1
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Aloisio GM, Nagaraj D, Murray AM, Schultz EM, McBride T, Aideyan L, Nicholson EG, Henke D, Ferlic-Stark L, Rajan A, Kambal A, Johnson HL, Mosa E, Stossi F, Blutt SE, Piedra PA, Avadhanula V. Pediatric human nose organoids demonstrate greater susceptibility, epithelial responses, and cytotoxicity than adults during RSV infection. bioRxiv 2024:2024.02.01.578466. [PMID: 38352333 PMCID: PMC10862794 DOI: 10.1101/2024.02.01.578466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Respiratory syncytial virus (RSV) is a common cause of respiratory infections, causing significant morbidity and mortality, especially in young children. Why RSV infection in children is more severe as compared to healthy adults is not fully understood. In the present study, we infect both pediatric and adult human nose organoid-air liquid interface (HNO-ALIs) cell lines with two contemporary RSV isolates and demonstrate how they differ in virus replication, induction of the epithelial cytokine response, cell injury, and remodeling. Pediatric HNO-ALIs were more susceptible to early RSV replication, elicited a greater overall cytokine response, demonstrated enhanced mucous production, and manifested greater cellular damage compared to their adult counterparts. Adult HNO-ALIs displayed enhanced mucus production and robust cytokine response that was well controlled by superior regulatory cytokine response and possibly resulted in lower cellular damage than in pediatric lines. Taken together, our data suggest substantial differences in how pediatric and adult upper respiratory tract epithelium responds to RSV infection. These differences in epithelial cellular response can lead to poor mucociliary clearance and predispose infants to a worse respiratory outcome of RSV infection.
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Affiliation(s)
- Gina M Aloisio
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Divya Nagaraj
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ashley M Murray
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Emily M Schultz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Trevor McBride
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Letisha Aideyan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Erin G Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Laura Ferlic-Stark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Amal Kambal
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hannah L Johnson
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas, USA
| | - Elina Mosa
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas, USA
| | - Fabio Stossi
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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2
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Avadhanula V, Creighton C, Ferlic-Stark L, Sucgang R, Zhang Y, Nagaraj D, Nicholson E, Rajan A, Menon V, Doddapaneni H, Muzny D, Metcalf G, Cregeen SJ, Hoffman K, Gibbs R, Petrosino J, Piedra P. Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. Res Sq 2023:rs.3.rs-2978272. [PMID: 37333115 PMCID: PMC10274945 DOI: 10.21203/rs.3.rs-2978272/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
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3
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Carter H, Clark J, Carlin LG, Vaughan E, Rajan A, Olvera A, Yu X, Zeng XL, Kambal A, Holder M, Qin X, Gibbs RA, Petrosino JF, Muzny DM, Doddapaneni H, Menon VK, Hoffman KL, Meng Q, Ross MC, Javornik Cregeen SJ, Metcalf G, Jenq R, Blutt S, Estes MK, Maresso A, Okhuysen PC. Functional Genomics of Gastrointestinal Escherichia coli Isolated from Patients with Cancer and Diarrhea. bioRxiv 2023:2023.05.31.543115. [PMID: 37398483 PMCID: PMC10312547 DOI: 10.1101/2023.05.31.543115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We describe the epidemiology and clinical characteristics of 29 patients with cancer and diarrhea in whom Enteroaggregative Escherichia coli (EAEC) was initially identified by GI BioFire panel multiplex. E. coli strains were successfully isolated from fecal cultures in 14 of 29 patients. Six of the 14 strains were identified as EAEC and 8 belonged to other diverse E. coli groups of unknown pathogenesis. We investigated these strains by their adherence to human intestinal organoids, cytotoxic responses, antibiotic resistance profile, full sequencing of their genomes, and annotation of their functional virulome. Interestingly, we discovered novel and enhanced adherence and aggregative patterns for several diarrheagenic pathotypes that were not previously seen when co-cultured with immortalized cell lines. EAEC isolates displayed exceptional adherence and aggregation to human colonoids compared not only to diverse GI E. coli , but also compared to prototype strains of other diarrheagenic E. coli . Some of the diverse E. coli strains that could not be classified as a conventional pathotype also showed an enhanced aggregative and cytotoxic response. Notably, we found a high carriage rate of antibiotic resistance genes in both EAEC strains and diverse GI E. coli isolates and observed a positive correlation between adherence to colonoids and the number of metal acquisition genes carried in both EAEC and the diverse E. coli strains. This work indicates that E. coli from cancer patients constitute strains of remarkable pathotypic and genomic divergence, including strains of unknown disease etiology with unique virulomes. Future studies will allow for the opportunity to re-define E. coli pathotypes with greater diagnostic accuracy and into more clinically relevant groupings.
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4
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Avadhanula V, Creighton CJ, Ferlic-Stark L, Sucgang R, Zhang Y, Nagaraj D, Nicholson EG, Rajan A, Menon VK, Doddapaneni H, Muzny DM, Metcalf G, Cregeen SJJ, Hoffman KL, Gibbs RA, Petrosino J, Piedra PA. Longitudinal host transcriptional responses to SARS-CoV-2 infection in adults with extremely high viral load. bioRxiv 2023:2023.05.24.542181. [PMID: 37292999 PMCID: PMC10245966 DOI: 10.1101/2023.05.24.542181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Current understanding of viral dynamics of SARS-CoV-2 and host responses driving the pathogenic mechanisms in COVID-19 is rapidly evolving. Here, we conducted a longitudinal study to investigate gene expression patterns during acute SARS-CoV-2 illness. Cases included SARS-CoV-2 infected individuals with extremely high viral loads early in their illness, individuals having low SARS-CoV-2 viral loads early in their infection, and individuals testing negative for SARS-CoV-2. We could identify widespread transcriptional host responses to SARS-CoV-2 infection that were initially most strongly manifested in patients with extremely high initial viral loads, then attenuating within the patient over time as viral loads decreased. Genes correlated with SARS-CoV-2 viral load over time were similarly differentially expressed across independent datasets of SARS-CoV-2 infected lung and upper airway cells, from both in vitro systems and patient samples. We also generated expression data on the human nose organoid model during SARS-CoV-2 infection. The human nose organoid-generated host transcriptional response captured many aspects of responses observed in the above patient samples, while suggesting the existence of distinct host responses to SARS-CoV-2 depending on the cellular context, involving both epithelial and cellular immune responses. Our findings provide a catalog of SARS-CoV-2 host response genes changing over time.
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Affiliation(s)
- Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J. Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laura Ferlic-Stark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard Sucgang
- Center for Health Data Science and Analytics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Divya Nagaraj
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Erin G. Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vipin Kumar Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harshavardhan Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Marie Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Kristi Louise Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
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5
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Edwards B, Dowinton O, Hall AE, Murgatroyd PAE, Buchberger S, Antonelli T, Siemann GR, Rajan A, Morales EA, Zivanovic A, Bigi C, Belosludov RV, Polley CM, Carbone D, Mayoh DA, Balakrishnan G, Bahramy MS, King PDC. Giant valley-Zeeman coupling in the surface layer of an intercalated transition metal dichalcogenide. Nat Mater 2023; 22:459-465. [PMID: 36658327 DOI: 10.1038/s41563-022-01459-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Spin-valley locking is ubiquitous among transition metal dichalcogenides with local or global inversion asymmetry, in turn stabilizing properties such as Ising superconductivity, and opening routes towards 'valleytronics'. The underlying valley-spin splitting is set by spin-orbit coupling but can be tuned via the application of external magnetic fields or through proximity coupling. However, only modest changes have been realized to date. Here, we investigate the electronic structure of the V-intercalated transition metal dichalcogenide V1/3NbS2 using microscopic-area spatially resolved and angle-resolved photoemission spectroscopy. Our measurements and corresponding density functional theory calculations reveal that the bulk magnetic order induces a giant valley-selective Ising coupling exceeding 50 meV in the surface NbS2 layer, equivalent to application of a ~250 T magnetic field. This energy scale is of comparable magnitude to the intrinsic spin-orbit splittings, and indicates how coupling of local magnetic moments to itinerant states of a transition metal dichalcogenide monolayer provides a powerful route to controlling their valley-spin splittings.
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Affiliation(s)
- B Edwards
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
| | - O Dowinton
- Department of Physics and Astronomy, University of Manchester, Manchester, UK
| | - A E Hall
- Department of Physics, University of Warwick, Coventry, United Kingdom
| | - P A E Murgatroyd
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
| | - S Buchberger
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
- Max Planck Institute for Chemical Physics of Solids, Dresden, Germany
| | - T Antonelli
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
| | - G-R Siemann
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
| | - A Rajan
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
| | - E Abarca Morales
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
- Max Planck Institute for Chemical Physics of Solids, Dresden, Germany
| | - A Zivanovic
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
- Max Planck Institute for Chemical Physics of Solids, Dresden, Germany
| | - C Bigi
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK
| | - R V Belosludov
- Institute for Materials Research, Tohoku University, Sendai, Japan
| | - C M Polley
- MAX IV Laboratory, Lund University, Lund, Sweden
| | - D Carbone
- MAX IV Laboratory, Lund University, Lund, Sweden
| | - D A Mayoh
- Department of Physics, University of Warwick, Coventry, United Kingdom
| | - G Balakrishnan
- Department of Physics, University of Warwick, Coventry, United Kingdom
| | - M S Bahramy
- Department of Physics and Astronomy, University of Manchester, Manchester, UK.
| | - P D C King
- SUPA, School of Physics and Astronomy, University of St Andrews, St Andrews, UK.
