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Mitelpunkt A, Stodola MA, Vargus-Adams J, Kurowski BG, Greve K, Bhatnagar S, Aronow B, Zahner J, Bailes AF. A big data approach to evaluate receipt of optimal care in childhood cerebral palsy. Disabil Rehabil 2024; 46:723-730. [PMID: 36755522 PMCID: PMC10406971 DOI: 10.1080/09638288.2023.2175919] [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: 05/20/2022] [Revised: 12/20/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023]
Abstract
PURPOSE Through automated electronic health record (EHR) data extraction and analysis, this project systematically quantified actual care delivery for children with cerebral palsy (CP) and evaluated alignment with current evidence-based recommendations. METHODS Utilizing EHR data for over 8000 children with CP, we developed an approach to define and quantify receipt of optimal care, and pursued proof-of-concept with two children with unilateral CP, Gross Motor Function Classification System (GMFCS) Level II. Optimal care was codified as a cluster of four components including physical medicine and rehabilitation (PMR) care, spasticity management, physical therapy (PT), and occupational therapy (OT). A Receipt of Care Score (ROCS) quantified the degree of adherence to recommendations and was compared with the Pediatric Outcomes Data Collection Instrument (PODCI) and Pediatric Quality of Life Inventory (PEDS QL). RESULTS The two children (12 year old female, 13 year old male) had nearly identical PMR and spasticity component scores while PT and OT scores were more divergent. Functional outcomes were higher for the child who had higher adjusted ROCS. CONCLUSIONS ROCSs demonstrate variation in real-world care delivered over time and differentiate between components of care. ROCSs reflect overall function and quality of life. The ROCS methods developed are novel, robust, and scalable and will be tested in a larger sample.IMPLICATIONS FOR REHABILITATIONOptimal practice, with an emphasis on integrated multidisciplinary care, can be defined and quantified utilizing evidence-based recommendations.Receipt of optimal care for childhood cerebral palsy can be scored using existing electronic health record data.Big Data approaches can contribute to the understanding of current care and inform approaches for improved care.
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Affiliation(s)
- Alexis Mitelpunkt
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Pediatric Rehabilitation, Department of Rehabilitation, Dana-Dwek Children’s Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Jilda Vargus-Adams
- Division of Pediatric Rehabilitation Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Brad G. Kurowski
- Division of Pediatric Rehabilitation Medicine, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kelly Greve
- Division of Occupational Therapy and Physical Therapy, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Rehabilitation, Exercise and Nutrition Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Surbhi Bhatnagar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Janet Zahner
- Department of Information Services, University of Cincinnati, Cincinnati, OH, USA
| | - Amy F. Bailes
- Division of Occupational Therapy and Physical Therapy, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Rehabilitation, Exercise and Nutrition Sciences, University of Cincinnati, Cincinnati, OH, USA
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2
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Sebastian R, Jin K, Pavon N, Bansal R, Potter A, Song Y, Babu J, Gabriel R, Sun Y, Aronow B, Pak C. Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids. Nat Commun 2023; 14:3770. [PMID: 37355690 PMCID: PMC10290702 DOI: 10.1038/s41467-023-39420-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/13/2023] [Indexed: 06/26/2023] Open
Abstract
De novo mutations and copy number deletions in NRXN1 (2p16.3) pose a significant risk for schizophrenia (SCZ). It is unclear how NRXN1 deletions impact cortical development in a cell type-specific manner and disease background modulates these phenotypes. Here, we leveraged human pluripotent stem cell-derived forebrain organoid models carrying NRXN1 heterozygous deletions in isogenic and SCZ patient genetic backgrounds and conducted single-cell transcriptomic analysis over the course of brain organoid development from 3 weeks to 3.5 months. Intriguingly, while both deletions similarly impacted molecular pathways associated with ubiquitin-proteasome system, alternative splicing, and synaptic signaling in maturing glutamatergic and GABAergic neurons, SCZ-NRXN1 deletions specifically perturbed developmental trajectories of early neural progenitors and accumulated disease-specific transcriptomic signatures. Using calcium imaging, we found that both deletions led to long-lasting changes in spontaneous and synchronous neuronal networks, implicating synaptic dysfunction. Our study reveals developmental-timing- and cell-type-dependent actions of NRXN1 deletions in unique genetic contexts.
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Affiliation(s)
- Rebecca Sebastian
- Graduate Program in Neuroscience & Behavior, UMass Amherst, Amherst, MA, 01003, USA
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Narciso Pavon
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Ruby Bansal
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Andrew Potter
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Yoonjae Song
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Juliana Babu
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Rafael Gabriel
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA, 01003, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, 45256, USA
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA.
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3
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Yagi H, Cui C, Saydmohammed M, Gabriel G, Baker C, Devine W, Wu Y, Lin JH, Malek M, Bais A, Murray S, Aronow B, Tsang M, Kostka D, Lo CW. Spatial transcriptome profiling uncovers metabolic regulation of left-right patterning. bioRxiv 2023:2023.04.21.537827. [PMID: 37131609 PMCID: PMC10153223 DOI: 10.1101/2023.04.21.537827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Left-right patterning disturbance can cause severe birth defects, but it remains least understood of the three body axes. We uncovered an unexpected role for metabolic regulation in left-right patterning. Analysis of the first spatial transcriptome profile of left-right patterning revealed global activation of glycolysis, accompanied by right-sided expression of Bmp7 and genes regulating insulin growth factor signaling. Cardiomyocyte differentiation was left-biased, which may underlie the specification of heart looping orientation. This is consistent with known Bmp7 stimulation of glycolysis and glycolysis suppression of cardiomyocyte differentiation. Liver/lung laterality may be specified via similar metabolic regulation of endoderm differentiation. Myo1d , found to be left-sided, was shown to regulate gut looping in mice, zebrafish, and human. Together these findings indicate metabolic regulation of left-right patterning. This could underlie high incidence of heterotaxy-related birth defects in maternal diabetes, and the association of PFKP, allosteric enzyme regulating glycolysis, with heterotaxy. This transcriptome dataset will be invaluable for interrogating birth defects involving laterality disturbance.
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Greve KR, Bailes AF, Zhang N, Long J, Aronow B, Mitelpunkt A. Outpatient hospital utilization after single event multi-level surgery in children with cerebral palsy. J Pediatr Rehabil Med 2023; 16:139-148. [PMID: 36847028 DOI: 10.3233/prm-220051] [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] [Indexed: 03/01/2023] Open
Abstract
PURPOSE This study aimed to examine outpatient hospital utilization (number of specialties seen and number of visits to each specialty) in the year after single event multi-level surgery (SEMLS) in children with cerebral palsy (CP), and to determine if utilization differs across the medical center in the year after compared to the year before SEMLS. METHODS This retrospective cross-sectional study used electronic medical record data of outpatient hospital utilization in children with CP who underwent SEMLS. RESULTS Thirty children with CP (Gross Motor Function Classification System Levels I-V, mean age of 9.9 years) were included. In the year after surgery, a significant difference (p = 0.001) was found for the number of specialties seen, with non-ambulatory children seeing more specialties than ambulatory children. No statistically significant difference was found between the number of outpatient visits to each specialty in the year after SEMLS. Compared to the year before SEMLS, fewer therapy visits occurred in the year after SEMLS (p < 0.001) but significantly more visits to orthopaedics (p = 0.001) and radiology (p = 0.001). CONCLUSION Children with CP had fewer therapy visits but more orthopaedic and radiology visits the year after SEMLS. Nearly half of the children were non-ambulatory. Examination of care needs in children with CP undergoing SEMLS is justified with consideration of ambulatory status, surgical burden, and post-operative immobilization.
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Affiliation(s)
- Kelly R Greve
- Division of Occupational Therapy and Physical Therapy, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Rehabilitation, Exerciseand Nutrition Sciences, University of Cincinnati College of Allied Health Sciences, Cincinnati, OH, USA
| | - Amy F Bailes
- Division of Occupational Therapy and Physical Therapy, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Rehabilitation, Exerciseand Nutrition Sciences, University of Cincinnati College of Allied Health Sciences, Cincinnati, OH, USA
| | - Nanhua Zhang
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Jason Long
- Division of Occupational Therapy and Physical Therapy, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Divison of Pediatric Orthopaedic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce Aronow
- College of Medicine, University of Cincinnati, Cincinnati, OH, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Alexis Mitelpunkt
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Rehabilitation, Pediatric Rehabilitation, Dana-Dwek Children's Hospital, Tel Aviv Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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5
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Greve K, Ni Y, Bailes AF, Vargus-Adams J, Miley AE, Aronow B, McMahon MM, Kurowski BG, Mitelpunkt A. Gross motor function prediction using natural language processing in cerebral palsy. Dev Med Child Neurol 2023; 65:100-106. [PMID: 35665923 PMCID: PMC9720038 DOI: 10.1111/dmcn.15301] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 01/12/2023]
Abstract
AIM To predict ambulatory status and Gross Motor Function Classification System (GMFCS) levels in patients with cerebral palsy (CP) by applying natural language processing (NLP) to electronic health record (EHR) clinical notes. METHOD Individuals aged 8 to 26 years with a diagnosis of CP in the EHR between January 2009 and November 2020 (~12 years of data) were included in a cross-sectional retrospective cohort of 2483 patients. The cohort was divided into train-test and validation groups. Positive predictive value, sensitivity, specificity, and area under the receiver operating curve (AUC) were calculated for prediction of ambulatory status and GMFCS levels. RESULTS The median age was 15 years (interquartile range 10-20 years) for the total cohort, with 56% being male and 75% White. The validation group resulted in 70% sensitivity, 88% specificity, 81% positive predictive value, and 0.89 AUC for predicting ambulatory status. NLP applied to the EHR differentiated between GMFCS levels I-II and III (15% sensitivity, 96% specificity, 46% positive predictive value, and 0.71 AUC); and IV and V (81% sensitivity, 51% specificity, 70% positive predictive value, and 0.75 AUC). INTERPRETATION NLP applied to the EHR demonstrated excellent differentiation between ambulatory and non-ambulatory status, and good differentiation between GMFCS levels I-II and III, and IV and V. Clinical use of NLP may help to individualize functional characterization and management. WHAT THIS PAPER ADDS Natural language processing (NLP) applied to the electronic health record (EHR) can predict ambulatory status in children with cerebral palsy (CP). NLP provides good prediction of Gross Motor Function Classification System level in children with CP using the EHR. NLP methods described could be integrated in an EHR system to provide real-time information.
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Affiliation(s)
- Kelly Greve
- Division of Occupational Therapy and Physical Therapy, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Rehabilitation, Exercise and Nutrition Sciences, University of Cincinnati College of Allied Health Sciences, Cincinnati, OH, USA
| | - Yizhao Ni
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Amy F. Bailes
- Division of Occupational Therapy and Physical Therapy, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Rehabilitation, Exercise and Nutrition Sciences, University of Cincinnati College of Allied Health Sciences, Cincinnati, OH, USA
| | - Jilda Vargus-Adams
- Division of Pediatric Rehabilitation Medicine, Cincinnati Children’s Hospital Medical Center, OH, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Aimee E. Miley
- Division of Pediatric Rehabilitation Medicine, Cincinnati Children’s Hospital Medical Center, OH, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Mary M. McMahon
- Division of Pediatric Rehabilitation Medicine, Cincinnati Children’s Hospital Medical Center, OH, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Brad G. Kurowski
- Division of Pediatric Rehabilitation Medicine, Cincinnati Children’s Hospital Medical Center, OH, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Alexis Mitelpunkt
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Pediatric Rehabilitation, Department of Rehabilitation, Dana-Dwek Children’s Hospital, Tel Aviv Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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6
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McSweeney D, Gabriel R, Jin K, Pang ZP, Aronow B, Pak C. CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons. iScience 2022; 25:105187. [PMID: 36262316 PMCID: PMC9574418 DOI: 10.1016/j.isci.2022.105187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022] Open
Abstract
Loss-of-function (LOF) mutations in CASK cause severe developmental phenotypes, including microcephaly with pontine and cerebellar hypoplasia, X-linked intellectual disability, and autism. Unraveling the pathological mechanisms of CASK-related disorders has been challenging owing to limited human cellular models to study the dynamic roles of this molecule during neuronal maturation and synapse development. Here, we investigate cell-autonomous functions of CASK in cortical excitatory induced neurons (iNs) generated from CASK knockout (KO) isogenic human embryonic stem cells (hESCs) using gene expression, morphometrics, and electrophysiology. While immature CASK KO iNs show robust neuronal outgrowth, mature CASK KO iNs display severe defects in synaptic transmission and synchronized network activity without compromising neuronal morphology and synapse numbers. In the developing human cortical excitatory neurons, CASK functions to promote both structural integrity and establishment of cortical excitatory neuronal networks. These results lay the foundation for future studies identifying suppressors of such phenotypes relevant to human patients.
