigned regions. These regions are predicted to have higher levels of disorder content than correctly assigned regions. This partially, albeit not completely, explains the observed discrepancy in predicted disorder content between confirmed and putative human proteins. Conclusions Our findings provide the first evidence that current practice of predicting disorder content in putative sequences should be reconsidered, as such estimates may be biased.
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Affiliation(s)
- Uros Midic
- Fels Institute for Cancer Research & Molecular Biology, Temple University School of Medicine, 3307 N, Broad St, Philadelphia, PA 19140, USA.
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Lee YS, VandeVoort CA, Gaughan JP, Midic U, Obradovic Z, Latham KE. Extensive effects of in vitro oocyte maturation on rhesus monkey cumulus cell transcriptome. Am J Physiol Endocrinol Metab 2011; 301:E196-209. [PMID: 21487073 PMCID: PMC3129840 DOI: 10.1152/ajpendo.00686.2010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [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] [Indexed: 11/22/2022]
Abstract
The elaboration of a quality oocyte is integrally linked to the correct developmental progression of cumulus cell phenotype. In humans and nonhuman primates, oocyte quality is diminished with in vitro maturation. To determine the changes in gene expression in rhesus monkey cumulus cells (CC) that occur during the final day prior to oocyte maturation and how these changes differ between in vitro (IVM) and in vivo maturation (VVM), we completed a detailed comparison of transcriptomes using the Affymetrix gene array. We observed a large number of genes differing in expression when comparing IVM-CC and VVM-CC directly but a much larger number of differences when comparing the transitions from the prematuration to the post-IVM and post-VVM states. We observed a truncation or delay in the normal pattern of gene regulation but also remarkable compensatory changes in gene expression during IVM. Among the genes affected by IVM are those that contribute to productive cell-cell interactions between cumulus cell and oocyte and between cumulus cells. Numerous genes involved in lipid metabolism are incorrectly regulated during IVM, and the synthesis of sex hormones appears not to be suppressed during IVM. We identified a panel of 24 marker genes, the expression of which should provide the foundation for understanding how IVM can be improved for monitoring IVM conditions and for diagnosing oocyte quality.
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Affiliation(s)
- Young S Lee
- Fels Institute for Cancer Research & Molecular Biology, Temple University School of Medicine, Philadelphia, PA 19140, USA
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Potireddy S, Midic U, Liang CG, Obradovic Z, Latham KE. Positive and negative cis-regulatory elements directing postfertilization maternal mRNA translational control in mouse embryos. Am J Physiol Cell Physiol 2010; 299:C818-27. [PMID: 20573994 DOI: 10.1152/ajpcell.00166.2010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mechanisms providing for temporally complex patterns of maternal mRNA translation after fertilization are poorly understood. We employed bioinformatics analysis to compare populations of mRNAs enriched specifically on polysomes at the metaphase II (MII) stage oocyte and late one-cell stages and a detailed deletion/truncation series to identify elements that regulate translation. We used the Bag4 3' untranslated region (UTR) as a model. Bioinformatics analysis revealed one conserved motif, subsequently confirmed by functional studies to be a key translation repressor element. The deletion/truncation studies revealed additional regulatory motifs, most notably a strong translation activator element of <30 nt. Analysis of mRNA secondary structure suggests that secondary structure plays a key role in translation repression. Additional bioinformatics analysis of the regulated mRNA population revealed a diverse collection of regulatory motifs found in small numbers of mRNAs, highlighting a high degree of sequence diversity and combinatorial complexity in the overall control of the maternal mRNA population. We conclude that translational control after fertilization is driven primarily by negative regulatory mechanisms opposing strong translational activators, with stage-specific release of the inhibitory influences to permit recruitment. The combination of bioinformatics analysis and deletion/truncation studies provides the necessary approach for dissecting postfertilization translation regulatory mechanisms.
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Affiliation(s)
- Santhi Potireddy
- Fels Institute for Cancer Research and Molecular Biology, Information Science and Technology Center, Temple University, Philadelphia, PA 19140, USA
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Midic U, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Unfoldomics of human genetic diseases: illustrative examples of ordered and intrinsically disordered members of the human diseasome. Protein Pept Lett 2010; 16:1533-47. [PMID: 20001916 DOI: 10.2174/092986609789839377] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute a recently recognized realm of atypical biologically active proteins that lack stable structure under physiological conditions, but are commonly involved in such crucial cellular processes as regulation, recognition, signaling and control. IDPs are very common among proteins associated with various diseases. Recently, we performed a systematic bioinformatics analysis of the human diseasome, a network that linked the human disease phenome (which includes all the human genetic diseases) with the human disease genome (which contains all the disease-related genes) (Goh, K. I., Cusick, M. E., Valle, D., Childs, B., Vidal, M., and Barabasi, A. L. (2007). The human disease network. Proc. Natl. Acad. Sci. U.S.A. 104, 8685-90). The analysis of this diseasome revealed that IDPs are abundant in proteins linked to human genetic diseases, and that different genetic disease classes varied dramatically in the IDP content (Midic U., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2009) Protein disorder in the human diseasome: Unfoldomics of human genetic diseases. BMC Genomics. In press). Furthermore, many of the genetic disease-related proteins were shown to contain at least one molecular recognition feature, which is a relatively short loosely structured protein region within a mostly disordered segment with the feature gaining structure upon binding to a partner. Finally, alternative splicing was shown to be abundant among the diseasome genes. Based on these observations the human-genetic-disease-associated unfoldome was created. This minireview describes several illustrative examples of ordered and intrinsically disordered members of the human diseasome.