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6
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Piedra FA, Henke D, Rajan A, Muzny DM, Doddapaneni H, Menon VK, Hoffman KL, Ross MC, Javornik Cregeen SJ, Metcalf G, Gibbs RA, Petrosino JF, Avadhanula V, Piedra PA. Modeling nonsegmented negative-strand RNA virus (NNSV) transcription with ejective polymerase collisions and biased diffusion. Front Mol Biosci 2023; 9:1095193. [PMID: 36699700 PMCID: PMC9868645 DOI: 10.3389/fmolb.2022.1095193] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Infections by non-segmented negative-strand RNA viruses (NNSV) are widely thought to entail gradient gene expression from the well-established existence of a single promoter at the 3' end of the viral genome and the assumption of constant transcriptional attenuation between genes. But multiple recent studies show viral mRNA levels in infections by respiratory syncytial virus (RSV), a major human pathogen and member of NNSV, that are inconsistent with a simple gradient. Here we integrate known and newly predicted phenomena into a biophysically reasonable model of NNSV transcription. Our model succeeds in capturing published observations of respiratory syncytial virus and vesicular stomatitis virus (VSV) mRNA levels. We therefore propose a novel understanding of NNSV transcription based on the possibility of ejective polymerase-polymerase collisions and, in the case of RSV, biased polymerase diffusion.
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Affiliation(s)
- Felipe-Andrés Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States,*Correspondence: Felipe-Andrés Piedra,
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Donna M. Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Vipin K. Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Matthew C. Ross
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Sara J. Javornik Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States,Department of Pediatrics, Baylor College of Medicine, Houston, TX, Unites States
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7
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Marques CA, Bahramy MS, Trainer C, Marković I, Watson MD, Mazzola F, Rajan A, Raub TD, King PDC, Wahl P. Tomographic mapping of the hidden dimension in quasi-particle interference. Nat Commun 2021; 12:6739. [PMID: 34795276 PMCID: PMC8602440 DOI: 10.1038/s41467-021-27082-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/04/2021] [Indexed: 11/12/2022] Open
Abstract
Quasiparticle interference (QPI) imaging is well established to study the low-energy electronic structure in strongly correlated electron materials with unrivalled energy resolution. Yet, being a surface-sensitive technique, the interpretation of QPI only works well for anisotropic materials, where the dispersion in the direction perpendicular to the surface can be neglected and the quasiparticle interference is dominated by a quasi-2D electronic structure. Here, we explore QPI imaging of galena, a material with an electronic structure that does not exhibit pronounced anisotropy. We find that the quasiparticle interference signal is dominated by scattering vectors which are parallel to the surface plane however originate from bias-dependent cuts of the 3D electronic structure. We develop a formalism for the theoretical description of the QPI signal and demonstrate how this quasiparticle tomography can be used to obtain information about the 3D electronic structure and orbital character of the bands.
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Affiliation(s)
- C A Marques
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK
| | - M S Bahramy
- Department of Physics and Astronomy, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - C Trainer
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK
| | - I Marković
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK
- Max Planck Institute for Chemical Physics of Solids, Nöthnitzer Strasse 40, 01187, Dresden, Germany
| | - M D Watson
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK
| | - F Mazzola
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK
| | - A Rajan
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK
| | - T D Raub
- School of Earth and Environmental Sciences, University of St Andrews, Irvine Building, St Andrews, KY16 9AL, UK
| | - P D C King
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK
| | - P Wahl
- SUPA, School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9SS, UK.
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8
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Criss ZK, Bhasin N, Di Rienzi SC, Rajan A, Deans-Fielder K, Swaminathan G, Kamyabi N, Zeng XL, Doddapaneni H, Menon VK, Chakravarti D, Estrella C, Yu X, Patil K, Petrosino JF, Fleet JC, Verzi MP, Christakos S, Helmrath MA, Arimura S, DePinho RA, Britton RA, Maresso AW, Grande-Allen KJ, Blutt SE, Crawford SE, Estes MK, Ramani S, Shroyer NF. Drivers of transcriptional variance in human intestinal epithelial organoids. Physiol Genomics 2021; 53:486-508. [PMID: 34612061 DOI: 10.1152/physiolgenomics.00061.2021] [Citation(s) in RCA: 13] [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] [Indexed: 01/01/2023] Open
Abstract
Human intestinal epithelial organoids (enteroids and colonoids) are tissue cultures used for understanding the physiology of the human intestinal epithelium. Here, we explored the effect on the transcriptome of common variations in culture methods, including extracellular matrix substrate, format, tissue segment, differentiation status, and patient heterogeneity. RNA-sequencing datasets from 276 experiments performed on 37 human enteroid and colonoid lines from 29 patients were aggregated from several groups in the Texas Medical Center. DESeq2 and gene set enrichment analysis (GSEA) were used to identify differentially expressed genes and enriched pathways. PERMANOVA, Pearson's correlation, and dendrogram analysis of the data originally indicated three tiers of influence of culture methods on transcriptomic variation: substrate (collagen vs. Matrigel) and format (3-D, transwell, and monolayer) had the largest effect; segment of origin (duodenum, jejunum, ileum, colon) and differentiation status had a moderate effect; and patient heterogeneity and specific experimental manipulations (e.g., pathogen infection) had the smallest effect. GSEA identified hundreds of pathways that varied between culture methods, such as IL1 cytokine signaling enriched in transwell versus monolayer cultures and E2F target genes enriched in collagen versus Matrigel cultures. The transcriptional influence of the format was furthermore validated in a synchronized experiment performed with various format-substrate combinations. Surprisingly, large differences in organoid transcriptome were driven by variations in culture methods such as format, whereas experimental manipulations such as infection had modest effects. These results show that common variations in culture conditions can have large effects on intestinal organoids and should be accounted for when designing experiments and comparing results between laboratories. Our data constitute the largest RNA-seq dataset interrogating human intestinal epithelial organoids.
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Affiliation(s)
- Zachary K Criss
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Nobel Bhasin
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Sara C Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Kali Deans-Fielder
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | | | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Deepavali Chakravarti
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Clarissa Estrella
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiaomin Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - James C Fleet
- Department of Nutrition Sciences, The University of Texas, Austin, Texas
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey
| | - Michael A Helmrath
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sumimasa Arimura
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | | | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Noah F Shroyer
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
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9
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Ye X, Angelo LS, Nicholson EG, Iwuchukwu OP, Cabral de Rezende W, Rajan A, Aideyan LO, McBride TJ, Bond N, Santarcangelo P, Rayford YJ, Ferlic-Stark L, Fragoso S, Momin Z, Liu H, Truong K, Lopez B, Conner ME, Rice AP, Kimata JT, Avadhanula V, Piedra PA. Serum IgG anti-SARS-CoV-2 Binding Antibody Level Is Strongly Associated With IgA and Functional Antibody Levels in Adults Infected With SARS-CoV-2. Front Immunol 2021; 12:693462. [PMID: 34691016 PMCID: PMC8531527 DOI: 10.3389/fimmu.2021.693462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/11/2021] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in December 2019 in Wuhan, China, and then rapidly spread causing an unprecedented pandemic. A robust serological assay is needed to evaluate vaccine candidates and better understand the epidemiology of coronavirus disease (COVID-19). Methods We used the full-length spike (S) protein of SARS-CoV-2 for the development of qualitative and quantitative IgG and IgA anti-S enzyme linked immunosorbent assays (ELISA). A total of 320 sera used for assay development were comprised of pandemic sera from SARS-CoV-2 infected adults (n=51) and pre-pandemic sera (n=269) including sera from endemic human coronavirus infected adults. Reverse cumulative curves and diagnostic test statistics were evaluated to define the optimal serum dilution and OD cutoff value for IgG anti-S and IgA anti-S ELISAs. The IgG and IgA anti-S, and three functional antibodies (ACE-2 receptor blocking antibody, lentipseudovirus-S neutralizing antibody, and SARS-CoV-2 neutralizing antibody) were measured using additional SARS-CoV-2 PCR positive sera (n=76) and surveillance sera (n=25). Lastly, the IgG and IgA anti-S levels were compared in different demographic groups. Results The optimal serum dilution for the qualitative IgG anti-S ELISA was at 1:1024 yielding a 99.6% specificity, 92.2% sensitivity, 92.9% positive predictive value (PPV), and 99.6% negative predictive value (NPV) at a SARS-CoV-2 seroprevalence of 5%. The optimal serum dilution for the qualitative IgA anti-S ELISA was at 1:128 yielding a 98.9% specificity, 76.5% sensitivity, 78.3% PPV, and 98.8% NPV at the same seroprevalence. Significant correlations were demonstrated between the IgG and IgA (r=0.833 for concentrations, r=0.840 for titers) as well as between IgG and three functional antibodies (r=0.811-0.924 for concentrations, r=0.795-0.917 for titers). The IgG and IgA anti-S levels were significantly higher in males than females (p<0.05), and in adults with moderate/severe symptoms than in adults with mild/moderate symptoms (p<0.001). Conclusion We developed a highly specific and sensitive IgG anti-S ELISA assay to SARS-CoV-2 using full length S protein. The IgG anti-S antibody level was strongly associated with IgA and functional antibody levels in adults with SARS-CoV-2 infection. Gender and disease severity, rather than age, play an important role in antibody levels.