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Affiliation(s)
- Danny McSweeney
- Graduate Program in Molecular and Cellular Biology, UMass Amherst, Amherst, MA 01003, USA,Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Rafael Gabriel
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Kang Jin
- Departments of Biomedical Informatics, Pediatrics, University of Cincinnati, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Zhiping P. Pang
- Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Bruce Aronow
- Departments of Biomedical Informatics, Pediatrics, University of Cincinnati, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA,Corresponding author
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7
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Xu X, Jin K, Bais AS, Zhu W, Yagi H, Feinstein TN, Nguyen PK, Criscione JD, Liu X, Beutner G, Karunakaran KB, Rao KS, He H, Adams P, Kuo CK, Kostka D, Pryhuber GS, Shiva S, Ganapathiraju MK, Porter GA, Lin JHI, Aronow B, Lo CW. Uncompensated mitochondrial oxidative stress underlies heart failure in an iPSC-derived model of congenital heart disease. Cell Stem Cell 2022; 29:840-855.e7. [PMID: 35395180 PMCID: PMC9302582 DOI: 10.1016/j.stem.2022.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 04/26/2021] [Revised: 11/19/2021] [Accepted: 03/08/2022] [Indexed: 12/14/2022]
Abstract
Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease with 30% mortality from heart failure (HF) in the first year of life, but the cause of early HF remains unknown. Induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CM) from patients with HLHS showed that early HF is associated with increased apoptosis, mitochondrial respiration defects, and redox stress from abnormal mitochondrial permeability transition pore (mPTP) opening and failed antioxidant response. In contrast, iPSC-CM from patients without early HF showed normal respiration with elevated antioxidant response. Single-cell transcriptomics confirmed that early HF is associated with mitochondrial dysfunction accompanied with endoplasmic reticulum (ER) stress. These findings indicate that uncompensated oxidative stress underlies early HF in HLHS. Importantly, mitochondrial respiration defects, oxidative stress, and apoptosis were rescued by treatment with sildenafil to inhibit mPTP opening or TUDCA to suppress ER stress. Together these findings point to the potential use of patient iPSC-CM for modeling clinical heart failure and the development of therapeutics.
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Affiliation(s)
- Xinxiu Xu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
| | - Abha S Bais
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wenjuan Zhu
- Centre for Cardiovascular Genomics and Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Hisato Yagi
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy N Feinstein
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Phong K Nguyen
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Joseph D Criscione
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - Xiaoqin Liu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gisela Beutner
- Departments of Pediatrics and Environmental Medicine University of Rochester Medical Center Rochester, NY USA
| | - Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
| | - Krithika S Rao
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haoting He
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Phillip Adams
- Anesthesiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Catherine K Kuo
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA; Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA; Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Computational & Systems Biology and Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gloria S Pryhuber
- Departments of Pediatrics and Environmental Medicine University of Rochester Medical Center Rochester, NY USA
| | - Sruti Shiva
- Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA; Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - George A Porter
- Pediatrics, Pharmacology, and Physiology, Aab Cardiovascular Research Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Jiuann-Huey Ivy Lin
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45256, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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Ware SM, Bhatnagar S, Dexheimer PJ, Wilkinson JD, Sridhar A, Fan X, Shen Y, Tariq M, Schubert JA, Colan SD, Shi L, Canter CE, Hsu DT, Bansal N, Webber SA, Everitt MD, Kantor PF, Rossano JW, Pahl E, Rusconi P, Lee TM, Towbin JA, Lal AK, Chung WK, Miller EM, Aronow B, Martin LJ, Lipshultz SE. The genetic architecture of pediatric cardiomyopathy. Am J Hum Genet 2022; 109:282-298. [PMID: 35026164 DOI: 10.1016/j.ajhg.2021.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/10/2021] [Indexed: 01/27/2023] Open
Abstract
To understand the genetic contribution to primary pediatric cardiomyopathy, we performed exome sequencing in a large cohort of 528 children with cardiomyopathy. Using clinical interpretation guidelines and targeting genes implicated in cardiomyopathy, we identified a genetic cause in 32% of affected individuals. Cardiomyopathy sub-phenotypes differed by ancestry, age at diagnosis, and family history. Infants < 1 year were less likely to have a molecular diagnosis (p < 0.001). Using a discovery set of 1,703 candidate genes and informatic tools, we identified rare and damaging variants in 56% of affected individuals. We see an excess burden of damaging variants in affected individuals as compared to two independent control sets, 1000 Genomes Project (p < 0.001) and SPARK parental controls (p < 1 × 10-16). Cardiomyopathy variant burden remained enriched when stratified by ancestry, variant type, and sub-phenotype, emphasizing the importance of understanding the contribution of these factors to genetic architecture. Enrichment in this discovery candidate gene set suggests multigenic mechanisms underlie sub-phenotype-specific causes and presentations of cardiomyopathy. These results identify important information about the genetic architecture of pediatric cardiomyopathy and support recommendations for clinical genetic testing in children while illustrating differences in genetic architecture by age, ancestry, and sub-phenotype and providing rationale for larger studies to investigate multigenic contributions.
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9
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Mast AE, Wolberg AS, Gailani D, Garvin MR, Alvarez C, Miller JI, Jones P, Aronow B, Jacobson D. Response to comment on 'SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung'. eLife 2022; 11:e74951. [PMID: 35014952 PMCID: PMC8752086 DOI: 10.7554/elife.74951] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022] Open
Abstract
Early in the SARS-CoV-2 pandemic, we compared transcriptome data from hospitalized COVID-19 patients and control patients without COVID-19. We found changes in procoagulant and fibrinolytic gene expression in the lungs of COVID-19 patients (Mast et al., 2021). These findings have been challenged based on issues with the samples (Fitzgerald and Jamieson, 2022). We have revisited our previous analyses in the light of this challenge and find that these new analyses support our original conclusions.
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Affiliation(s)
- Alan E Mast
- Versiti Blood Research Institute, Department of Cell Biology Neurobiology and Anatomy Medical College of WisconsinMilwaukeeUnited States
| | - Alisa S Wolberg
- Department of Pathology and Laboratory Medicine and UNC Blood Research CenterChapel HillUnited States
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashvilleUnited States
| | - Michael R Garvin
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - Christiane Alvarez
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - J Izaak Miller
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - Piet Jones
- University of Tennessee Knoxville, The Bredesen Center for Interdisciplinary Research and Graduate EducationKnoxvilleUnited States
| | - Bruce Aronow
- Biomedical Informatics, Cincinnati Children’s Hospital Research Foundation, University of CincinnatiCincinnatiUnited States
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
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10
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Karlebach G, Aronow B, Baylin SB, Butler D, Foox J, Levy S, Meydan C, Mozsary C, Saravia-Butler AM, Taylor DM, Wurtele E, Mason CE, Beheshti A, Robinson PN. Betacoronavirus-specific alternate splicing. Genomics 2022; 114:110270. [PMID: 35074468 PMCID: PMC8782732 DOI: 10.1016/j.ygeno.2022.110270] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/15/2021] [Accepted: 01/16/2022] [Indexed: 11/04/2022]
Abstract
Viruses can subvert a number of cellular processes including splicing in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection, datasets from the betacoronaviruses SARS-CoV and MERS, as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification, and have a smaller number of exons as compared with differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by differential alternative splicing and gene expression in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS. The alternative splicing changes observed in betacoronaviruses infection potentially modify a broad range of cellular functions, via changes in the functions of the products of a diverse set of genes involved in different biological processes.
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11
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Bondoc A, Glaser K, Jin K, Lake C, Cairo S, Geller J, Tiao G, Aronow B. Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma. Commun Biol 2021; 4:1049. [PMID: 34497364 PMCID: PMC8426487 DOI: 10.1038/s42003-021-02562-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 08/16/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatoblastoma (HB) is the most common primary liver malignancy of childhood, and molecular investigations are limited and effective treatment options for chemoresistant disease are lacking. There is a knowledge gap in the investigation of key driver cells of HB in tumor. Here we show single cell ribonucleic acid sequencing (scRNAseq) analysis of human tumor, background liver, and patient derived xenograft (PDX) to demonstrate gene expression patterns within tumor and to identify intratumor cell subtype heterogeneity to define differing roles in pathogenesis based on intracellular signaling in pediatric HB. We have identified a driver tumor cell cluster in HB by genetic expression which can be examined to define disease mechanism and treatments. Identification of both critical mechanistic pathways combined with unique cell populations provide the basis for discovery and investigation of novel treatment strategies in vitro and in vivo.
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Affiliation(s)
- Alexander Bondoc
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital, Medical Center, Cincinnati, OH, USA.
| | - Kathryn Glaser
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital, Medical Center, Cincinnati, OH, USA
| | - Kang Jin
- Division of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
| | - Charissa Lake
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital, Medical Center, Cincinnati, OH, USA
| | - Stefano Cairo
- Research and Development Unit, XenTech, Genopole-Campus 3, Fontaine, France
- Istituto di Ricerca Pediatrica (IRP), Corso Stati Uniti, Padua, Italy
| | - James Geller
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gregory Tiao
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital, Medical Center, Cincinnati, OH, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
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12
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Karlebach G, Aronow B, Baylin SB, Butler D, Foox J, Levy S, Meydan C, Mozsary C, Saravia-Butler AM, Taylor DM, Wurtele E, Mason CE, Beheshti A, Robinson PN. Betacoronavirus-specific alternate splicing. bioRxiv 2021. [PMID: 34230929 PMCID: PMC8259905 DOI: 10.1101/2021.07.02.450920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viruses can subvert a number of cellular processes in order to block innate antiviral responses, and many viruses interact with cellular splicing machinery. SARS-CoV-2 infection was shown to suppress global mRNA splicing, and at least 10 SARS-CoV-2 proteins bind specifically to one or more human RNAs. Here, we investigate 17 published experimental and clinical datasets related to SARS-CoV-2 infection as well as datasets from the betacoronaviruses SARS-CoV and MERS as well as Streptococcus pneumonia, HCV, Zika virus, Dengue virus, influenza H3N2, and RSV. We show that genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those of SARS-CoV and MERS and affect a diverse set of genes and biological functions, including many closely related to virus biology. Additionally, the differentially spliced transcripts of cells infected by coronaviruses were more likely to undergo intron-retention, contain a pseudouridine modification and a smaller number of exons than differentially spliced transcripts in the control groups. Viral load in clinical COVID-19 samples was correlated with isoform distribution of differentially spliced genes. A significantly higher number of ribosomal genes are affected by DAS and DGE in betacoronavirus samples, and the betacoronavirus differentially spliced genes are depleted for binding sites of RNA-binding proteins. Our results demonstrate characteristic patterns of differential splicing in cells infected by SARS-CoV-2, SARS-CoV, and MERS, potentially modifying a broad range of cellular functions and affecting a diverse set of genes and biological functions.
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13
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Lewis CS, Karve A, Matiash K, Stone T, Li J, Wang J, Versteeg H, Aronow B, Ahmad S, Desai P, Bogdanov V. Abstract 908: Preclinical in vivo characterization of a first-in-class humanized antibody targeting alternatively spliced tissue factor. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tissue Factor, the initiator of the extrinsic pathway of coagulation, and its isoform alternatively spliced Tissue Factor (asTF) are often overexpressed in cancer cells. Previously, we have shown that RabMab1, a rabbit monoclonal antibody specific for human asTF, disrupts the binding of asTF to beta-integrins and thereby inhibits the growth of breast cancer and pancreatic ductal adenocarcinoma (PDAC) cell lines in vitro and in vivo. Here, we report on humanization of RabMab1, assessment of its binding characteristics, and determination of its in vivo properties. The variable regions of the heavy and light chains of hybridoma derived RabMab1 were cloned and used to generate a rabbit/human chimera (cRabMab1). Substitutions of species-specific residues were then carried out to produce humanized RabMab1 (hRabMab1; IgG1 isotype). Antigen binding was assessed via anti-human IgG Fc capture biosensor assays. cRabMab1 was found to have a KD of 4.24 nM whereas hRabMab1 was found to have a KD in the low picomolar range, which could not be precisely measured due to an extremely slow off-rate. The in vivo half-lives of each were determined to be 280 and 908 hours, respectively. Orthotopic co-implantation of cRabMab1 with high-grade, human PDAC cell line Pt45.P1 in athymic nude mice resulted in tumors that were 82% and 92% smaller than tumors in the vehicle and IgG control group groups, respectively, with no statistical difference between vehicle and IgG isotype control groups. Intravenous administration of hRabMab1 slowed the growth of pre-formed orthotopic Pt45.P1 tumors in athymic nude mice by 64% and 61% compared to vehicle and isotype control groups, respectively; again, there was no difference between vehicle and IgG isotype control groups. Immunohistochemical analysis of tumor tissue revealed a statistically significant 68% reduction in neovascularization (CD31), a 58% reduction in M2-polarized macrophages (CD206), and a 24% reduction in proliferating cells (Ki67) in the hRabMab1 cohort. RNAseq analysis of tumor tissue revealed that components of the focal adhesion system were the most affected by hRabMab1 treatment. In addition, a significant suppression of pathways that promote mitosis and the cell cycle was seen in hRabMab1-treated tumors. By qRT-PCR, we validated a greater than 82% reduction in the expression of HBEGF, a gene encoding a cell surface mitogen, and a greater than 68% reduction in the expression of STN1, a gene encoding a component of the CST-complex, a telomere replication and maintenance structure. This is the first proof-of-concept study whereby a novel biologic that inhibits asTF has been used as a systemically administered single agent, with encouraging results. Because hRabMab1 has a favorable pharmacokinetic profile and is able to suppress PDAC tumor cell growth in vivo, it is an attractive candidate for further clinical development.