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Affiliation(s)
- Uros Midic
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 410 W. 10th Street, Indianapolis, IN 46202, USA.
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Uversky VN, Oldfield CJ, Midic U, Xie H, Xue B, Vucetic S, Iakoucheva LM, Obradovic Z, Dunker AK. Unfoldomics of human diseases: linking protein intrinsic disorder with diseases. BMC Genomics 2009; 10 Suppl 1:S7. [PMID: 19594884 PMCID: PMC2709268 DOI: 10.1186/1471-2164-10-s1-s7] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack stable tertiary and/or secondary structure yet fulfills key biological functions. The recent recognition of IDPs and IDRs is leading to an entire field aimed at their systematic structural characterization and at determination of their mechanisms of action. Bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. These activities complement the functions of structured proteins. IDPs and IDRs were shown to participate in both one-to-many and many-to-one signaling. Alternative splicing and posttranslational modifications are frequently used to tune the IDP functionality. Several individual IDPs were shown to be associated with human diseases, such as cancer, cardiovascular disease, amyloidoses, diabetes, neurodegenerative diseases, and others. This raises questions regarding the involvement of IDPs and IDRs in various diseases. RESULTS IDPs and IDRs were shown to be highly abundant in proteins associated with various human maladies. As the number of IDPs related to various diseases was found to be very large, the concepts of the disease-related unfoldome and unfoldomics were introduced. Novel bioinformatics tools were proposed to populate and characterize the disease-associated unfoldome. Structural characterization of the members of the disease-related unfoldome requires specialized experimental approaches. IDPs possess a number of unique structural and functional features that determine their broad involvement into the pathogenesis of various diseases. CONCLUSION Proteins associated with various human diseases are enriched in intrinsic disorder. These disease-associated IDPs and IDRs are real, abundant, diversified, vital, and dynamic. These proteins and regions comprise the disease-related unfoldome, which covers a significant part of the human proteome. Profound association between intrinsic disorder and various human diseases is determined by a set of unique structural and functional characteristics of IDPs and IDRs. Unfoldomics of human diseases utilizes unrivaled bioinformatics and experimental techniques, paves the road for better understanding of human diseases, their pathogenesis and molecular mechanisms, and helps develop new strategies for the analysis of disease-related proteins.
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Affiliation(s)
- Vladimir N Uversky
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Uros Midic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Hongbo Xie
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Bin Xue
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Slobodan Vucetic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Lilia M Iakoucheva
- Laboratory of Statistical Genetics, The Rockefeller University, New York, NY 10065 USA
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Abstract
BACKGROUND Intrinsically disordered proteins lack stable structure under physiological conditions, yet carry out many crucial biological functions, especially functions associated with regulation, recognition, signaling and control. Recently, human genetic diseases and related genes were organized into a bipartite graph (Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690). This diseasome network revealed several significant features such as the common genetic origin of many diseases. METHODS AND FINDINGS We analyzed the abundance of intrinsic disorder in these diseasome network proteins by means of several prediction algorithms, and we analyzed the functional repertoires of these proteins based on prior studies relating disorder to function. Our analyses revealed that (i) Intrinsic disorder is common in proteins associated with many human genetic diseases; (ii) Different disease classes vary in the IDP contents of their associated proteins; (iii) Molecular recognition features, which are relatively short loosely structured protein regions within mostly disordered sequences and which gain structure upon binding to partners, are common in the diseasome, and their abundance correlates with the intrinsic disorder level; (iv) Some disease classes have a significant fraction of genes affected by alternative splicing, and the alternatively spliced regions in the corresponding proteins are predicted to be highly disordered; and (v) Correlations were found among the various diseasome graph-related properties and intrinsic disorder. CONCLUSION These observations provide the basis for the construction of the human-genetic-disease-associated unfoldome.
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Affiliation(s)
- Uros Midic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Christopher J Oldfield
- Center for Computational Biology and Bioinformatics, Indiana University School of Informatics, Indianapolis, IN 46202, USA
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122, USA
| | - Vladimir N Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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Midic U, Oldfield C, Dunker A, Obradovic Z, Uversky V. Unfoldomics of Human Genetic Diseases. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.1594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Abstract
Methods for 3-class secondary-structure prediction are thought to be reaching the highest achievable accuracy. Their accuracy on beta-sheet residue class is considerably lower than for the other two classes. We analysed the relevance of 315 individual input attributes for a predictor with the usual framework of using sequence-profile based data with an input window of fixed size. We propose two alternative knowledge representations with significantly smaller sets of input attributes. We also investigated the possibility of exploiting the prediction of connected pairs of beta-sheet residues and the prediction of residue contact maps for the improvement of accuracy of secondary-structure prediction.
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Affiliation(s)
- Uros Midic
- Center for Information Science and Technology, Temple University, 1805 N. Broad St., 303 Wachman Hall, Philadelphia, PA 19129, USA.
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