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Affiliation(s)
- Xunyan Ye
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Laura S Angelo
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Erin G Nicholson
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Obinna P Iwuchukwu
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Wanderson Cabral de Rezende
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, United States
| | - Anubama Rajan
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Letisha O Aideyan
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Trevor J McBride
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Nanette Bond
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Patricia Santarcangelo
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Yolanda J Rayford
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Laura Ferlic-Stark
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Sonia Fragoso
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Zoha Momin
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Hongbing Liu
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Khanghy Truong
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Brianna Lopez
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Margaret E Conner
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Andrew P Rice
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Jason T Kimata
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Pedro A Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, United States.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, United States.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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10
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Swaminathan G, Kamyabi N, Carter HE, Rajan A, Karandikar U, Criss ZK, Shroyer NF, Robertson MJ, Coarfa C, Huang C, Shannon TE, Tadros M, Estes MK, Maresso AW, Grande-Allen KJ. Effect of substrate stiffness on human intestinal enteroids' infectivity by enteroaggregative Escherichia coli. Acta Biomater 2021; 132:245-259. [PMID: 34280559 DOI: 10.1016/j.actbio.2021.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/24/2021] [Accepted: 07/12/2021] [Indexed: 01/08/2023]
Abstract
Human intestinal enteroids (HIE) models have contributed significantly to our understanding of diarrheal diseases and other intestinal infections, but their routine culture conditions fail to mimic the mechanical environment of the native intestinal wall. Because the mechanical characteristics of the intestine significantly alter how pathogens interact with the intestinal epithelium, we used different concentrations of polyethylene glycol (PEG) to generate soft (~2 kPa), medium (~10 kPa), and stiff (~100 kPa) hydrogel biomaterial scaffolds. The height of HIEs cultured in monolayers atop these hydrogels was 18 µm whereas HIEs grown on rigid tissue culture surfaces (with stiffness in the GPa range) were 10 µm. Substrate stiffness also influenced the amount of enteroaggregative E. coli (EAEC strain 042) adhered to the HIEs. We quantified a striking difference in adherence pattern; on the medium and soft gels, the bacteria formed clusters of > 100 and even > 1000 on both duodenal and jejunal HIEs (such as would be found in biofilms), but did not on glass slides and stiff hydrogels. All hydrogel cultured HIEs showed significant enrichment for gene and signaling pathways related to epithelial differentiation, cell junctions and adhesions, extracellular matrix, mucins, and cell signaling compared to the HIEs cultured on rigid tissue culture surfaces. Collectively, these results indicate that the HIE monolayers cultured on the hydrogels are primed for a robust engagement with their mechanical environment, and that the soft hydrogels promote the formation of larger EAEC aggregates, likely through an indirect differential effect on mucus. STATEMENT OF SIGNIFICANCE: Enteroids are a form of in vitro experimental mini-guts created from intestinal stem cells. Enteroids are usually cultured in 3D within Matrigel atop rigid glass or plastic substrates, which fail to mimic the native intestinal mechanical environment. Because intestinal mechanics significantly alter how pathogens interact with the intestinal epithelium, we grew human intestinal enteroids in 2D atop polyethylene glycol (PEG) hydrogel scaffolds that were soft, medium, or stiff. Compared with enteroids grown in 2D atop glass or plastic, the enteroids grown on hydrogels were taller and more enriched in mechanobiology-related gene signaling pathways. Additionally, enteroids on the softest hydrogels supported adhesion of large aggregates of enteroaggregative E. coli. Thus, this platform offers a more biomimetic model for studying enteric diseases.
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11
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One 2021; 16:e0244468. [PMID: 34432798 PMCID: PMC8386831 DOI: 10.1371/journal.pone.0244468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/07/2020] [Accepted: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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12
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Rajan A, Weaver AM, Aloisio GM, Jelinski J, Johnson HL, Venable SF, McBride T, Aideyan L, Piedra FA, Ye X, Melicoff-Portillo E, Yerramilli MRK, Zeng XL, Mancini MA, Stossi F, Maresso AW, Kotkar SA, Estes MK, Blutt S, Avadhanula V, Piedra PA. The human nose organoid respiratory virus model: an ex-vivo human challenge model to study RSV and SARS-CoV-2 pathogenesis and evaluate therapeutics. bioRxiv 2021. [PMID: 34341793 DOI: 10.1101/2021.07.28.453844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
There is an unmet need for pre-clinical models to understand the pathogenesis of human respiratory viruses; and predict responsiveness to immunotherapies. Airway organoids can serve as an ex-vivo human airway model to study respiratory viral pathogenesis; however, they rely on invasive techniques to obtain patient samples. Here, we report a non-invasive technique to generate human nose organoids (HNOs) as an alternate to biopsy derived organoids. We made air liquid interface (ALI) cultures from HNOs and assessed infection with two major human respiratory viruses, respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Infected HNO-ALI cultures recapitulate aspects of RSV and SARS-CoV-2 infection, including viral shedding, ciliary damage, innate immune responses, and mucus hyper-secretion. Next, we evaluated the feasibility of the HNO-ALI respiratory virus model system to test the efficacy of palivizumab to prevent RSV infection. Palivizumab was administered in the basolateral compartment (circulation) while viral infection occurred in the apical ciliated cells (airways), simulating the events in infants. In our model, palivizumab effectively prevented RSV infection in a concentration dependent manner. Thus, the HNO-ALI model can serve as an alternate to lung organoids to study respiratory viruses and testing therapeutics.
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13
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Olvera A, Carter H, Rajan A, Carlin LG, Yu X, Zeng XL, Shelburne S, Bhatti M, Blutt SE, Shroyer NF, Jenq R, Estes MK, Maresso A, Okhuysen PC. Enteropathogenic Escherichia coli Infection in Cancer and Immunosuppressed Patients. Clin Infect Dis 2021; 72:e620-e629. [PMID: 32930708 DOI: 10.1093/cid/ciaa1394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The role of enteropathogenic Escherichia coli (EPEC) as a cause of diarrhea in cancer and immunocompromised patients is controversial. Quantitation of fecal bacterial loads has been proposed as a method to differentiate colonized from truly infected patients. METHODS We studied 77 adult cancer and immunosuppressed patients with diarrhea and EPEC identified in stools by FilmArray, 25 patients with pathogen-negative diarrhea, and 21 healthy adults without diarrhea. Stools were studied by quantitative polymerase chain reaction (qRT-PCR) for EPEC genes eaeA and lifA/efa-1 and strains characterized for virulence factors and adherence to human intestinal enteroids (HIEs). RESULTS Patients with EPEC were more likely to have community-acquired diarrhea (odds ratio, 3.82 [95% confidence interval, 1.5-10.0]; P = .008) compared with pathogen-negative cases. Although EPEC was identified in 3 of 21 (14%) healthy subjects by qPCR, the bacterial burden was low compared to patients with diarrhea (≤55 vs median, 6 × 104 bacteria/mg stool; P < .001). Among EPEC patients, the bacterial burden was higher in those who were immunosuppressed (median, 6.7 × 103 vs 55 bacteria/mg; P < .001) and those with fecal lifA/ifa-1 (median, 5 × 104 vs 120 bacteria/mg; P = .015). Response to antimicrobial therapy was seen in 44 of 48 (92%) patients with EPEC as the sole pathogen. Antimicrobial resistance was common and strains exhibited distinct patterns of adherence with variable cytotoxicity when studied in HIEs. Cancer care was delayed in 13% of patients. CONCLUSIONS Immunosuppressed cancer patients with EPEC-associated diarrhea carry high burden of EPEC with strains that are resistant to antibiotics, exhibit novel patterns of adherence when studied in HIEs, and interfere with cancer care.