Citation Format: Clayton S. Lewis, Aniruddha Karve, Kateryna Matiash, Timothy Stone, Jingxing Li, Jordan Wang, Henri Versteeg, Bruce Aronow, Syed Ahmad, Pankaj Desai, Vladimir Bogdanov. Preclinical in vivo characterization of a first-in-class humanized antibody targeting alternatively spliced tissue factor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 908.
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Affiliation(s)
| | - Aniruddha Karve
- 2University of Cincinnati College of Pharmacy, Cincinnati, OH
| | | | - Timothy Stone
- 1University of Cincinnati College of Medicine, Cincinnati, OH
| | | | | | | | - Bruce Aronow
- 5Cincinnati Children's Hospital and Medical Center, Cincinnati, OH
| | - Syed Ahmad
- 1University of Cincinnati College of Medicine, Cincinnati, OH
| | - Pankaj Desai
- 2University of Cincinnati College of Pharmacy, Cincinnati, OH
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14
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Ware SM, Wilkinson JD, Tariq M, Schubert JA, Sridhar A, Colan SD, Shi L, Canter CE, Hsu DT, Webber SA, Dodd DA, Everitt MD, Kantor PF, Addonizio LJ, Jefferies JL, Rossano JW, Pahl E, Rusconi P, Chung WK, Lee T, Towbin JA, Lal AK, Bhatnagar S, Aronow B, Dexheimer PJ, Martin LJ, Miller EM, Sleeper LA, Razoky H, Czachor J, Lipshultz SE. Genetic Causes of Cardiomyopathy in Children: First Results From the Pediatric Cardiomyopathy Genes Study. J Am Heart Assoc 2021; 10:e017731. [PMID: 33906374 PMCID: PMC8200745 DOI: 10.1161/jaha.120.017731] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Pediatric cardiomyopathy is a genetically heterogeneous disease with substantial morbidity and mortality. Current guidelines recommend genetic testing in children with hypertrophic, dilated, or restrictive cardiomyopathy, but practice variations exist. Robust data on clinical testing practices and diagnostic yield in children are lacking. This study aimed to identify the genetic causes of cardiomyopathy in children and to investigate clinical genetic testing practices. Methods and Results Children with familial or idiopathic cardiomyopathy were enrolled from 14 institutions in North America. Probands underwent exome sequencing. Rare sequence variants in 37 known cardiomyopathy genes were assessed for pathogenicity using consensus clinical interpretation guidelines. Of the 152 enrolled probands, 41% had a family history of cardiomyopathy. Of 81 (53%) who had undergone clinical genetic testing for cardiomyopathy before enrollment, 39 (48%) had a positive result. Genetic testing rates varied from 0% to 97% between sites. A positive family history and hypertrophic cardiomyopathy subtype were associated with increased likelihood of genetic testing (P=0.005 and P=0.03, respectively). A molecular cause was identified in an additional 21% of the 63 children who did not undergo clinical testing, with positive results identified in both familial and idiopathic cases and across all phenotypic subtypes. Conclusions A definitive molecular genetic diagnosis can be made in a substantial proportion of children for whom the cause and heritable nature of their cardiomyopathy was previously unknown. Practice variations in genetic testing are great and should be reduced. Improvements can be made in comprehensive cardiac screening and predictive genetic testing in first‐degree relatives. Overall, our results support use of routine genetic testing in cases of both familial and idiopathic cardiomyopathy. Registration URL: https://www.clinicaltrials.gov; Unique identifier: NCT01873963.
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Affiliation(s)
- Stephanie M Ware
- Departments of Pediatrics and Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | | | - Muhammad Tariq
- Faculty of Applied Medical Sciences University of Tabuk Kingdom of Saudi Arabia
| | - Jeffrey A Schubert
- Departments of Pediatrics and Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | - Arthi Sridhar
- Departments of Pediatrics and Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | - Steven D Colan
- Department of Cardiology and Harvard Medical School Boston Children's Hospital Boston MA
| | - Ling Shi
- New England Research Institutes Watertown MA
| | | | - Daphne T Hsu
- Albert Einstein College of Medicine and Children's Hospital at Montefiore Bronx NY
| | - Steven A Webber
- Monroe Carell Jr. Children's Hospital at Vanderbilt Nashville TN
| | - Debra A Dodd
- Monroe Carell Jr. Children's Hospital at Vanderbilt Nashville TN
| | | | - Paul F Kantor
- Keck School of Medicine and Children's Hospital Los Angeles University of Southern California Los Angeles CA
| | | | | | | | - Elfriede Pahl
- Ann and Robert H. Lurie Children's Hospital Chicago IL
| | - Paolo Rusconi
- University of Miami Miller School of Medicine Miami FL
| | | | - Teresa Lee
- Columbia University Medical Center New York NY
| | | | | | - Surbhi Bhatnagar
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Bruce Aronow
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Phillip J Dexheimer
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Lisa J Martin
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Erin M Miller
- University of Cincinnati School of Medicine and Cincinnati Children's Hospital Medical Center Cincinnati OH
| | - Lynn A Sleeper
- Department of Cardiology and Harvard Medical School Boston Children's Hospital Boston MA
| | - Hiedy Razoky
- Wayne State University School of Medicine Detroit MI
| | - Jason Czachor
- Wayne State University School of Medicine Detroit MI
| | - Steven E Lipshultz
- Jacobs School of Medicine and Biomedical Sciences at University at Buffalo NY.,John R. Oishei Children's Hospital Buffalo NY
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15
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Bailes AF, Greve K, Long J, Kurowski BG, Vargus-Adams J, Aronow B, Mitelpunkt A. Describing the Delivery of Evidence-Based Physical Therapy Intervention to Individuals With Cerebral Palsy. Pediatr Phys Ther 2021; 33:65-72. [PMID: 33770793 PMCID: PMC10141519 DOI: 10.1097/pep.0000000000000783] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE To characterize by evidence grades and examine variation in type of physical therapy intervention delivered in routine clinical care in individuals with cerebral palsy (CP). METHODS Retrospective data collection from the electronic record over 1 year at a tertiary care pediatric outpatient therapy division. RESULTS Four hundred sixty-five individuals with CP received 28 344 interventions during 4335 treatment visits. Sixty-six percent of interventions were evidence-based interventions (EBIs). Significant variation was demonstrated across Gross Motor Function Classification System levels, with children classified as level V receiving the least and level III the most. The most frequent EBIs delivered were caregiver education, motor control, functional strengthening, ankle-foot orthoses, treadmill training, and fit of adaptive equipment. CONCLUSIONS Further work is needed to determine whether amount of EBI is related to better outcomes. Combining this information with other aspects of dose (intensity, time, and frequency) may elucidate the contribution of each with outcomes.
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Affiliation(s)
- Amy F Bailes
- Division of Occupational Therapy and Physical Therapy (Drs Bailes, Greve, and Long), Division of Orthopaedic Surgery Motion Analysis Laboratory (Dr Long), and Division of Biomedical Informatics (Drs Aronow and Mitelpunkt), Cincinnati Children's Hospital, Cincinnati, Ohio; Department of Rehabilitation Science (Dr Bailes), University of Cincinnati, Cincinnati, Ohio; Division of Pediatric Rehabilitation Medicine (Drs Kurowski and Vargus-Adams), Departments of Pediatrics and Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Sackler Faculty of Medicine (Dr Mitelpunkt), Tel Aviv University, Tel Aviv, Israel
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16
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Mast AE, Wolberg AS, Gailani D, Garvin MR, Alvarez C, Miller JI, Aronow B, Jacobson D. SARS-CoV-2 suppresses anticoagulant and fibrinolytic gene expression in the lung. eLife 2021; 10:e64330. [PMID: 33683204 PMCID: PMC8049742 DOI: 10.7554/elife.64330] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/06/2021] [Indexed: 12/13/2022] Open
Abstract
Extensive fibrin deposition in the lungs and altered levels of circulating blood coagulation proteins in COVID-19 patients imply local derangement of pathways that limit fibrin formation and/or promote its clearance. We examined transcriptional profiles of bronchoalveolar lavage fluid (BALF) samples to identify molecular mechanisms underlying these coagulopathies. mRNA levels for regulators of the kallikrein-kinin (C1-inhibitor), coagulation (thrombomodulin, endothelial protein C receptor), and fibrinolytic (urokinase and urokinase receptor) pathways were significantly reduced in COVID-19 patients. While transcripts for several coagulation proteins were increased, those encoding tissue factor, the protein that initiates coagulation and whose expression is frequently increased in inflammatory disorders, were not increased in BALF from COVID-19 patients. Our analysis implicates enhanced propagation of coagulation and decreased fibrinolysis as drivers of the coagulopathy in the lungs of COVID-19 patients.
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Affiliation(s)
- Alan E Mast
- Versiti Blood Research Institute, Department of Cell Biology Neurobiology and Anatomy Medical College of WisconsinMilwaukeeUnited States
| | - Alisa S Wolberg
- Department of Pathology and Laboratory Medicine and UNC Blood Research CenterChapel HillUnited States
| | - David Gailani
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashvilleUnited States
| | - Michael R Garvin
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - Christiane Alvarez
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - J Izaak Miller
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - Bruce Aronow
- University of Tennessee Knoxville, The Bredesen Center for Interdisciplinary Research and Graduate EducationKnoxvilleUnited States
- Biomedical Informatics, Cincinnati Children’s Hospital Research FoundationCincinnatiUnited States
- University of CincinnatiCincinnatiUnited States
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
- University of Tennessee Knoxville, The Bredesen Center for Interdisciplinary Research and Graduate EducationKnoxvilleUnited States
- University of Tennessee Knoxville, Department of PsychologyKnoxvilleUnited States
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17
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Masci AM, White S, Neely B, Ardini-Polaske M, Hill CB, Misra RS, Aronow B, Gaddis N, Yang L, Wert SE, Palmer SM, Chan C. Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. BMC Bioinformatics 2021; 22:82. [PMID: 33622235 PMCID: PMC7901098 DOI: 10.1186/s12859-021-04008-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 02/08/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Immunofluorescent confocal microscopy uses labeled antibodies as probes against specific macromolecules to discriminate between multiple cell types. For images of the developmental mouse lung, these cells are themselves organized into densely packed higher-level anatomical structures. These types of images can be challenging to segment automatically for several reasons, including the relevance of biomedical context, dependence on the specific set of probes used, prohibitive cost of generating labeled training data, as well as the complexity and dense packing of anatomical structures in the image. The use of an application ontology helps surmount these challenges by combining image data with its metadata to provide a meaningful biological context, modeled after how a human expert would make use of contextual information to identify histological structures, that constrains and simplifies the process of segmentation and object identification. RESULTS We propose an innovative approach for the semi-supervised analysis of complex and densely packed anatomical structures from immunofluorescent images that utilizes an application ontology to provide a simplified context for image segmentation and object identification. We describe how the logical organization of biological facts in the form of an ontology can provide useful constraints that facilitate automatic processing of complex images. We demonstrate the results of ontology-guided segmentation and object identification in mouse developmental lung images from the Bioinformatics REsource ATlas for the Healthy lung database of the Molecular Atlas of Lung Development (LungMAP1) program CONCLUSION: We describe a novel ontology-guided approach to segmentation and classification of complex immunofluorescence images of the developing mouse lung. The ontology is used to automatically generate constraints for each image based on its biomedical context, which facilitates image segmentation and classification.