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Affiliation(s)
- Adilene Olvera
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hannah Carter
- Department of Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Anubama Rajan
- Department of Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Lily G Carlin
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiaomin Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Samuel Shelburne
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Micah Bhatti
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah E Blutt
- Department of Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Noah F Shroyer
- Department of Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas, USA
| | - Robert Jenq
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anthony Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Pablo C Okhuysen
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Section of Infectious Diseases, Baylor College of Medicine, Houston, Texas, USA
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14
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Takahashi N, Tlemsani C, Pongor L, Rajapakse V, Tyagi M, Wen X, Fasaye G, Schmidt K, Kim C, Rajan A, Swift S, Sciuto L, Vilimas R, Webb S, Nichols S, Figg W, Pommier Y, Calzone K, Steinberg S, Wei J, Guha U, Turner C, Khan J, Thomas A. OA11.05 Whole Exome Sequencing Reveals the Potential Role of Hereditary Predisposition in Small Cell Lung Cancer, a Tobacco-Related Cancer. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Green SI, Gu Liu C, Yu X, Gibson S, Salmen W, Rajan A, Carter HE, Clark JR, Song X, Ramig RF, Trautner BW, Kaplan HB, Maresso AW. Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract. mBio 2021; 12:e03474-20. [PMID: 33563833 PMCID: PMC7885116 DOI: 10.1128/mbio.03474-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/21/2022] Open
Abstract
The human gastrointestinal mucosal surface consists of a eukaryotic epithelium, a prokaryotic microbiota, and a carbohydrate-rich interface that separates them. In the gastrointestinal tract, the interaction of bacteriophages (phages) and their prokaryotic hosts influences the health of the mammalian host, especially colonization with invasive pathobionts. Antibiotics may be used, but they also kill protective commensals. Here, we report a novel phage whose lytic cycle is enhanced in intestinal environments. The tail fiber gene, whose protein product binds human heparan sulfated proteoglycans and localizes the phage to the epithelial cell surface, positions it near its bacterial host, a type of locational targeting mechanism. This finding offers the prospect of developing mucosal targeting phage to selectively remove invasive pathobiont species from mucosal surfaces.IMPORTANCE Invasive pathobionts or microbes capable of causing disease can reside deep within the mucosal epithelium of our gastrointestinal tract. Targeted effective antibacterial therapies are needed to combat these disease-causing organisms, many of which may be multidrug resistant. Here, we isolated a lytic bacteriophage (phage) that can localize to the epithelial surface by binding heparan sulfated glycans, positioning it near its host, Escherichia coli This targeted therapy can be used to selectively remove invasive pathobionts from the gastrointestinal tract, preventing the development of disease.
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Affiliation(s)
- Sabrina I Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Carmen Gu Liu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Xue Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Shelley Gibson
- Department of Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Wilhem Salmen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hannah E Carter
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Justin R Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Xuezheng Song
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Robert F Ramig
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Barbara W Trautner
- Michael E. Debakey Veterans Affairs Medical Center, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Heidi B Kaplan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
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16
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Wilson RL, Hewes SA, Rajan A, Lin SC, Bomidi C, Iida T, Estes MK, Maresso AW, Grande-Allen KJ. A Millifluidic Perfusion Cassette for Studying the Pathogenesis of Enteric Infections Using Ex-Vivo Organoids. Ann Biomed Eng 2021; 49:1233-1244. [PMID: 33409849 DOI: 10.1007/s10439-020-02705-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
To generate physiologically-relevant experimental models, the study of enteric diarrheal diseases is turning increasingly to advanced in vitro models that combine ex vivo, stem cell-derived "organoid" cell lines with bioengineered culture environments that expose them to mechanical stimuli, such as fluid flow. However, such approaches require considerable technical expertise with both microfabrication and organoid culture, and are, therefore, inaccessible to many researchers. For this reason, we have developed a perfusion system that is simple to fabricate, operate, and maintain. Its dimensions approximate the volume and cell culture area of traditional 96-well plates and allow the incorporation of fastidious primary, stem cell-derived cell lines with only minimal adaptation of their established culture techniques. We show that infections with enteroaggregative E. coli and norovirus, common causes of infectious diarrhea, in the system display important differences from static models, and in some ways better recreate the pathophysiology of in vivo infections. Furthermore, commensal strains of bacteria can be added alongside the pathogens to simulate the effects of a host microbiome on the infectious process. For these reasons, we believe that this perfusion system is a powerful, yet easily accessible tool for studying host-pathogen interactions in the human intestine.
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Affiliation(s)
- Reid L Wilson
- Department of Bioengineering, Rice University, 6100 Main St, MS-142, Houston, TX, 77005, USA.,Medical Scientist Training Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sarah A Hewes
- Department of Bioengineering, Rice University, 6100 Main St, MS-142, Houston, TX, 77005, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shih-Ching Lin
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Carolyn Bomidi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Takanori Iida
- Department of Bioengineering, Rice University, 6100 Main St, MS-142, Houston, TX, 77005, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - K Jane Grande-Allen
- Department of Bioengineering, Rice University, 6100 Main St, MS-142, Houston, TX, 77005, USA.
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17
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Rafie K, Lenman A, Fuchs J, Rajan A, Arnberg N, Carlson LA. The structure of enteric human adenovirus 41-A leading cause of diarrhea in children. Sci Adv 2021; 7:7/2/eabe0974. [PMID: 33523995 PMCID: PMC7793593 DOI: 10.1126/sciadv.abe0974] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/17/2020] [Indexed: 05/05/2023]
Abstract
Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ notably in tissue tropism and pathogenicity from respiratory and ocular adenoviruses, but the structural basis for this divergence has been unknown. Here, we present the first structure of an enteric HAdV-HAdV-F41-determined by cryo-electron microscopy to a resolution of 3.8 Å. The structure reveals extensive alterations to the virion exterior as compared to nonenteric HAdVs, including a unique arrangement of capsid protein IX. The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of core protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Our findings provide the structural basis for adaptation of enteric HAdVs to a fundamentally different tissue tropism.
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Affiliation(s)
- K Rafie
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - A Lenman
- Department of Clinical Microbiology, Section of Virology, Umeå University, Umeå, Sweden
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - J Fuchs
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - A Rajan
- Department of Clinical Microbiology, Section of Virology, Umeå University, Umeå, Sweden
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - N Arnberg
- Department of Clinical Microbiology, Section of Virology, Umeå University, Umeå, Sweden.
| | - L-A Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
- Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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18
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals. bioRxiv 2020:2020.12.11.421057. [PMID: 33330863 PMCID: PMC7743067 DOI: 10.1101/2020.12.11.421057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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19
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Strauss J, Rajan A, Apolo A, Lee J, Thomas A, Chen A, Coyne GO, Madan R, Bilusic M, Karzai F, Sater HA, Redman J, Gatti-Mays M, Floudas C, Marte J, Cordes L, Schlom J, Gulley J. Impact of angiotensin II pathway inhibition on tumor response to anti PD(L)1 based therapy. Eur J Cancer 2020. [DOI: 10.1016/s0959-8049(20)31091-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Rajan A, Robertson MJ, Carter HE, Poole NM, Clark JR, Green SI, Criss ZK, Zhao B, Karandikar U, Xing Y, Margalef-Català M, Jain N, Wilson RL, Bai F, Hyser JM, Petrosino J, Shroyer NF, Blutt SE, Coarfa C, Song X, Prasad BVV, Amieva MR, Grande-Allen J, Estes MK, Okhuysen PC, Maresso AW. Enteroaggregative E. coli Adherence to Human Heparan Sulfate Proteoglycans Drives Segment and Host Specific Responses to Infection. PLoS Pathog 2020; 16:e1008851. [PMID: 32986782 PMCID: PMC7553275 DOI: 10.1371/journal.ppat.1008851] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/13/2020] [Accepted: 08/01/2020] [Indexed: 02/06/2023] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) is a significant cause of acute and chronic diarrhea, foodborne outbreaks, infections of the immunocompromised, and growth stunting in children in developing nations. There is no vaccine and resistance to antibiotics is rising. Unlike related E. coli pathotypes that are often associated with acute bouts of infection, EAEC is associated with persistent diarrhea and subclinical long-term colonization. Several secreted virulence factors have been associated with EAEC pathogenesis and linked to disease in humans, less certain are the molecular drivers of adherence to the intestinal mucosa. We previously established human intestinal enteroids (HIEs) as a model system to study host-EAEC interactions and aggregative adherence fimbriae A (AafA) as a major driver of EAEC adherence to HIEs. Here, we report a large-scale assessment of the host response to EAEC adherence from all four segments of the intestine across at least three donor lines for five E. coli pathotypes. The data demonstrate that the host response in the duodenum is driven largely by the infecting pathotype, whereas the response in the colon diverges in a patient-specific manner. Major pathways altered in gene expression in each of the four enteroid segments differed dramatically, with responses observed for inflammation, apoptosis and an overwhelming response to different mucin genes. In particular, EAEC both associated with large mucus droplets and specific mucins at the epithelial surface, binding that was ameliorated when mucins were removed, a process dependent on AafA. Pan-screening for glycans for binding to purified AafA identified the human ligand as heparan sulfate proteoglycans (HSPGs). Removal of HSPG abrogated EAEC association with HIEs. These results may mean that the human intestine responds remarkably different to distinct pathobionts that is dependent on the both the individual and intestinal segment in question, and uncover a major role for surface heparan sulfate proteoglycans as tropism-driving factor in adherence and/or colonization.