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Affiliation(s)
- Anna Maria Masci
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
| | - Scott White
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Ben Neely
- Duke Crucible, Duke University, Durham, NC, USA
| | | | - Carol B Hill
- Duke Clinical Research Institute, Duke School of Medicine, Durham, NC, USA
| | - Ravi S Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Bruce Aronow
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Lina Yang
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Susan E Wert
- Department of Pediatrics Perinatal Institute Divisions of Neonatology, Perinatal and Pulmonary Biology Cincinnati Children's Hospital Medical Center/Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Scott M Palmer
- Vice Chair for Research, Department of Medicine, Director, Respiratory Research, Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
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18
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Riccetti M, Gokey JJ, Aronow B, Perl AKT. The elephant in the lung: Integrating lineage-tracing, molecular markers, and single cell sequencing data to identify distinct fibroblast populations during lung development and regeneration. Matrix Biol 2020; 91-92:51-74. [PMID: 32442602 PMCID: PMC7434667 DOI: 10.1016/j.matbio.2020.05.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 11/08/2019] [Revised: 05/08/2020] [Accepted: 05/08/2020] [Indexed: 12/26/2022]
Abstract
During lung development, the mesenchyme and epithelium are dependent on each other for instructive morphogenic cues that direct proliferation, cellular differentiation and organogenesis. Specification of epithelial and mesenchymal cell lineages occurs in parallel, forming cellular subtypes that guide the formation of both transitional developmental structures and the permanent architecture of the adult lung. While epithelial cell types and lineages have been relatively well-defined in recent years, the definition of mesenchymal cell types and lineage relationships has been more challenging. Transgenic mouse lines with permanent and inducible lineage tracers have been instrumental in identifying lineage relationships among epithelial progenitor cells and their differentiation into distinct airway and alveolar epithelial cells. Lineage tracing experiments with reporter mice used to identify fibroblast progenitors and their lineage trajectories have been limited by the number of cell specific genes and the developmental timepoint when the lineage trace was activated. In this review, we discuss major developmental mesenchymal lineages, focusing on time of origin, major cell type, and other lineage derivatives, as well as the transgenic tools used to find and define them. We describe lung fibroblasts using function, location, and molecular markers in order to compare and contrast cells with similar functions. The temporal and cell-type specific expression of fourteen "fibroblast lineage" genes were identified in single-cell RNA-sequencing data from LungMAP in the LGEA database. Using these lineage signature genes as guides, we clustered murine lung fibroblast populations from embryonic day 16.5 to postnatal day 28 (E16.5-PN28) and generated heatmaps to illustrate expression of transcription factors, signaling receptors and ligands in a temporal and population specific manner.
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Affiliation(s)
- Matthew Riccetti
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Jason J Gokey
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Bruce Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, United States
| | - Anne-Karina T Perl
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, United States.
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19
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Garvin MR, Alvarez C, Miller JI, Prates ET, Walker AM, Amos BK, Mast AE, Justice A, Aronow B, Jacobson D. A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm. eLife 2020; 9:e59177. [PMID: 32633718 PMCID: PMC7410499 DOI: 10.7554/elife.59177] [Citation(s) in RCA: 236] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Neither the disease mechanism nor treatments for COVID-19 are currently known. Here, we present a novel molecular mechanism for COVID-19 that provides therapeutic intervention points that can be addressed with existing FDA-approved pharmaceuticals. The entry point for the virus is ACE2, which is a component of the counteracting hypotensive axis of RAS. Bradykinin is a potent part of the vasopressor system that induces hypotension and vasodilation and is degraded by ACE and enhanced by the angiotensin1-9 produced by ACE2. Here, we perform a new analysis on gene expression data from cells in bronchoalveolar lavage fluid (BALF) from COVID-19 patients that were used to sequence the virus. Comparison with BALF from controls identifies a critical imbalance in RAS represented by decreased expression of ACE in combination with increases in ACE2, renin, angiotensin, key RAS receptors, kinogen and many kallikrein enzymes that activate it, and both bradykinin receptors. This very atypical pattern of the RAS is predicted to elevate bradykinin levels in multiple tissues and systems that will likely cause increases in vascular dilation, vascular permeability and hypotension. These bradykinin-driven outcomes explain many of the symptoms being observed in COVID-19.
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Affiliation(s)
- Michael R Garvin
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - Christiane Alvarez
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - J Izaak Miller
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - Erica T Prates
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
| | - Angelica M Walker
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
- University of Tennessee Knoxville, The Bredesen Center for Interdisciplinary Research and Graduate EducationKnoxvilleUnited States
| | - B Kirtley Amos
- University of Kentucky, Department of HorticultureLexingtonUnited States
| | - Alan E Mast
- Versiti Blood Research Institute, Medical College of WisconsinMilwaukeeUnited States
| | - Amy Justice
- VA Connecticut Healthcare/General Internal Medicine, Yale University School of MedicineWest HavenUnited States
| | - Bruce Aronow
- University of CincinnatiCincinnatiUnited States
- Biomedical Informatics, Cincinnati Children’s Hospital Research FoundationCincinnatiUnited States
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences DivisionOak RidgeUnited States
- University of Tennessee Knoxville, The Bredesen Center for Interdisciplinary Research and Graduate EducationKnoxvilleUnited States
- University of Tennessee Knoxville, Department of Psychology, Austin Peay BuildingKnoxvilleUnited States
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20
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Abstract
e17078 Background: The Cancer Genome Atlas project has become a leading source for data that has allowed the identification of a broad range of human cancer tumor types and subtypes and has revealed deep complexity with respect to the differentiation, or lack thereof, among human cancers. In particular, differential gene expression analyses have revealed a wealth of active oncogenic pathways, underlying gene mutation drivers, discriminative markers, and candidate therapeutic targets. Despite its rich composition, several factors have led to it not attaining the utility it would seem to offer. Methods: To study this, we dissected molecular subtypes in the TCGA and used the Pan-Kidney (n = 1022 samples) Portion within it to determine where obstacles seem to limit its utility. We re-clustered the renal carcinomas to create more appropriate histology annotations for these samples. The molecular subtypes were then found through K-means using differentially expressed known developmental regulators per histological annotation. After deriving these new annotations, the histology and molecular subtypes were compared to one another via T-test to generate gene modules that characterize these classes/subclasses. Results: We identified a number of factors that include inconsistent metadata attributes, apparent misclassification of histological subtypes, and molecular subtypes that do not match with that obtained by focused approaches to rederive principle subclasses. Our gene modules showed a molecular subtype of clear cell renal carcinoma that was enriched for vascular development and nephron development. In general, the clear cell renal carcinoma and papillary renal cell carcinoma cohorts both showed significant co-expression with atlases that were enriched for genes involved in kidney development. Conclusions: Our atlas highlights the limitations of the current TCGA atlas and provides another tool to capture the rich insights from the TCGA repository through the efforts explained above, highlighted by its use in kidney carcinoma.
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Affiliation(s)
| | - James I. Geller
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Bruce Aronow
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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21
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Woodle E, Tremblay S, Brailey P, Girnita A, Alloway R, Aronow B, Dasgupta N, Ebstein F, Kloetzel P, Lee M, Kim K, Singh H, Driscoll J. Proteasomal adaptations underlying carfilzomib-resistance in human bone marrow plasma cells. Am J Transplant 2020; 20:399-410. [PMID: 31595669 PMCID: PMC6984988 DOI: 10.1111/ajt.15634] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 08/30/2018] [Revised: 09/15/2019] [Accepted: 09/15/2019] [Indexed: 01/25/2023]
Abstract
Donor-specific antibodies (DSAs) have a deleterious effect on allografts and remain a major immunologic barrier in transplantation. Current therapies to eliminate DSAs are ineffective in highly HLA-sensitized patients. Proteasome inhibitors have been employed as a strategy to target bone marrow plasma cells (BMPCs), the source of long-term antibody production; however, their efficacy has been limited by poorly defined drug-resistance mechanisms. Here, we performed transcriptomic profiling of CD138+ BMPCs that survived in vivo desensitization therapy with the proteasome inhibitor carfilzomib to identify mechanisms of drug resistance. The results revealed a genomic signature that included increased expression of the immunoproteasome, a highly specialized proteasomal variant. Western blotting and functional studies demonstrated that catalytically active immunoproteasomes and the immunoproteasome activator PA28 were upregulated in carfilzomib-resistant BMPCs. Carfilzomib-resistant BMPCs displayed reduced sensitivity to the proteasome inhibitors carfilzomib, bortezomib, and ixazomib, but enhanced sensitivity to an immunoproteasome-specific inhibitor ONX-0914. Finally, in vitro carfilzomib treatment of BMPCs from HLA-sensitized patients increased levels of the immunoproteasome β5i (PSMB8) catalytic subunit suggesting that carfilzomib therapy directly induces an adaptive immunoproteasome response. Taken together, our results indicate that carfilzomib induces structural changes in proteasomes and immunoproteasome formation.
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Affiliation(s)
- E.S. Woodle
- Division of Transplantation, Department of Surgery, Cincinnati, OH, 45267, USA,Corresponding authors: E. Steve Woodle, MD; James J. Driscoll, MD, PhD; driscojs@ UCMAIL.UC.EDU
| | - S. Tremblay
- Division of Transplantation, Department of Surgery, Cincinnati, OH, 45267, USA,Department of Environmental Health, Division of Epidemiology, Cincinnati, OH, 45229, USA
| | - P. Brailey
- Hoxworth Blood Center, Transplant Immunology Division, Cincinnati, OH, 45229, USA
| | - A. Girnita
- Division of Transplantation, Department of Surgery, Cincinnati, OH, 45267, USA,Hoxworth Blood Center, Transplant Immunology Division, Cincinnati, OH, 45229, USA
| | - R.R. Alloway
- Division of Transplantation, Department of Surgery, Cincinnati, OH, 45267, USA
| | - B. Aronow
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - N. Dasgupta
- Department of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - F. Ebstein
- Institute for Biochemistry, Charité - University Medicine Berlin, Berlin, Germany
| | - P.M. Kloetzel
- Institute for Biochemistry, Charité - University Medicine Berlin, Berlin, Germany
| | - M.J. Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - K.B. Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, USA
| | - H. Singh
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - J.J. Driscoll
- Department of Internal Medicine, Division of Hematology and Oncology, Cincinnati, OH, 45267, USA,University of Cincinnati Cancer Institute, Cincinnati, OH, 45267, USA,Corresponding authors: E. Steve Woodle, MD; James J. Driscoll, MD, PhD; driscojs@ UCMAIL.UC.EDU
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22
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Lu YC, Sanada C, Xavier-Ferrucio J, Wang L, Zhang PX, Grimes HL, Venkatasubramanian M, Chetal K, Aronow B, Salomonis N, Krause DS. The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. Cell Rep 2019; 25:2083-2093.e4. [PMID: 30463007 PMCID: PMC6336197 DOI: 10.1016/j.celrep.2018.10.084] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [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: 04/19/2018] [Revised: 08/14/2018] [Accepted: 10/24/2018] [Indexed: 12/25/2022] Open
Abstract
Megakaryocytic-erythroid progenitors (MEPs) give rise to the cells that produce red blood cells and platelets. Although the mechanisms underlying megakaryocytic (MK) and erythroid (E) maturation have been described, those controlling their specification from MEPs are unknown. Single-cell RNA sequencing of primary human MEPs, common myeloid progenitors (CMPs), megakaryocyte progenitors, and E progenitors revealed a distinct transitional MEP signature. Inferred regulatory transcription factors (TFs) were associated with differential expression of cell cycle regulators. Genetic manipulation of selected TFs validated their role in lineage specification and demonstrated coincident modulation of the cell cycle. Genetic and pharmacologic modulation demonstrated that cell cycle activation is sufficient to promote E versus MK specification. These findings, obtained from healthy human cells, lay a foundation to study the mechanisms underlying benign and malignant disease states of the megakaryocytic and E lineages. Bipotent megakaryocytic-erythroid progenitors (MEPs) produce megakaryocytic and erythroid cells. Using single-cell RNA sequencing of primary human MEPs and their upstream and downstream progenitors, Lu et al. show that MEPs are a unique transitional population. Functional and molecular studies show that MEP lineage fate is toggled by cell cycle speed.