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Affiliation(s)
- Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Matthew J. Robertson
- Molecular and Cell Biology-Mol. Regulation, Baylor College of Medicine, Houston, TX, United States of America
| | - Hannah E. Carter
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Nina M. Poole
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Sabrina I. Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Zachary K. Criss
- Department of Medicine Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, United States of America
| | - Boyang Zhao
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Umesh Karandikar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Mar Margalef-Català
- Department of Pediatrics, Division of Infectious Diseases, Stanford University, Stanford, CA, United States of America
| | - Nikhil Jain
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Reid L. Wilson
- Department of Bioengineering, Rice University, Houston, TX, United States of America
| | - Fan Bai
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Joseph Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Noah F. Shroyer
- Department of Medicine Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, United States of America
| | - Sarah E. Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Cristian Coarfa
- Molecular and Cell Biology-Mol. Regulation, Baylor College of Medicine, Houston, TX, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States of America
| | - Xuezheng Song
- Department of Biochemistry, Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, United States of America
| | - BV Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Manuel R. Amieva
- Department of Pediatrics, Division of Infectious Diseases, Stanford University, Stanford, CA, United States of America
| | - Jane Grande-Allen
- Department of Bioengineering, Rice University, Houston, TX, United States of America
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
| | - Pablo C. Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX, United States of America
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States of America
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21
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. bioRxiv 2020:2020.07.27.223495. [PMID: 32766579 PMCID: PMC7402036 DOI: 10.1101/2020.07.27.223495] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA, 77030
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
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22
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Vimala A, Rajan A, Babu J, Nair SS, Jose R. SUN-065 HYPONATREMIA AMONG PATIENTS ADMITTED IN CRICAL CARE UNIT AT TERTIARY CARE HOSPITALS. Kidney Int Rep 2020. [DOI: 10.1016/j.ekir.2020.02.590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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23
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Kim C, Xi L, Cultraro C, Wei F, Cheng J, Shafiei A, Pham T, Roper N, Akoth E, Strom C, Tu M, Liao W, Chia D, Morris C, Rajan A, Bagheri M, Jones G, Wong D, Raffeld M, Guha U. P1.01-27 Serial Circulating Tumor DNA (ctDNA) Analysis of Blood and Saliva Predicts Osimertinib Response and Resistance in EGFR-Mutant NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Rajan A, Gray J, Devarakonda S, Gurtler J, Birhiray R, Paschold E, Dasgupta A, Heery C, Pico-Navarro C, Piechatzek M, Wagner E, Menius E, Donahue R, Schlom J, Gulley J. Phase I trial of CV301 in combination with anti-PD-1 therapy in non-squamous NSCLC. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz253.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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25
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Affiliation(s)
- A Rajan
- David Geffen School of Medicine at UCLA, 885 Tiverton Drive, Los Angeles, CA, 90095, USA
| | - J Grotts
- Department of Medicine Statistics Core, University of California at Los Angeles, Los Angeles, CA, USA
| | - C Goh
- Division of Dermatology, University of California Los Angeles David Geffen School of Medicine, 200 Medical Plaza Suite 465, Los Angeles, CA, USA
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26
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Kim C, Xi L, Cultraro C, Pham T, Roper N, Bagheri M, Rajan A, Beeler J, Jones G, Raffeld M, Guha U. P1.01-46 Circulating Tumor DNA Analysis for Predicting Response to Osimertinib and Disease Progression in EGFR-Mutant Non-Small-Cell Lung Cancer. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Rajan A, Shi H, Xue B. Class I and II Histone Deacetylase Inhibitors Differentially Regulate Thermogenic Gene Expression in Brown Adipocytes. Sci Rep 2018; 8:13072. [PMID: 30166563 PMCID: PMC6117331 DOI: 10.1038/s41598-018-31560-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/17/2018] [Indexed: 01/04/2023] Open
Abstract
Class I histone deacetylase inhibitors (HDACis) enhance whole body energy expenditure and attenuate high fat diet-induced insulin resistance. However, it is not clear whether this is exerted directly through activating brown fat thermogenesis. Here, we find that pan-HDACi TSA exerts paradoxical effects on brown fat gene expression, as it inhibits the expression of Ucp1, Pparγ and Prdm16 in brown adipocytes, while promoting the expression of other brown fat-specific genes such as Pgc1α, Pgc1β, Acox1 and Cidea. Further studies indicate that class I HDACi MS-275 significantly increases; whereas class II HDACi MC-1568 markedly reduces, the expression of Ucp1 and other brown fat-specific genes in treated brown adipocytes. ChIP assay reveals an enhanced H3 acetylation at the Pgc1α promoter in MS-275-treated brown adipocytes; whereas the effect of MC-1568 is associated with up-regulation of retinoblastoma protein (Rb) and an enhanced acetylation of H3K27 at the Rb promoter. Loss of function studies indicate that Pgc1α up-regulation largely mediates the stimulatory effect of class I HDACis on the thermogenic program, whereas up-regulation of Rb may be responsible for the inhibitory effect of class II HDACis. Thus, our data suggest that class I and II HDACis have differential effects on brown fat thermogenic gene expression.
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Affiliation(s)
- Anubama Rajan
- Center for Obesity Reversal, Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Hang Shi
- Center for Obesity Reversal, Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Bingzhong Xue
- Center for Obesity Reversal, Department of Biology, Georgia State University, Atlanta, GA, 30303, USA.
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28
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Abstract
Adherence, invasion, and translocation to and through the intestinal epithelium are important drivers of disease for many enteric bacteria. However, most work has been limited to transformed intestinal cell lines or murine models that often do not faithfully recapitulate key elements associated with human disease. The recent technological advances in organotypic tissue and cell culture are providing unparalleled access to systems with human physiology and complexity. Human intestinal enteroids (HIEs), derived from patient biopsy or surgical specimens of intestinal tissues, are organotypic cultures now being adapted to the study of enteric infections. HIEs are comprised of the dominant cell types of the human gastrointestinal epithelium, can be grown in two- or three-dimensional structures, form a crypt-villus axis with defined apical and basolateral compartments, and undergo physiologic responses to many different stimuli. Here, we describe a series of protocols that encompass the use of human enteroids for the measurement of the adherence, invasion, and translocation of E. coli to and through the intestinal epithelium. We also outline the steps needed to grow and prepare enteroids for this purpose and highlight some common problems to troubleshoot. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nina M Poole
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
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29
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Makary M, Rajan A, Miller R, Elliott E, Guy G. Abstract No. 463 Interventional radiology symposium increases medical student interest and identifies target recruitment candidates. J Vasc Interv Radiol 2018. [DOI: 10.1016/j.jvir.2018.01.508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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30
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Roper N, Zhang X, Maity T, Gao S, Venugopalan A, Biswas R, Cultraro C, Kim C, Padiernos E, Rajan A, Thomas A, Hassan R, Kleiner D, Hewitt S, Khan J, Guha U. P1.02-063 Tumor Heterogeneity Analyzes by Integrated Proteo-Genomics of Thoracic Tumors from Sequential Biopsies and Warm Autopsies. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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31
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Brahmer J, Johnson M, Awad M, Rajan A, Allred A, Knoblauch R, Zudaire E, Lorenzi M, Hassan R. P2.07-058 First-In-Human Study of JNJ-64041757, a Live Attenuated Listeria Monocytogenes Immunotherapy, for Non-Small Cell Lung Cancer. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.1314] [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: 11/24/2022]
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32
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Kesarwala A, Kim C, Jones J, Kaushal A, Roper N, Hoang C, Szabo E, Connolly M, Padiernos E, Cultraro C, Waris M, Gao S, Steinberg S, Khan J, Rajan A, Guha U. Radiation As a Local Ablative Therapy Option for Oligoprogressive EGFR-Mutant Non-Small Cell Lung Cancer after Treatment with Osimertinib. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Lindley RI, Anderson CS, Billot L, Forster A, Hackett ML, Harvey LA, Jan S, Li Q, Liu H, Langhorne P, Maulik PK, Murthy GVS, Walker MF, Pandian JD, Alim M, Felix C, Syrigapu A, Tugnawat DK, Verma SJ, Shamanna BR, Hankey G, Thrift A, Bernhardt J, Mehndiratta MM, Jeyaseelan L, Donnelly P, Byrne D, Steley S, Santhosh V, Chilappagari S, Mysore J, Roy J, Padma MV, John L, Aaron S, Borah NC, Vijaya P, Kaul S, Khurana D, Sylaja PN, Halprashanth DS, Madhusudhan BK, Nambiar V, Sureshbabu S, Khanna MC, Narang GS, Chakraborty D, Chakraborty SS, Biswas B, Kaura S, Koundal H, Singh P, Andrias A, Thambu DS, Ramya I, George J, Prabhakar AT, Kirubakaran P, Anbalagan P, Ghose M, Bordoloi K, Gohain P, Reddy NM, Reddy KV, Rao TNM, Alladi S, Jalapu VRR, Manchireddy K, Rajan A, Mehta S, Katoch C, Das B, Jangir A, Kaur T, Sreedharan S, Sivasambath S, Dinesh S, Shibi BS, Thangaraj A, Karunanithi A, Sulaiman SMS, Dehingia K, Das K, Nandini C, Thomas NJ, Dhanya TS, Thomas N, Krishna R, Aneesh V, Krishna R, Khullar S, Thouman S, Sebastian I. Family-led rehabilitation after stroke in India (ATTEND): a randomised controlled trial. Lancet 2017; 390:588-599. [PMID: 28666682 DOI: 10.1016/s0140-6736(17)31447-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/17/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Most people with stroke in India have no access to organised rehabilitation services. The effectiveness of training family members to provide stroke rehabilitation is uncertain. Our primary objective was to determine whether family-led stroke rehabilitation, initiated in hospital and continued at home, would be superior to usual care in a low-resource setting. METHODS The Family-led Rehabilitation after Stroke in India (ATTEND) trial was a prospectively randomised open trial with blinded endpoint done across 14 hospitals in India. Patients aged 18 years or older who had had a stroke within the past month, had residual disability and reasonable expectation of survival, and who had an informal family-nominated caregiver were randomly assigned to intervention or usual care by site coordinators using a secure web-based system with minimisation by site and stroke severity. The family members of participants in the intervention group received additional structured rehabilitation training-including information provision, joint goal setting, carer training, and task-specific training-that was started in hospital and continued at home for up to 2 months. The primary outcome was death or dependency at 6 months, defined by scores 3-6 on the modified Rankin scale (range, 0 [no symptoms] to 6 [death]) as assessed by masked observers. Analyses were by intention to treat. This trial is registered with Clinical Trials Registry-India (CTRI/2013/04/003557), Australian New Zealand Clinical Trials Registry (ACTRN12613000078752), and Universal Trial Number (U1111-1138-6707). FINDINGS Between Jan 13, 2014, and Feb 12, 2016, 1250 patients were randomly assigned to intervention (n=623) or control (n=627) groups. 33 patients were lost to follow-up (14 intervention, 19 control) and five patients withdrew (two intervention, three control). At 6 months, 285 (47%) of 607 patients in the intervention group and 287 (47%) of 605 controls were dead or dependent (odds ratio 0·98, 95% CI 0·78-1·23, p=0·87). 72 (12%) patients in the intervention group and 86 (14%) in the control group died (p=0·27), and we observed no difference in rehospitalisation (89 [14%]patients in the intervention group vs 82 [13%] in the control group; p=0·56). We also found no difference in total non-fatal events (112 events in 82 [13%] intervention patients vs 110 events in 79 [13%] control patients; p=0·80). INTERPRETATION Although task shifting is an attractive solution for health-care sustainability, our results do not support investment in new stroke rehabilitation services that shift tasks to family caregivers, unless new evidence emerges. A future avenue of research should be to investigate the effects of task shifting to health-care assistants or team-based community care. FUNDING The National Health and Medical Research Council of Australia.
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Qin M, Rajan A, Shin Y, Ogawa H, Kulkarni R. 815 Evaluating the role of AIM2 expression in melanoma. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Gutierrez M, Giaccone G, Liu S, Rajan A, Guha U, Halfdanarson T, Curtis K, Kunz P, Gabrail N, Hinson J, Orlemans E. Phase I, open-label, dose-escalation study of SNX-5422 plus everolimus in neuroendocrine tumors (NETs). Ann Oncol 2016. [DOI: 10.1093/annonc/mdw369.08] [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: 11/12/2022] Open
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Rajan A, Berns A, Ringborg U, Celis J, Ponder B, Caldas C, Livingston D, Bristow RG, Hecht TT, Tursz T, van Luenen H, Bono P, Helander T, Seamon K, Smyth JF, Louvard D, Eggermont A, van Harten WH. Excellent translational research in oncology: A journey towards novel and more effective anti-cancer therapies. Mol Oncol 2016; 10:645-51. [PMID: 26797050 PMCID: PMC5423159 DOI: 10.1016/j.molonc.2015.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 09/06/2015] [Revised: 12/06/2015] [Accepted: 12/07/2015] [Indexed: 12/02/2022] Open
Abstract
Comprehensive Cancer Centres (CCCs) serve as critical drivers for improving cancer survival. In Europe, we have developed an Excellence Designation System (EDS) consisting of criteria to assess "excellence" of CCCs in translational research (bench to bedside and back), with the expectation that many European CCCs will aspire to this status.
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Affiliation(s)
- A Rajan
- The Netherlands Cancer Institute, The Netherlands
| | - A Berns
- The Netherlands Cancer Institute, The Netherlands
| | | | - J Celis
- Danish Cancer Society, Denmark
| | | | | | | | | | - T T Hecht
- Translational Research Program, National Cancer Institute, USA
| | - T Tursz
- Institut Gustave Roussy, France
| | - H van Luenen
- The Netherlands Cancer Institute, The Netherlands
| | - P Bono
- Helsinki University Central Hospital Cancer Center, Finland
| | - T Helander
- Helsinki University Central Hospital Cancer Center, Finland
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Carter CA, Rajan A, Keen C, Szabo E, Khozin S, Thomas A, Brzezniak C, Guha U, Doyle LA, Steinberg SM, Xi L, Raffeld M, Tomita Y, Lee MJ, Lee S, Trepel JB, Reckamp KL, Koehler S, Gitlitz B, Salgia R, Gandara D, Vokes E, Giaccone G. Selumetinib with and without erlotinib in KRAS mutant and KRAS wild-type advanced nonsmall-cell lung cancer. Ann Oncol 2016; 27:693-9. [PMID: 26802155 DOI: 10.1093/annonc/mdw008] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/27/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND KRAS mutations in NSCLC are associated with a lack of response to epidermal growth factor receptor inhibitors. Selumetinib (AZD6244; ARRY-142886) is an oral selective MEK kinase inhibitor of the Ras/Raf/MEK/ERK pathway. PATIENTS AND METHODS Advanced nonsmall-cell lung cancer (NSCLC) patients failing one to two prior regimens underwent KRAS profiling. KRAS wild-type patients were randomized to erlotinib (150 mg daily) or a combination of selumetinib (150 mg daily) with erlotinib (100 mg daily). KRAS mutant patients were randomized to selumetinib (75 mg b.i.d.) or the combination. The primary end points were progression-free survival (PFS) for the KRAS wild-type cohort and objective response rate (ORR) for the KRAS mutant cohort. Biomarker studies of ERK phosphorylation and immune subsets were carried out. RESULTS From March 2010 to May 2013, 89 patients were screened; 41 KRAS mutant and 38 KRAS wild-type patients were enrolled. Median PFS in the KRAS wild-type arm was 2.4 months [95% confidence interval (CI) 1.3-3.7] for erlotinib alone and 2.1 months (95% CI 1.8-5.1) for the combination. The ORR in the KRAS mutant group was 0% (95% CI 0.0% to 33.6%) for selumetinib alone and 10% (95% CI 2.1% to 26.3%) for the combination. Combination therapy resulted in increased toxicities, requiring dose reductions (56%) and discontinuation (8%). Programmed cell death-1 expression on regulatory T cells (Tregs), Tim-3 on CD8+ T cells and Th17 levels were associated with PFS and overall survival in patients receiving selumetinib. CONCLUSIONS This study failed to show improvement in ORR or PFS with combination therapy of selumetinib and erlotinib over monotherapy in KRAS mutant and KRAS wild-type advanced NSCLC. The association of immune subsets and immune checkpoint receptor expression with selumetinib may warrant further studies.