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Affiliation(s)
- Yi-Chien Lu
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA.
| | - Chad Sanada
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Juliana Xavier-Ferrucio
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Lin Wang
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Ping-Xia Zhang
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Meenakshi Venkatasubramanian
- Division of Biomedical Informatics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Bruce Aronow
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Diane S Krause
- Department of Laboratory Medicine and Yale Stem Cell Center, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
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23
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Turnier JL, Brunner HI, Bennett M, Aleed A, Gulati G, Haffey WD, Thornton S, Wagner M, Devarajan P, Witte D, Greis KD, Aronow B. Discovery of SERPINA3 as a candidate urinary biomarker of lupus nephritis activity. Rheumatology (Oxford) 2019; 58:321-330. [PMID: 30285245 DOI: 10.1093/rheumatology/key301] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Indexed: 12/11/2022] Open
Abstract
Objectives We used an unbiased proteomics approach to identify candidate urine biomarkers (CUBMs) predictive of LN chronicity and pursued their validation in a larger cohort. Methods In this cross-sectional pilot study, we selected urine collected at kidney biopsy from 20 children with varying levels of LN damage (discovery cohort) and performed proteomic analysis using isobaric tags for relative and absolute quantification (iTRAQ). We identified differentially excreted proteins based on degree of LN chronicity and sought to distinguish markers exhibiting different relative expression patterns using hierarchically clustered log10-normalized relative abundance data with linked and distinct functions by biological network analyses. For each CUBM, we performed specific ELISAs on urine from a validation cohort (n = 41) and analysis of variance to detect differences between LN chronicity, with LN activity adjustment. We evaluated for CUBM expression in LN biopsies with immunohistochemistry. Results iTRAQ detected 112 proteins in urine from the discovery cohort, 51 quantifiable in all replicates. Simple analysis of variance revealed four differentially expressed, chronicity-correlated proteins (P-values < 0.05). Further correlation and network analyses led to selection of seven CUBMs for LN chronicity. In the validation cohort, none of the CUBMs distinguished LN chronicity degree; however, urine SERPINA3 demonstrated a moderate positive correlation with LN histological activity. Immunohistochemistry further demonstrated SERPINA3 staining in proximal tubular epithelial and endothelial cells. Conclusion We identified SERPINA3, a known inhibitor of neutrophil cathepsin G and angiotensin II production, as a potential urine biomarker to help quantify LN activity.
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Affiliation(s)
- Jessica L Turnier
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hermine I Brunner
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael Bennett
- Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ashwaq Aleed
- Department of Pediatrics, Qassim University College of Medicine, Qassim, Saudi Arabia
| | - Gaurav Gulati
- Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Wendy D Haffey
- Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sherry Thornton
- Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael Wagner
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Prasad Devarajan
- Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - David Witte
- Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth D Greis
- Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Bruce Aronow
- Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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24
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Schrode N, Ho SM, Yamamuro K, Dobbyn A, Huckins L, Matos MR, Cheng E, Deans PJM, Flaherty E, Barretto N, Topol A, Alganem K, Abadali S, Gregory J, Hoelzli E, Phatnani H, Singh V, Girish D, Aronow B, Mccullumsmith R, Hoffman GE, Stahl EA, Morishita H, Sklar P, Brennand KJ. Synergistic effects of common schizophrenia risk variants. Nat Genet 2019; 51:1475-1485. [PMID: 31548722 PMCID: PMC6778520 DOI: 10.1038/s41588-019-0497-5] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/13/2019] [Indexed: 12/19/2022]
Abstract
The mechanisms by which common risk variants of small effect interact to contribute to complex genetic disorders are unclear. Here, we apply a genetic approach, using isogenic human induced pluripotent stem cells, to evaluate the effects of schizophrenia (SZ)-associated common variants predicted to function as SZ expression quantitative trait loci (eQTLs). By integrating CRISPR-mediated gene editing, activation and repression technologies to study one putative SZ eQTL (FURIN rs4702) and four top-ranked SZ eQTL genes (FURIN, SNAP91, TSNARE1 and CLCN3), our platform resolves pre- and postsynaptic neuronal deficits, recapitulates genotype-dependent gene expression differences and identifies convergence downstream of SZ eQTL gene perturbations. Our observations highlight the cell-type-specific effects of common variants and demonstrate a synergistic effect between SZ eQTL genes that converges on synaptic function. We propose that the links between rare and common variants implicated in psychiatric disease risk constitute a potentially generalizable phenomenon occurring more widely in complex genetic disorders.
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Affiliation(s)
- Nadine Schrode
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seok-Man Ho
- Department of Stem Cell and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kazuhiko Yamamuro
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Dobbyn
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Huckins
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marliette R Matos
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Esther Cheng
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P J Michael Deans
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Erin Flaherty
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie Barretto
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aaron Topol
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Khaled Alganem
- Department of Neurosciences, Institute in the College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Sonya Abadali
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Gregory
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Emily Hoelzli
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Hemali Phatnani
- Center for Genomics of Neurodegenerative Disease, New York Genome Center, New York, NY, USA
| | - Vineeta Singh
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Deeptha Girish
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Bruce Aronow
- UC Department of Pediatrics Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert Mccullumsmith
- Department of Neurosciences, Institute in the College of Medicine & Life Sciences, The University of Toledo, Toledo, OH, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hirofumi Morishita
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pamela Sklar
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Stem Cell and Regenerative Biology, 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
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Stem Cell and Regenerative Biology, 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.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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25
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Peters AL, Luo Z, Li J, Mourya R, Wang Y, Dexheimer P, Shivakumar P, Aronow B, Bezerra JA. Single cell RNA sequencing reveals regional heterogeneity of hepatobiliary innate lymphoid cells in a tissue-enriched fashion. PLoS One 2019; 14:e0215481. [PMID: 31022195 PMCID: PMC6483339 DOI: 10.1371/journal.pone.0215481] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/02/2019] [Indexed: 12/29/2022] Open
Abstract
IL-33 promotes type 2 immunity, epithelial repair, and tissue fibrosis by activating group 2 innate lymphoid cells (ILC2). ILC2 lack all known surface markers of mature T, B, NK, and myeloid cell lineages (Linneg), express the IL-33 receptor ST2, and release type 2 cytokines which contribute to cholangiocyte proliferation and activation of hepatic stellate cells. This pathway results in massive proliferation of the extrahepatic bile duct (EHBD) but also exacerbates liver fibrosis, suggesting that there may be tissue-specific subpopulations of IL-33-induced ILC. To determine the tissue-specific subsets of ILC in the hepatobiliary system, we analyzed CD45+Linneg mononuclear cells from IL-33 treated adult Balb/c mouse liver or EHBD by single cell RNA sequencing. Principal component analysis identified 6 major CD45+Linneg cell classes, two of which were restricted to the EHBD. One of these classes, biliary immature myeloid (BIM) cells, was predicted to interact with ILC2 by a network of shared receptor-ligand pairs. BIM highly expressed Gp49 and ST2 receptors on the cell surface while lacking surface expression of markers for mature myeloid cells. In conclusion, single cell RNA sequencing identified IL-33 responsive cell groups regionally confined to the liver or extrahepatic bile duct, including a novel population of CD45+Linneg Gp49-expressing mononuclear cells.
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Affiliation(s)
- Anna L. Peters
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Zhenhua Luo
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jun Li
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Reena Mourya
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Yunguan Wang
- Department of Pediatrics, Division of Bioinformatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Phillip Dexheimer
- Department of Pediatrics, Division of Bioinformatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Pranav Shivakumar
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Bruce Aronow
- Department of Pediatrics, Division of Bioinformatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jorge A. Bezerra
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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26
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Roy S, Rai P, Eiymo Mwa Mpollo MS, Chang KH, Rizvi T, Shanmukhappa SK, VandenHeuvel K, Aronow B, Inagami T, Cancelas JA, Malik P. Angiotensin receptor signaling in sickle cell anemia has a reno-protective effect on urine concentrating ability but results in sickle glomerulopathy. Am J Hematol 2018; 93:E177-E181. [PMID: 29675906 DOI: 10.1002/ajh.25118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/15/2018] [Accepted: 04/17/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Swarnava Roy
- Division of Experimental Hematology and Cancer Biology; Cancer and Blood Diseases Institute, Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
| | - Parul Rai
- Division of Experimental Hematology and Cancer Biology; Cancer and Blood Diseases Institute, Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
- Division of Hematology; Cancer and Blood Diseases Institute, Hoxworth Blood Center; Cincinnati Ohio 45267
| | - Marthe-Sandrine Eiymo Mwa Mpollo
- Division of Experimental Hematology and Cancer Biology; Cancer and Blood Diseases Institute, Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
| | - Kyung-Hee Chang
- Division of Experimental Hematology and Cancer Biology; Cancer and Blood Diseases Institute, Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
| | - Tilat Rizvi
- Division of Experimental Hematology and Cancer Biology; Cancer and Blood Diseases Institute, Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
| | - Shiva Kumar Shanmukhappa
- Division of Pathology; Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
| | - Katherine VandenHeuvel
- Division of Pathology; Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
| | - Bruce Aronow
- Division of Bioinformatics; Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
| | - Tadashi Inagami
- Vanderbilt University School of Medicine; Nashville Tennessee
| | - Jose A. Cancelas
- Division of Experimental Hematology and Cancer Biology; Cancer and Blood Diseases Institute, Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
- University of Cincinnati College of Medicine; Hoxworth Blood Center; Cincinnati Ohio 45267
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology; Cancer and Blood Diseases Institute, Cincinnati Children's Research Foundation, Cincinnati Children's Hospital Medical Center; Cincinnati Ohio 45229
- Division of Hematology; Cancer and Blood Diseases Institute, Hoxworth Blood Center; Cincinnati Ohio 45267
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27
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Xu J, Hartley BJ, Kurup P, Phillips A, Topol A, Xu M, Ononenyi C, Foscue E, Ho SM, Baguley TD, Carty N, Barros CS, Müller U, Gupta S, Gochman P, Rapoport J, Ellman JA, Pittenger C, Aronow B, Nairn AC, Nestor MW, Lombroso PJ, Brennand KJ. Inhibition of STEP 61 ameliorates deficits in mouse and hiPSC-based schizophrenia models. Mol Psychiatry 2018; 23:271-281. [PMID: 27752082 PMCID: PMC5395367 DOI: 10.1038/mp.2016.163] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 07/13/2016] [Accepted: 08/11/2016] [Indexed: 02/03/2023]
Abstract
The brain-specific tyrosine phosphatase, STEP (STriatal-Enriched protein tyrosine Phosphatase) is an important regulator of synaptic function. STEP normally opposes synaptic strengthening by increasing N-methyl D-aspartate glutamate receptor (NMDAR) internalization through dephosphorylation of GluN2B and inactivation of the kinases extracellular signal-regulated kinase 1/2 and Fyn. Here we show that STEP61 is elevated in the cortex in the Nrg1+/- knockout mouse model of schizophrenia (SZ). Genetic reduction or pharmacological inhibition of STEP prevents the loss of NMDARs from synaptic membranes and reverses behavioral deficits in Nrg1+/- mice. STEP61 protein is also increased in cortical lysates from the central nervous system-specific ErbB2/4 mouse model of SZ, as well as in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons and Ngn2-induced excitatory neurons, from two independent SZ patient cohorts. In these selected SZ models, increased STEP61 protein levels likely reflect reduced ubiquitination and degradation. These convergent findings from mouse and hiPSC SZ models provide evidence for STEP61 dysfunction in SZ.