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Affiliation(s)
- C A Carter
- John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda
| | - A Rajan
- Medical Oncology Branch, Center for Cancer Research
| | - C Keen
- Medical Oncology Branch, Center for Cancer Research
| | - E Szabo
- Lung & Upper Aerodigestive Cancer Research Group Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda
| | - S Khozin
- Medical Oncology Branch, Center for Cancer Research
| | - A Thomas
- Medical Oncology Branch, Center for Cancer Research
| | - C Brzezniak
- John P. Murtha Cancer Center, Walter Reed National Military Medical Center, Bethesda
| | - U Guha
- Medical Oncology Branch, Center for Cancer Research
| | - L A Doyle
- Cancer Therapy Evaluation Program, National Institutes of Health, Bethesda
| | - S M Steinberg
- Biostatistics and Data Management Section, Office of the Clinical Director, Center for Cancer Research
| | - L Xi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda
| | - M Raffeld
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda
| | - Y Tomita
- Medical Oncology Branch, Center for Cancer Research
| | - M J Lee
- Medical Oncology Branch, Center for Cancer Research
| | - S Lee
- Medical Oncology Branch, Center for Cancer Research
| | - J B Trepel
- Medical Oncology Branch, Center for Cancer Research
| | - K L Reckamp
- Department of Hematology and Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte
| | - S Koehler
- Department of Hematology and Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte
| | - B Gitlitz
- Department of Internal Medicine, University of Southern California, Los Angeles
| | - R Salgia
- Radiation and Cellular Oncology, University of Chicago, Medicine and Biological Sciences, Chicago
| | - D Gandara
- Division of Hematology and Oncology, University of California at Davis Cancer Center, Sacramento
| | - E Vokes
- Radiation and Cellular Oncology, University of Chicago, Medicine and Biological Sciences, Chicago
| | - G Giaccone
- Medical Oncology Branch, Center for Cancer Research Lombardi Comprehensive Cancer Center, Georgetown University, Washington, USA
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Håkansson B, Montgomery M, Cadiere GB, Rajan A, Bruley des Varannes S, Lerhun M, Coron E, Tack J, Bischops R, Thorell A, Arnelo U, Lundell L. Randomised clinical trial: transoral incisionless fundoplication vs. sham intervention to control chronic GERD. Aliment Pharmacol Ther 2015; 42:1261-70. [PMID: 26463242 DOI: 10.1111/apt.13427] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 08/08/2015] [Accepted: 09/21/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Until recently only two therapeutic options have been available to control symptoms and the esophagitis in chronic gastro-oesophageal reflux disease (GERD), i.e. lifelong proton pump inhibitor (PPI) therapy or anti-reflux surgery. Lately, transoral incisionless fundoplication (TIF) has been developed and found to offer a therapeutic alternative for these patients. AIM To perform a double-blind sham-controlled study in GERD patients who were chronic PPI users. METHODS We studied patients with objectively confirmed GERD and persistent moderate to severe GERD symptoms without PPI therapy. Of 121 patients screened, we finally randomised 44 patients with 22 patients in each group. Those allocated to TIF had the TIF2 procedure completed during general anaesthesia by the EsophyX device with SerosaFuse fasteners. The sham procedure consisted of upper GI endoscopy under general anaesthesia. Neither the patient nor the assessor was aware of the patients' group affiliation. The primary effectiveness endpoint was the proportion of patients in clinical remission after 6-month follow-up. Secondary outcomes were: PPI consumption, oesophageal acid exposure, reduction in Quality of Life in Reflux and Dyspepsia and Gastrointestinal Symptom Rating Scale scores and healing of reflux esophagitis. RESULTS The time (average days) in remission offered by the TIF2 procedure (197) was significantly longer compared to those submitted to the sham intervention (107), P < 0.001. After 6 months 13/22 (59%) of the chronic GERD patients remained in clinical remission after the active intervention. Likewise, the secondary outcome measures were all in favour of the TIF2 procedure. No safety issues were raised. CONCLUSION Transoral incisionless fundoplication (TIF2) is effective in chronic PPI-dependent GERD patients when followed up for 6 months. Clinicaltrials.gov: CT01110811.
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Affiliation(s)
- B Håkansson
- Department of Surgery, Ersta Hospital, Karolinska Institutet, Danderyds Hospital, Stockholm, Sweden
| | - M Montgomery
- Department of Surgery, Ersta Hospital, Karolinska Institutet, Danderyds Hospital, Stockholm, Sweden
| | - G B Cadiere
- Department of Surgery and Gastroenterology, Park Leopold Clinic, CHIREC, Brussels, Belgium
| | - A Rajan
- Department of Surgery and Gastroenterology, Park Leopold Clinic, CHIREC, Brussels, Belgium
| | | | - M Lerhun
- CHU Hotel Dieu Institut des Maladies de l' Appareil Digestif, Nantes, France
| | - E Coron
- CHU Hotel Dieu Institut des Maladies de l' Appareil Digestif, Nantes, France
| | - J Tack
- Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
| | - R Bischops
- Department of Gastroenterology, University Hospitals Leuven, Leuven, Belgium
| | - A Thorell
- Department of Surgery, Ersta Hospital, Karolinska Institutet, Danderyds Hospital, Stockholm, Sweden
| | - U Arnelo
- Department of Surgery, Centre for Digestive Diseases, Karolinska University Huddinge Hospital, Karolinska Institutet, Stockholm, Sweden
| | - L Lundell
- Department of Surgery, Centre for Digestive Diseases, Karolinska University Huddinge Hospital, Karolinska Institutet, Stockholm, Sweden
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Macintosh B, Graham JR, Barman T, De Rosa RJ, Konopacky Q, Marley MS, Marois C, Nielsen EL, Pueyo L, Rajan A, Rameau J, Saumon D, Wang JJ, Patience J, Ammons M, Arriaga P, Artigau E, Beckwith S, Brewster J, Bruzzone S, Bulger J, Burningham B, Burrows AS, Chen C, Chiang E, Chilcote JK, Dawson RI, Dong R, Doyon R, Draper ZH, Duchêne G, Esposito TM, Fabrycky D, Fitzgerald MP, Follette KB, Fortney JJ, Gerard B, Goodsell S, Greenbaum AZ, Hibon P, Hinkley S, Cotten TH, Hung LW, Ingraham P, Johnson-Groh M, Kalas P, Lafreniere D, Larkin JE, Lee J, Line M, Long D, Maire J, Marchis F, Matthews BC, Max CE, Metchev S, Millar-Blanchaer MA, Mittal T, Morley CV, Morzinski KM, Murray-Clay R, Oppenheimer R, Palmer DW, Patel R, Perrin MD, Poyneer LA, Rafikov RR, Rantakyrö FT, Rice EL, Rojo P, Rudy AR, Ruffio JB, Ruiz MT, Sadakuni N, Saddlemyer L, Salama M, Savransky D, Schneider AC, Sivaramakrishnan A, Song I, Soummer R, Thomas S, Vasisht G, Wallace JK, Ward-Duong K, Wiktorowicz SJ, Wolff SG, Zuckerman B. Discovery and spectroscopy of the young jovian planet 51 Eri b with the Gemini Planet Imager. Science 2015; 350:64-7. [DOI: 10.1126/science.aac5891] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 08/03/2015] [Indexed: 11/02/2022]
Affiliation(s)
- B. Macintosh
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, Stanford, CA 94305, USA
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94040, USA
| | - J. R. Graham
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - T. Barman
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721, USA
| | - R. J. De Rosa
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - Q. Konopacky
- Center for Astrophysics and Space Sciences, University of California–San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - M. S. Marley
- NASA Ames Research Center, MS 245-3, Moffett Field, CA 94035, USA
| | - C. Marois
- National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, British Columbia V9E 2E7, Canada
- Department of Physics and Astronomy, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - E. L. Nielsen
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, Stanford, CA 94305, USA
- Search for Extraterrestrial Intelligence Institute, Carl Sagan Center, 189 Bernardo Avenue, Mountain View, CA 94043, USA
| | - L. Pueyo
- Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA
| | - A. Rajan
- School of Earth and Space Exploration, Arizona State University, Post Office Box 871404, Tempe, AZ 85287, USA
| | - J. Rameau
- Institut de Recherche sur les Exoplanètes, Départment de Physique, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - D. Saumon
- Los Alamos National Laboratory, Post Office Box 1663, MS F663, Los Alamos, NM 87545, USA
| | - J. J. Wang
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - J. Patience
- School of Earth and Space Exploration, Arizona State University, Post Office Box 871404, Tempe, AZ 85287, USA
| | - M. Ammons
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94040, USA
| | - P. Arriaga
- Department of Physics and Astronomy, University of California–Los Angeles, 430 Portola Plaza, Los Angeles, CA 90095, USA
| | - E. Artigau
- Institut de Recherche sur les Exoplanètes, Départment de Physique, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - S. Beckwith
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - J. Brewster
- Search for Extraterrestrial Intelligence Institute, Carl Sagan Center, 189 Bernardo Avenue, Mountain View, CA 94043, USA
| | - S. Bruzzone
- Department of Physics and Astronomy, Centre for Planetary Science and Exploration, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - J. Bulger
- School of Earth and Space Exploration, Arizona State University, Post Office Box 871404, Tempe, AZ 85287, USA
- Subaru Telescope, 650 North A'ohoku Place, Hilo, HI 96720, USA
| | - B. Burningham
- NASA Ames Research Center, MS 245-3, Moffett Field, CA 94035, USA
- Science and Technology Research Institute, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - A. S. Burrows
- Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544, USA
| | - C. Chen
- Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA
| | - E. Chiang
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - J. K. Chilcote
- Dunlap Institute for Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, Ontario M5S 3H4, Canada