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Affiliation(s)
- J Xu
- Child Study Center, Yale University, New Haven, CT, USA
| | - B J Hartley
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - P Kurup
- Child Study Center, Yale University, New Haven, CT, USA
| | - A Phillips
- Hussman Institute for Autism, Baltimore, MD, USA
| | - A Topol
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Xu
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - C Ononenyi
- Child Study Center, Yale University, New Haven, CT, USA
| | - E Foscue
- Child Study Center, Yale University, New Haven, CT, USA
| | - S-M Ho
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Developmental and Stem Cell Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - T D Baguley
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - N Carty
- Child Study Center, Yale University, New Haven, CT, USA
| | - C S Barros
- Dorris Neuroscience Center, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA,Plymouth University School of Medicine, Plymouth UK
| | - U Müller
- Dorris Neuroscience Center, Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - S Gupta
- UC Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - P Gochman
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - J Rapoport
- Childhood Psychiatry Branch, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - J A Ellman
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - C Pittenger
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - B Aronow
- UC Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - A C Nairn
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - M W Nestor
- Hussman Institute for Autism, Baltimore, MD, USA
| | - P J Lombroso
- Child Study Center, Yale University, New Haven, CT, USA,Department of Psychiatry, Yale University, New Haven, CT, USA,Department of Neurobiology, Yale University, New Haven, CT, USA,Department of Psychiatry, Yale University, New Haven, CT, USA E-mail:
| | - K J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA. E-mail:
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Haberman Y, BenShoshan M, Di Segni A, Dexheimer PJ, Braun T, Weiss B, Walters TD, Baldassano RN, Noe JD, Markowitz J, Rosh J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Kellermayer R, Patel A, Otley A, Steiner SJ, Gulati AS, Guthery SL, LeLeiko N, Moulton D, Kirschner BS, Snapper S, Avivi C, Barshack I, Oliva-Hemker M, Cohen SA, Keljo DJ, Ziring D, Anikster Y, Aronow B, Hyams JS, Kugathasan S, Denson LA. Long ncRNA Landscape in the Ileum of Treatment-Naive Early-Onset Crohn Disease. Inflamm Bowel Dis 2018; 24:346-360. [PMID: 29361088 PMCID: PMC6231367 DOI: 10.1093/ibd/izx013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 07/14/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Long noncoding RNAs (lncRNA) are key regulators of gene transcription and many show tissue-specific expression. We previously defined a novel inflammatory and metabolic ileal gene signature in treatment-naive pediatric Crohn disease (CD). We now extend our analyses to include potential regulatory lncRNA. METHODS Using RNAseq, we systematically profiled lncRNAs and protein-coding gene expression in 177 ileal biopsies. Co-expression analysis was used to identify functions and tissue-specific expression. RNA in situ hybridization was used to validate expression. Real-time polymerase chain reaction was used to test lncRNA regulation by IL-1β in Caco-2 enterocytes. RESULTS We characterize widespread dysregulation of 459 lncRNAs in the ileum of CD patients. Using only the lncRNA in discovery and independent validation cohorts showed patient classification as accurate as the protein-coding genes, linking lncRNA to CD pathogenesis. Co-expression and functional annotation enrichment analyses across several tissues and cell types 1showed that the upregulated LINC01272 is associated with a myeloid pro-inflammatory signature, whereas the downregulated HNF4A-AS1 exhibits association with an epithelial metabolic signature. We confirmed tissue-specific expression in biopsies using in situ hybridization, and validated regulation of prioritized lncRNA upon IL-1β exposure in differentiated Caco-2 cells. Finally, we identified significant correlations between LINC01272 and HNF4A-AS1 expression and more severe mucosal injury. CONCLUSIONS We systematically define differentially expressed lncRNA in the ileum of newly diagnosed pediatric CD. We show lncRNA utility to correctly classify disease or healthy states and demonstrate their regulation in response to an inflammatory signal. These lncRNAs, after mechanistic exploration, may serve as potential new tissue-specific targets for RNA-based interventions.
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Affiliation(s)
- Yael Haberman
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Sheba Medical Center, Israel,Address correspondence to: Yael Haberman, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, MLC 2010, 3333 Burnet Avenue, Cincinnati, OH 45229 ()
| | | | | | | | | | - Batia Weiss
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | - Thomas D Walters
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Joel Rosh
- Goryeb Children’s Hospital/Atlantic Health, Morristown, New Jersey
| | - Melvin B Heyman
- University of California, San Francisco, San Francisco, California
| | - Anne M Griffiths
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | | | - David R Mack
- Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | | | - Ashish Patel
- UT Southwestern Medical Center at Dallas, Dallas, Texas
| | | | | | - Ajay S Gulati
- University of North Carolina, Chapel Hill, North Carolina
| | | | | | | | | | | | | | - Iris Barshack
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | | | - Stanley A Cohen
- Children’s Center for Digestive Healthcare, Atlanta, Georgia
| | - David J Keljo
- Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Yair Anikster
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | - Bruce Aronow
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Jeffrey S Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut
| | | | - Lee A Denson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
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29
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Lee JM, Govindarajah V, Goddard B, Hinge A, Muench DE, Filippi MD, Aronow B, Cancelas JA, Salomonis N, Grimes HL, Reynaud D. Obesity alters the long-term fitness of the hematopoietic stem cell compartment through modulation of Gfi1 expression. J Exp Med 2017; 215:627-644. [PMID: 29282250 PMCID: PMC5789409 DOI: 10.1084/jem.20170690] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [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: 04/13/2017] [Revised: 08/31/2017] [Accepted: 11/16/2017] [Indexed: 12/13/2022] Open
Abstract
Lee et al. show that established obesity alters the composition and long-term fitness of the hematopoietic stem cell (HSC) compartment, in part through a Gfi1-dependent HSC regulatory program that is activated by the chronic oxidative stress associated with this condition. Obesity is a chronic organismal stress that disrupts multiple systemic and tissue-specific functions. In this study, we describe the impact of obesity on the activity of the hematopoietic stem cell (HSC) compartment. We show that obesity alters the composition of the HSC compartment and its activity in response to hematopoietic stress. The impact of obesity on HSC function is progressively acquired but persists after weight loss or transplantation into a normal environment. Mechanistically, we establish that the oxidative stress induced by obesity dysregulates the expression of the transcription factor Gfi1 and that increased Gfi1 expression is required for the abnormal HSC function induced by obesity. These results demonstrate that obesity produces durable changes in HSC function and phenotype and that elevation of Gfi1 expression in response to the oxidative environment is a key driver of the altered HSC properties observed in obesity. Altogether, these data provide phenotypic and mechanistic insight into durable hematopoietic dysregulations resulting from obesity.
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Affiliation(s)
- Jung-Mi Lee
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Vinothini Govindarajah
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Bryan Goddard
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Ashwini Hinge
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - David E Muench
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Marie-Dominique Filippi
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Jose A Cancelas
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Hoxworth Blood Center, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Damien Reynaud
- Stem Cell Program, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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30
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Huang W, Rainbow DB, Wu Y, Adams D, Shivakumar P, Kottyan L, Karns R, Aronow B, Bezerra J, Gershwin ME, Peterson LB, Wicker LS, Ridgway WM. A Novel Pkhd1 Mutation Interacts with the Nonobese Diabetic Genetic Background To Cause Autoimmune Cholangitis. J Immunol 2017; 200:147-162. [PMID: 29158418 DOI: 10.4049/jimmunol.1701087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/19/2017] [Indexed: 12/13/2022]
Abstract
We previously reported that NOD.c3c4 mice develop spontaneous autoimmune biliary disease (ABD) with anti-mitochondrial Abs, histopathological lesions, and autoimmune T lymphocytes similar to human primary biliary cholangitis. In this article, we demonstrate that ABD in NOD.c3c4 and related NOD ABD strains is caused by a chromosome 1 region that includes a novel mutation in polycystic kidney and hepatic disease 1 (Pkhd1). We show that a long terminal repeat element inserted into intron 35 exposes an alternative polyadenylation site, resulting in a truncated Pkhd1 transcript. A novel NOD congenic mouse expressing aberrant Pkhd1, but lacking the c3 and c4 chromosomal regions (NOD.Abd3), reproduces the immunopathological features of NOD ABD. RNA sequencing of NOD.Abd3 common bile duct early in disease demonstrates upregulation of genes involved in cholangiocyte injury/morphology and downregulation of immunoregulatory genes. Consistent with this, bone marrow chimera studies show that aberrant Pkhd1 must be expressed in the target tissue (cholangiocytes) and the immune system (bone marrow). Mutations of Pkhd1 produce biliary abnormalities in mice but have not been previously associated with autoimmunity. In this study, we eliminate clinical biliary disease by backcrossing this Pkhd1 mutation onto the C57BL/6 genetic background; thus, the NOD genetic background (which promotes autoimmunity) is essential for disease. We propose that loss of functional Pkhd1 on the NOD background produces early bile duct abnormalities, initiating a break in tolerance that leads to autoimmune cholangitis in NOD.Abd3 congenic mice. This model is important for understanding loss of tolerance to cholangiocytes and is relevant to the pathogenesis of several human cholangiopathies.
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Affiliation(s)
- Wenting Huang
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Daniel B Rainbow
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Wellcome Trust Center for Human Genetics, Nuffield Department of Medicine, National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Yuehong Wu
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - David Adams
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Pranavkumar Shivakumar
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Leah Kottyan
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Rebekah Karns
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Jorge Bezerra
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, Davis, CA 95616; and
| | | | - Linda S Wicker
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Wellcome Trust Center for Human Genetics, Nuffield Department of Medicine, National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - William M Ridgway
- Division of Immunology, Allergy and Rheumatology, University of Cincinnati College of Medicine, Cincinnati, OH 45267;
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31
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Hartung F, Wang Y, Aronow B, Weber GF. A core program of gene expression characterizes cancer metastases. Oncotarget 2017; 8:102161-102175. [PMID: 29254233 PMCID: PMC5731943 DOI: 10.18632/oncotarget.22240] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/31/2017] [Indexed: 11/25/2022] Open
Abstract
While aberrant expression or splicing of metastasis genes conveys to cancers the ability to break through tissue barriers and disseminate, the genetic basis for organ preference in metastasis formation has remained incompletely understood. Utilizing the gene expression profiles from 653 GEO datasets, we investigate whether the signatures by diverse cancers in various metastatic sites display common features. We corroborate the meta-analysis in a murine model. Metastases are generally characterized by a core program of gene expression that induces the oxidative metabolism, activates vascularization/tissue remodeling, silences extracellular matrix interactions, and alters ion homeostasis. This program distinguishes metastases from their originating primary tumors as well as from their target host tissues. Site-selectivity is accomplished through specific components that adjust to the target micro-environment. The same functional groups of gene expression programs are activated in the metastases of B16-F10 cells to various target organs. It remains to be investigated whether these genetic signatures precede implantation and thus determine organ preference or are shaped by the target site and are thus a consequence of implantation. Conceivably, chemotherapy of disseminated cancer might be more efficacious if selected to match the genetic makeup of the metastases rather than the organ of origin by the primary tumor.
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Affiliation(s)
- Franz Hartung
- University of Cincinnati Academic Health Center, Cincinnati, OH, USA
| | - Yunguan Wang
- Computational Medicine Center, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Bruce Aronow
- Computational Medicine Center, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Georg F Weber
- University of Cincinnati Academic Health Center, Cincinnati, OH, USA
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32
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Jain AK, Xi Y, McCarthy R, Allton K, Akdemir KC, Patel LR, Aronow B, Lin C, Li W, Yang L, Barton MC. LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56. Mol Cell 2017; 64:967-981. [PMID: 27912097 DOI: 10.1016/j.molcel.2016.10.039] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [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: 07/04/2016] [Revised: 09/07/2016] [Accepted: 10/28/2016] [Indexed: 12/12/2022]
Abstract
Recent evidence suggests that lncRNAs play an integral regulatory role in numerous functions, including determination of cellular identity. We determined global expression (RNA-seq) and genome-wide profiles (ChIP-seq) of histone post-translational modifications and p53 binding in human embryonic stem cells (hESCs) undergoing differentiation to define a high-confidence set of 40 lncRNAs, which are p53 transcriptional targets. We focused on lncRNAs highly expressed in pluripotent hESCs and repressed by p53 during differentiation to identify lncPRESS1 as a p53-regulated transcript that maintains hESC pluripotency in concert with core pluripotency factors. RNA-seq of hESCs depleted of lncPRESS1 revealed that lncPRESS1 controls a gene network that promotes pluripotency. Further, we found that lncPRESS1 physically interacts with SIRT6 and prevents SIRT6 chromatin localization, which maintains high levels of histone H3K56 and H3K9 acetylation at promoters of pluripotency genes. In summary, we describe a p53-regulated, pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity.
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Affiliation(s)
- Abhinav K Jain
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Yuanxin Xi
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ryan McCarthy
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kendra Allton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kadir C Akdemir
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lalit R Patel
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Stem Cell and Development Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
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33
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Sarangdhar M, Aronow B, Jegga AG, Turpin B, Breese EH, Perentesis JP. Large scale adverse event data mining for targeted therapies development. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.2538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2538 Background: Targeted anti-cancer small molecule drugs & immune therapies have had a dramatic impact in improving outcomes & the approach to clinical trials. Increasingly, regulatory approvals are expedited with small studies designed to identify strong efficacy signals. However, this may limit the extent of safety profiling. The use of large scale/big data meta-analyses can identify novel safety & efficacy signals in "real-world" medical settings. Methods: We used AERSMine, an open-source data mining platform to identify drug toxicity signatures in the FDA’s Adverse Event Reporting System of 8.6 million patients. We identified patients (n = 732,198) who received either traditional and targeted cancer therapy & identified therapy-specific toxicity patterns. Patients were classified based on exposures: anthracyclines (n = 83,179), platinum (117,993), antimetabolites (93,062), alkylators (81,507), antimicrotubule agents (97,726), HER2 inhibitors (40,040), VEGFis (79,144), VEGF-TKis (90,734), multi TKis (34,457), anaplastic lymphoma Kis (7,635), PI3K-AKT-mTOR inhibitors (33,864), Bruton TKis (9,247), MEKis (4,018), immunomodulatory agents (174,810), proteasome inhibitors (44,681), immune checkpoint inhibitors (20,287). Pharmacovigilance metrics [Relative Risks & safety signals] were used to establish statistical correlation & toxicity signatures were differentiated using the Kolmogorov–Smirnov test. Results: To validate the use of the AERSMine to detect AEs, we focused on cardiotoxicity. It identified classic drug associated AEs (e.g. ventricular dysfunction with anthracyclines, HER2is & VEGFis; VEGFi hypertension & vascular toxicity; multi TKIs vascular events). AERSMine also identified recently reported uncommon toxicities of myositis/myocarditis with immune checkpoint inhibitors. It indicated a higher frequency of myositis/myocarditis with combination immune checkpoint therapy, paralleling industry corporate safety databases. These toxicities were reported at higher frequencies in patients > 65 yrs. Conclusions: AERSMine “big data” analyses provide a sensitive tool to detect potential new patterns of AEs simultaneously across multiple clinical trials & in the real-world setting.
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Affiliation(s)
| | - Bruce Aronow
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Anil Goud Jegga
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Brian Turpin
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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34
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Du Y, Kitzmiller JA, Sridharan A, Perl AK, Bridges JP, Misra RS, Pryhuber GS, Mariani TJ, Bhattacharya S, Guo M, Potter SS, Dexheimer P, Aronow B, Jobe AH, Whitsett JA, Xu Y. Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development. Thorax 2017; 72:481-484. [PMID: 28070014 PMCID: PMC5520249 DOI: 10.1136/thoraxjnl-2016-209598] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/30/2016] [Accepted: 12/08/2016] [Indexed: 11/03/2022]
Abstract
'LungGENS', our previously developed web tool for mapping single-cell gene expression in the developing lung, has been well received by the pulmonary research community. With continued support from the 'LungMAP' consortium, we extended the scope of the LungGENS database to accommodate transcriptomics data from pulmonary tissues and cells from human and mouse at different stages of lung development. Lung Gene Expression Analysis (LGEA) web portal is an extended version of LungGENS useful for the analysis, display and interpretation of gene expression patterns obtained from single cells, sorted cell populations and whole lung tissues. The LGEA web portal is freely available at http://research.cchmc.org/pbge/lunggens/mainportal.html.
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Affiliation(s)
- Yina Du
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Joseph A Kitzmiller
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Anusha Sridharan
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Anne K Perl
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - James P Bridges
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ravi S Misra
- Department of Pediatrics, University of Rochester, Rochester, New York, USA
| | - Gloria S Pryhuber
- Department of Pediatrics, University of Rochester, Rochester, New York, USA
| | - Thomas J Mariani
- Department of Pediatrics, University of Rochester, Rochester, New York, USA
| | | | - Minzhe Guo
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - S Steven Potter
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Phillip Dexheimer
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Alan H Jobe
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jeffrey A Whitsett
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Yan Xu
- The Perinatal Institute and Section of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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35
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Karns R, Sarangdhar M, Aronow B, Basu M, Schwartz CL, Kelly KM, Friedman DL, Perentesis JP. Pharmacogenomic prediction of treatment-induced severe lung toxicity in Hodgkin lymphoma (HL). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.7522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Rebekah Karns
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | | | - Mitali Basu
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | | | - Debra L. Friedman
- Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN
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36
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Fulford L, Milewski D, Ustiyan V, Ravishankar N, Cai Y, Le T, Masineni S, Kasper S, Aronow B, Kalinichenko VV, Kalin TV. The transcription factor FOXF1 promotes prostate cancer by stimulating the mitogen-activated protein kinase ERK5. Sci Signal 2016; 9:ra48. [DOI: 10.1126/scisignal.aad5582] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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37
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Jain AK, Akdemir KC, Xi Y, McCarthy RL, Allton K, Aronow B, Lin C, Li W, Yang L, Barton MC. Abstract A06: Characterization of a novel p53-regulated embryonic stem cell-specific lncRNA that safeguards pluripotency. Cancer Res 2016. [DOI: 10.1158/1538-7445.nonrna15-a06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent work shows that long non-coding RNAs (lncRNAs), transcribed from 80% of our genomes, play important roles in gene regulation and are associated with disease pathogenesis. However, there is a broad gap in our knowledge regarding any contributions of lncRNAs in mediating p53 response or regulating stem cell state. Here, we report our discovery of lncRNAs that fine-tune p53's transcriptional outcomes in differentiating human embryonic stem cells (hESCs). By integrating RNA-Seq with p53 ChIP-Seq analyses along with active or repressive histone marks of hESCs undergoing differentiation, we defined a high-confidence set of 40 lncRNAs that are p53 transcriptional targets. We found that p53 directly regulates nuclear lncRNAs, which are either activated (HOTAIRM1) or repressed (lncPRESS-1) during hESC differentiation. Single-cell gene expression analysis during lineage-specific hESC differentiation revealed that lncPRESS-1 is a novel pluripotency-specific, p53-regulated transcript with expression tightly correlated with OCT4, NANOG and PRDM14. Loss-of-function of lncPRESS-1 results in diminished pluripotency and spontaneous differentiation of hESCs. In addition, mass cytometry-based multi-parametric analysis at a single cell level revealed that depletion of lncPRESS-1 results in overall loss of hESC pluripotency with marked induction of an ectoderm specific gene-signature. Further, we show that lncPRESS-1 physically interacts with SIRT6 and restrains its chromatin localization to maintain high levels of histone H3 Lys-56 (H3K56) and Lys-9 (H3K9) acetylation at promoters of pluripotency genes to sustain a chromatin architecture that favors pluripotency. In summary, we describe a novel pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity. Since lncPRESS-1 is repressed by p53, we believe that cancers that harbor mutant TP53 will have robust expression of this lncRNA. Further investigations are underway to determine the disease relevance of lncPRESS-1 and correlation with p53-mutations.
Citation Format: Abhinav K. Jain, Kadir C. Akdemir, Yuanxin Xi, Ryan L. McCarthy, Kendra Allton, Bruce Aronow, Chunru Lin, Wei Li, Liuqing Yang, Michelle C. Barton. Characterization of a novel p53-regulated embryonic stem cell-specific lncRNA that safeguards pluripotency. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A06.
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Affiliation(s)
- Abhinav K. Jain
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Kadir C. Akdemir
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Yuanxin Xi
- 2Baylor College of Medicine, Houston, TX,
| | - Ryan L. McCarthy
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Kendra Allton
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Bruce Aronow
- 3Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Chunru Lin
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
| | - Wei Li
- 2Baylor College of Medicine, Houston, TX,
| | - Liuqing Yang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX,
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Hoffman LM, DeWire M, Ryall S, Buczkowicz P, Leach J, Miles L, Ramani AK, Brudno M, Kumar SS, Drissi R, Dexheimer P, Salloum R, Chow L, Hummel T, Stevenson C, Lu QR, Jones B, Witte D, Aronow B, Hawkins CE, Fouladi M. Erratum: Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics. Acta Neuropathol Commun 2016; 4:13. [PMID: 26860432 PMCID: PMC4748490 DOI: 10.1186/s40478-016-0283-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 01/25/2016] [Indexed: 11/26/2022] Open
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Hoffman LM, DeWire M, Ryall S, Buczkowicz P, Leach J, Miles L, Ramani A, Brudno M, Kumar SS, Drissi R, Dexheimer P, Salloum R, Chow L, Hummel T, Stevenson C, Lu QR, Jones B, Witte D, Aronow B, Hawkins CE, Fouladi M. Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics. Acta Neuropathol Commun 2016; 4:1. [PMID: 26727948 PMCID: PMC4700584 DOI: 10.1186/s40478-015-0269-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/20/2015] [Indexed: 11/20/2022] Open
Abstract
Introduction Diffuse intrinsic pontine glioma (DIPG) and midline high-grade glioma (mHGG) are lethal childhood brain tumors. Spatial genomic heterogeneity has been well-described in adult HGG but has not been comprehensively characterized in pediatric HGG. We performed whole exome sequencing on 38-matched primary, contiguous, and metastatic tumor sites from eight children with DIPG (n = 7) or mHGG (n = 1) collected using a unique MRI-guided autopsy protocol. Validation was performed using Sanger sequencing, Droplet Digital polymerase-chain reaction, immunohistochemistry, and fluorescent in-situ hybridization. Results Median age at diagnosis was 6.1 years (range: 2.9–23.3 years). Median overall survival was 13.2 months (range: 11.2–32.2 months). Contiguous tumor infiltration and distant metastases were observed in seven and six patients, respectively, including leptomeningeal dissemination in three DIPGs. Histopathological heterogeneity was evident in seven patients, including intra-pontine heterogeneity in two DIPGs, ranging from World Health Organization grade II to IV astrocytoma. We found conservation of heterozygous K27M mutations in H3F3A (n = 4) or HIST1H3B (n = 3) across all primary, contiguous, and metastatic tumor sites in all DIPGs. ACVR1 (n = 2), PIK3CA (n = 2), FGFR1 (n = 2), and MET (n = 1) were also intra-tumorally conserved. ACVR1 was co-mutated with HIST1H3B (n = 2). In contrast, PDGFRA amplification and mutation were spatially heterogeneous, as were mutations in BCOR (n = 1), ATRX (n = 2), and MYC (n = 1). TP53 aberrations (n = 3 patients) varied by type and location between primary and metastatic tumors sites but were intra-tumorally conserved. Conclusion Spatial conservation of prognostically-relevant and therapeutically-targetable somatic mutations in DIPG and mHGG contrasts the significant heterogeneity of driver mutations seen in adult HGG and supports uniform implementation of diagnostic biopsy in DIPG and mHGG to classify molecular risk groups and guide therapeutic strategy. Electronic supplementary material The online version of this article (doi:10.1186/s40478-015-0269-0) contains supplementary material, which is available to authorized users.
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Sumegi J, Nestheide S, Aronow B, Fletcher D, Keddache M, Villanueva J, Zhang K, Filipovich AH. MicroRNA activation signature in patients with hemophagocytic lymphohistiocytosis and reversibility with disease-specific therapy. J Allergy Clin Immunol 2016; 137:309-312. [DOI: 10.1016/j.jaci.2015.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 05/14/2015] [Accepted: 06/04/2015] [Indexed: 12/11/2022]
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Cooke JP, Meng S, Wong WT, Sayed N, Ospino F, Lee J, Jha A, Dexheimer P, Aronow B. Response to Letter Regarding Article "Transdifferentiation of Human Fibroblasts to Endothelial Cells: Role of Innate Immunity". Circulation 2015; 132:e197. [PMID: 26459087 DOI: 10.1161/circulationaha.115.016792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- John P Cooke
- Center for Cardiovascular Regeneration Houston Methodist Research Institute Houston, TX
| | - Shu Meng
- Center for Cardiovascular Regeneration Houston Methodist Research Institute Houston, TX
| | - Wing Tak Wong
- Center for Cardiovascular Regeneration Houston Methodist Research Institute Houston, TX
| | - Nazish Sayed
- Center for Cardiovascular Regeneration Houston Methodist Research Institute Houston, TX
| | - Frank Ospino
- Center for Cardiovascular Regeneration Houston Methodist Research Institute Houston, TX
| | - Jieun Lee
- Division of Cardiovascular Medicine Stanford University School of Medicine Stanford, CA
| | - Arshi Jha
- Division of Cardiovascular Medicine Stanford University School of Medicine Stanford, CA
| | - Philip Dexheimer
- Division of Biomedical Informatics Cincinnati Children's Hospital Medical Center Cincinnati, OH
| | - Bruce Aronow
- Division of Biomedical Informatics Cincinnati Children's Hospital Medical Center Cincinnati, OH
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Berry RL, Ozdemir DD, Aronow B, Lindström NO, Dudnakova T, Thornburn A, Perry P, Baldock R, Armit C, Joshi A, Jeanpierre C, Shan J, Vainio S, Baily J, Brownstein D, Davies J, Hastie ND, Hohenstein P. Deducing the stage of origin of Wilms' tumours from a developmental series of Wt1-mutant mice. Development 2015. [DOI: 10.1242/dev.129239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Cutler DJ, Zwick ME, Okou DT, Prahalad S, Walters T, Guthery SL, Dubinsky M, Baldassano R, Crandall WV, Rosh J, Markowitz J, Stephens M, Kellermayer R, Pfefferkorn M, Heyman MB, LeLeiko N, Mack D, Moulton D, Kappelman MD, Kumar A, Prince J, Bose P, Mondal K, Ramachandran D, Bohnsack JF, Griffiths AM, Haberman Y, Essers J, Thompson SD, Aronow B, Keljo DJ, Hyams JS, Denson LA, Kugathasan S. Dissecting Allele Architecture of Early Onset IBD Using High-Density Genotyping. PLoS One 2015; 10:e0128074. [PMID: 26098103 PMCID: PMC4476779 DOI: 10.1371/journal.pone.0128074] [Citation(s) in RCA: 33] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 04/23/2015] [Indexed: 01/15/2023] Open
Abstract
Background The inflammatory bowel diseases (IBD) are common, complex disorders in which genetic and environmental factors are believed to interact leading to chronic inflammatory responses against the gut microbiota. Earlier genetic studies performed in mostly adult population of European descent identified 163 loci affecting IBD risk, but most have relatively modest effect sizes, and altogether explain only ~20% of the genetic susceptibility. Pediatric onset represents about 25% of overall incident cases in IBD, characterized by distinct disease physiology, course and risks. The goal of this study is to compare the allelic architecture of early onset IBD with adult onset in population of European descent. Methods We performed a fine mapping association study of early onset IBD using high-density Immunochip genotyping on 1008 pediatric-onset IBD cases (801 Crohn’s disease; 121 ulcerative colitis and 86 IBD undetermined) and 1633 healthy controls. Of the 158 SNP genotypes obtained (out of the 163 identified in adult onset), this study replicated 4% (5 SNPs out of 136) of the SNPs identified in the Crohn’s disease (CD) cases and 0.8% (1 SNP out of 128) in the ulcerative colitis (UC) cases. Replicated SNPs implicated the well known NOD2 and IL23R. The point estimate for the odds ratio (ORs) for NOD2 was above and outside the confidence intervals reported in adult onset. A polygenic liability score weakly predicted the age of onset for a larger collection of CD cases (p< 0.03, R2= 0.007), but not for the smaller number of UC cases. Conclusions The allelic architecture of common susceptibility variants for early onset IBD is similar to that of adult onset. This immunochip genotyping study failed to identify additional common variants that may explain the distinct phenotype that characterize early onset IBD. A comprehensive dissection of genetic loci is necessary to further characterize the genetic architecture of early onset IBD.
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Affiliation(s)
- David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Michael E. Zwick
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - David T. Okou
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Sampath Prahalad
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | | | - Stephen L. Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | - Marla Dubinsky
- Icahn School of Medicine, Mount Sinai Hospital, New York, New York, United States of America
| | - Robert Baldassano
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | | | - Joel Rosh
- Goryeb Children’s Hospital, Morristown, New Jersey, United States of America
| | - James Markowitz
- Cohen Children’s Medical Center, New Hyde Park, New York, United States of America
| | - Michael Stephens
- Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Richard Kellermayer
- Baylor College School of Medicine, Texas Children’s Hospital, Houston, Texas, United States of America
| | - Marian Pfefferkorn
- Riley Children’s Hospital, Indiannapolis, Indianapolis, United States of America
| | - Melvin B. Heyman
- University of California, San Francisco, California, United States of America
| | - Neal LeLeiko
- Hasbro Children’s Hospital, Providence, Rhode Island, United States of America
| | - David Mack
- Children’s Hospital of Eastern Ontario, Ottawa, Canada
| | - Dedrick Moulton
- Vanderbilt Children’s Hospital, Nashville, Tennessee, United States of America
| | - Michael D. Kappelman
- University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Archana Kumar
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Jarod Prince
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Promita Bose
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Kajari Mondal
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - Dhanya Ramachandran
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
| | - John F. Bohnsack
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
| | | | - Yael Haberman
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Jonah Essers
- Children’s Hospital of Boston, Boston, Massachusetts, United States of America
| | - Susan D. Thompson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Bruce Aronow
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - David J. Keljo
- Children Hospital of Pittsburgh, Pittsburg, Pennsylvania, United States of America
| | - Jeffrey S. Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut, United States of America
| | - Lee A. Denson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | | | - Subra Kugathasan
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
- Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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Turpin B, Karns R, Sarangdhar M, Weiss BD, Geller JI, Absalon M, O'Brien MM, Nagarajan R, Phillips CL, Chow LM, DeWire MD, Adams D, Burns KC, Hummel TR, Fouladi M, Hammill AM, Mangino J, Pressey JG, Aronow B, Perentesis JP. Next generation sequencing (NGS) to identify targetable recurring mutations and exceptional responders in relapsed and high-risk childhood and adolescent/young adult (AYA) malignancies. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.11011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Brian Turpin
- Cincinnati Children's Hosp Medcl Ctr, Cincinnati, OH
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | | | | | - Michael Absalon
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | | | | | | | | | | | | | | | - Maryam Fouladi
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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Wright J, Karns R, Mizuno T, Basu M, Weiss BD, Adams D, Vinks A, Aronow B, Perentesis JP. Pharmacogenetic variants associated with differential sirolimus clearance in pediatric patients. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.2562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Rebekah Karns
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Tomoyuki Mizuno
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Mitali Basu
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | | | | | - A.a. Vinks
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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Fowler T, Garruss AS, Ghosh A, De S, Becker KG, Wood WH, Weirauch MT, Smale ST, Aronow B, Sen R, Roy AL. Divergence of transcriptional landscape occurs early in B cell activation. Epigenetics Chromatin 2015; 8:20. [PMID: 25987903 PMCID: PMC4434543 DOI: 10.1186/s13072-015-0012-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 03/05/2015] [Accepted: 05/01/2015] [Indexed: 12/15/2022] Open
Abstract
Background Signaling via B cell receptor (BCR) and Toll-like receptors (TLRs) results in activation of B cells with distinct physiological outcomes, but transcriptional regulatory mechanisms that drive activation and distinguish these pathways remain unknown. Results Two hours after ligand exposure RNA-seq, ChIP-seq and computational methods reveal that BCR- or TLR-mediated activation of primary resting B cells proceeds via a large set of shared and a smaller subset of distinct signal-selective transcriptional responses. BCR stimulation resulted in increased global recruitment of RNA Pol II to promoters that appear to transit slowly to downstream regions. Conversely, lipopolysaccharide (LPS) stimulation involved an enhanced RNA Pol II transition from initiating to elongating mode accompanied by greater H3K4me3 activation markings compared to BCR stimulation. These rapidly diverging transcriptomic landscapes also show distinct repressing (H3K27me3) histone signatures, mutually exclusive transcription factor binding in promoters, and unique miRNA profiles. Conclusions Upon examination of genome-wide transcription and regulatory elements, we conclude that the B cell commitment to different activation states occurs much earlier than previously thought and involves a multi-faceted receptor-specific transcriptional landscape. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0012-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Trent Fowler
- Department of Developmental, Chemical and Molecular Biology, Sackler School of Biomedical Science, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111 USA
| | - Alexander S Garruss
- Wyss Institute for Biologically Inspired Engineering, Harvard University and Department of Genetics, Harvard Medical School, Boston, MA 02115 USA
| | - Amalendu Ghosh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA
| | - Supriyo De
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA ; Gene Expression Unit, Laboratory of Genetics, National Institute on Aging, Baltimore, MD 21224 USA
| | - Kevin G Becker
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA ; Gene Expression Unit, Laboratory of Genetics, National Institute on Aging, Baltimore, MD 21224 USA
| | - William H Wood
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA ; Gene Expression Unit, Laboratory of Genetics, National Institute on Aging, Baltimore, MD 21224 USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095 USA
| | - Bruce Aronow
- Center for Autoimmune Genomics and Etiology (CAGE) and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224 USA
| | - Ananda L Roy
- Department of Developmental, Chemical and Molecular Biology, Sackler School of Biomedical Science, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111 USA
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Berry RL, Ozdemir DD, Aronow B, Lindström NO, Dudnakova T, Thornburn A, Perry P, Baldock R, Armit C, Joshi A, Jeanpierre C, Shan J, Vainio S, Baily J, Brownstein D, Davies J, Hastie ND, Hohenstein P. Deducing the stage of origin of Wilms' tumours from a developmental series of Wt1-mutant mice. Dis Model Mech 2015; 8:903-17. [PMID: 26035382 PMCID: PMC4527280 DOI: 10.1242/dmm.018523] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 05/07/2015] [Indexed: 12/28/2022] Open
Abstract
Wilms' tumours, paediatric kidney cancers, are the archetypal example of tumours caused through the disruption of normal development. The genetically best-defined subgroup of Wilms' tumours is the group caused by biallelic loss of the WT1 tumour suppressor gene. Here, we describe a developmental series of mouse models with conditional loss of Wt1 in different stages of nephron development before and after the mesenchymal-to-epithelial transition (MET). We demonstrate that Wt1 is essential for normal development at all kidney developmental stages under study. Comparison of genome-wide expression data from the mutant mouse models with human tumour material of mutant or wild-type WT1 datasets identified the stage of origin of human WT1-mutant tumours, and emphasizes fundamental differences between the two human tumour groups due to different developmental stages of origin. Summary: The comparison of different nephron-specific Wt1-knockout mouse models identifies the stage of origin of human WT1-mutant Wilms' tumours.
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Affiliation(s)
- Rachel L Berry
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Derya D Ozdemir
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Bruce Aronow
- Department of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nils O Lindström
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Tatiana Dudnakova
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Anna Thornburn
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Paul Perry
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Richard Baldock
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Chris Armit
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Anagha Joshi
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Cécile Jeanpierre
- INSERM, UMR 1163, Laboratory of Inherited Kidney Diseases, Paris 75015, France Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | - Jingdong Shan
- Biocenter Oulu, InfoTech Oulu, Faculty of Biochemistry and Molecular Medicine, Aapistie 5A, University of Oulu, PO Box 5000, Oulu 90014, Finland
| | - Seppo Vainio
- Biocenter Oulu, InfoTech Oulu, Faculty of Biochemistry and Molecular Medicine, Aapistie 5A, University of Oulu, PO Box 5000, Oulu 90014, Finland
| | - James Baily
- Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - David Brownstein
- Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Jamie Davies
- Centre for Integrative Physiology, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, EH8 9XD, UK
| | - Nicholas D Hastie
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Peter Hohenstein
- MRC Human Genetics Unit, MRC Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA. Corrigendum. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest 2015; 125:1363. [PMID: 25729854 DOI: 10.1172/jci79657] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Su S, Bangar H, Saldanha R, Pemberton A, Aronow B, Dean GE, Lamkin TJ, Hassett DJ. Construction and characterization of stable, constitutively expressed, chromosomal green and red fluorescent transcriptional fusions in the select agents, Bacillus anthracis, Yersinia pestis, Burkholderia mallei, and Burkholderia pseudomallei. Microbiologyopen 2014; 3:610-29. [PMID: 25044501 PMCID: PMC4234255 DOI: 10.1002/mbo3.192] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/23/2014] [Accepted: 05/29/2014] [Indexed: 11/09/2022] Open
Abstract
Here, we constructed stable, chromosomal, constitutively expressed, green and red fluorescent protein (GFP and RFP) as reporters in the select agents, Bacillus anthracis, Yersinia pestis, Burkholderia mallei, and Burkholderia pseudomallei. Using bioinformatic approaches and other experimental analyses, we identified P0253 and P1 as potent promoters that drive the optimal expression of fluorescent reporters in single copy in B. anthracis and Burkholderia spp. as well as their surrogate strains, respectively. In comparison, Y. pestis and its surrogate strain need two chromosomal copies of cysZK promoter (P2cysZK) for optimal fluorescence. The P0253-, P2cysZK-, and P1-driven GFP and RFP fusions were first cloned into the vectors pRP1028, pUC18R6KT-mini-Tn7T-Km, pmini-Tn7-gat, or their derivatives. The resultant constructs were delivered into the respective surrogates and subsequently into the select agent strains. The chromosomal GFP- and RFP-tagged strains exhibited bright fluorescence at an exposure time of less than 200 msec and displayed the same virulence traits as their wild-type parental strains. The utility of the tagged strains was proven by the macrophage infection assays and lactate dehydrogenase release analysis. Such strains will be extremely useful in high-throughput screens for novel compounds that could either kill these organisms, or interfere with critical virulence processes in these important bioweapon agents and during infection of alveolar macrophages.
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Affiliation(s)
- Shengchang Su
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of MedicineCincinnati, Ohio, 45267
| | - Hansraj Bangar
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of MedicineCincinnati, Ohio, 45267
| | | | | | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical CenterCincinnati, Ohio, 45229-3039
| | - Gary E Dean
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of MedicineCincinnati, Ohio, 45267
| | - Thomas J Lamkin
- Air Force Research Laboratory, 711th HPW/RHXBC, Molecular Signatures SectionWright-Patterson AFB, Ohio, 45433-7913
| | - Daniel J Hassett
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of MedicineCincinnati, Ohio, 45267
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Grimes HL, Olsson A, Aronow B, Chaudhri V, Dexheimer P, Singh H. Single cell transcriptome-based dissection of lineage fate decisions in myelopoiesis. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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