| | - R. I. Dawson
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - R. Dong
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - R. Doyon
- Institut de Recherche sur les Exoplanètes, Départment de Physique, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Z. H. Draper
- National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, British Columbia V9E 2E7, Canada
- Department of Physics and Astronomy, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - G. Duchêne
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
- Institut de Planétologie et d’Astrophysique de Grenoble, Université Grenoble Alpes, Centre National de la Recherche Scientifique, 38000 Grenoble, France
| | - T. M. Esposito
- Department of Physics and Astronomy, University of California–Los Angeles, 430 Portola Plaza, Los Angeles, CA 90095, USA
| | - D. Fabrycky
- Department of Astronomy and Astrophysics, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637, USA
| | - M. P. Fitzgerald
- Department of Physics and Astronomy, University of California–Los Angeles, 430 Portola Plaza, Los Angeles, CA 90095, USA
| | - K. B. Follette
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, Stanford, CA 94305, USA
| | - J. J. Fortney
- Department of Astronomy and Astrophysics, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - B. Gerard
- National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, British Columbia V9E 2E7, Canada
- Department of Physics and Astronomy, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - S. Goodsell
- Department of Physics, Durham University, Stockton Road, Durham DH1, UK
- Gemini Observatory, Casilla 603, La Serena, Chile
| | - A. Z. Greenbaum
- Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA
- Department of Physics and Astronomy, Johns Hopkins University, 3600 North Charles Street, Baltimore, MD 21218, USA
| | - P. Hibon
- Gemini Observatory, Casilla 603, La Serena, Chile
| | - S. Hinkley
- University of Exeter, Astrophysics Group, Physics Building, Stocker Road, Exeter EX4 4QL, UK
| | - T. H. Cotten
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA
| | - L.-W. Hung
- Department of Physics and Astronomy, University of California–Los Angeles, 430 Portola Plaza, Los Angeles, CA 90095, USA
| | - P. Ingraham
- Large Synoptic Survey Telescope, 950 North Cherry Avenue, Tucson, AZ 85719, USA
| | - M. Johnson-Groh
- National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, British Columbia V9E 2E7, Canada
- Department of Physics and Astronomy, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - P. Kalas
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
- Search for Extraterrestrial Intelligence Institute, Carl Sagan Center, 189 Bernardo Avenue, Mountain View, CA 94043, USA
| | - D. Lafreniere
- Institut de Recherche sur les Exoplanètes, Départment de Physique, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - J. E. Larkin
- Department of Physics and Astronomy, University of California–Los Angeles, 430 Portola Plaza, Los Angeles, CA 90095, USA
| | - J. Lee
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA
| | - M. Line
- Department of Astronomy and Astrophysics, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - D. Long
- Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA
| | - J. Maire
- Dunlap Institute for Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, Ontario M5S 3H4, Canada
| | - F. Marchis
- Search for Extraterrestrial Intelligence Institute, Carl Sagan Center, 189 Bernardo Avenue, Mountain View, CA 94043, USA
| | - B. C. Matthews
- National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, British Columbia V9E 2E7, Canada
- Department of Physics and Astronomy, University of Victoria, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
| | - C. E. Max
- Department of Astronomy and Astrophysics, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - S. Metchev
- Department of Physics and Astronomy, Centre for Planetary Science and Exploration, The University of Western Ontario, London, Ontario N6A 3K7, Canada
- Department of Physics and Astronomy, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794-3800, USA
| | - M. A. Millar-Blanchaer
- Department of Astronomy and Astrophysics, University of Toronto, Toronto, Ontario M5S 3H4, Canada
| | - T. Mittal
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - C. V. Morley
- Department of Astronomy and Astrophysics, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - K. M. Morzinski
- Steward Observatory, 933 North Cherry Avenue, University of Arizona, Tucson, AZ 85721, USA
| | - R. Murray-Clay
- Department of Physics, University of California–Santa Barbara, Broida Hall, Santa Barbara, CA 93106-9530, USA
| | - R. Oppenheimer
- Department of Astrophysics, American Museum of Natural History, New York, NY 10024, USA
| | - D. W. Palmer
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94040, USA
| | - R. Patel
- Department of Physics and Astronomy, Stony Brook University, 100 Nicolls Road, Stony Brook, NY 11794-3800, USA
| | - M. D. Perrin
- Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA
| | - L. A. Poyneer
- Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94040, USA
| | - R. R. Rafikov
- Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544, USA
| | | | - E. L. Rice
- Department of Astrophysics, American Museum of Natural History, New York, NY 10024, USA
- Department of Engineering Science and Physics, College of Staten Island, City University of New York, Staten Island, NY 10314, USA
| | - P. Rojo
- Departamento de Astronomía, Universidad de Chile, Camino El Observatorio 1515, Casilla 36-D, Las Condes, Santiago, Chile
| | - A. R. Rudy
- Department of Astronomy and Astrophysics, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - J.-B. Ruffio
- Kavli Institute for Particle Astrophysics and Cosmology, Stanford University, Stanford, CA 94305, USA
- Search for Extraterrestrial Intelligence Institute, Carl Sagan Center, 189 Bernardo Avenue, Mountain View, CA 94043, USA
| | - M. T. Ruiz
- Departamento de Astronomía, Universidad de Chile, Camino El Observatorio 1515, Casilla 36-D, Las Condes, Santiago, Chile
| | - N. Sadakuni
- Gemini Observatory, Casilla 603, La Serena, Chile
- Stratospheric Observatory for Infrared Astronomy, Universities Space Research Association, NASA Armstrong Flight Research Center, 2825 East Avenue P, Palmdale, CA 93550, USA
| | - L. Saddlemyer
- National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, British Columbia V9E 2E7, Canada
| | - M. Salama
- Department of Astronomy, University of California–Berkeley, Berkeley, CA 94720, USA
| | - D. Savransky
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14853, USA
| | - A. C. Schneider
- Physics and Astronomy, University of Toledo, 2801 West Bancroft Street, Toledo, OH 43606, USA
| | - A. Sivaramakrishnan
- Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA
| | - I. Song
- Department of Physics and Astronomy, University of Georgia, Athens, GA 30602, USA
| | - R. Soummer
- Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA
| | - S. Thomas
- Large Synoptic Survey Telescope, 950 North Cherry Avenue, Tucson, AZ 85719, USA
| | - G. Vasisht
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109, USA
| | - J. K. Wallace
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109, USA
| | - K. Ward-Duong
- School of Earth and Space Exploration, Arizona State University, Post Office Box 871404, Tempe, AZ 85287, USA
| | - S. J. Wiktorowicz
- Department of Astronomy and Astrophysics, University of California–Santa Cruz, Santa Cruz, CA 95064, USA
| | - S. G. Wolff
- Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218, USA
- Department of Physics and Astronomy, Johns Hopkins University, 3600 North Charles Street, Baltimore, MD 21218, USA
| | - B. Zuckerman
- Department of Physics and Astronomy, University of California–Los Angeles, 430 Portola Plaza, Los Angeles, CA 90095, USA
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Gulley J, Rajan A, Spigel D, Iannotti N, Chandler J, Wong D, Leach J, Edenfield W, Wang D, Bajars M, Von Heydebreck A, Kelly K. 3090 Avelumab (MSB0010718C), an anti-PD-L1 antibody, in patients with metastatic or recurrent non-small-cell lung cancer progressing after platinum-based chemotherapy: A phase Ib trial. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31731-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Karuppiah C, Muthupandi K, Chen SM, Ali MA, Palanisamy S, Rajan A, Prakash P, Al-Hemaid FMA, Lou BS. Green synthesized silver nanoparticles decorated on reduced graphene oxide for enhanced electrochemical sensing of nitrobenzene in waste water samples. RSC Adv 2015. [DOI: 10.1039/c5ra00992h] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the present work, an electrochemical sensor for nitrobenzene has been developed based on a green synthesized silver nanoparticle (AgNP) decorated reduced graphene oxide (RGO) modified glassy carbon electrode (GCE).
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Affiliation(s)
- Chelladurai Karuppiah
- Electroanalysis and Bioelectrochemistry Lab
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 106
- People's Republic of China
| | - K. Muthupandi
- Department of Chemistry
- Thiagarajar College
- Madurai-625009
- India
| | - Shen-Ming Chen
- Electroanalysis and Bioelectrochemistry Lab
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 106
- People's Republic of China
| | - M. Ajmal Ali
- Department of Botany and Microbiology
- College of Science
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | - Selvakumar Palanisamy
- Electroanalysis and Bioelectrochemistry Lab
- Department of Chemical Engineering and Biotechnology
- National Taipei University of Technology
- Taipei 106
- People's Republic of China
| | - A. Rajan
- Department of Chemistry
- Thiagarajar College
- Madurai-625009
- India
| | - P. Prakash
- Department of Chemistry
- Thiagarajar College
- Madurai-625009
- India
| | - Fahad M. A. Al-Hemaid
- Department of Botany and Microbiology
- College of Science
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | - Bih-Show Lou
- Chemistry Division
- Center for General Education
- Chang Gung University
- Tao-Yuan
- Taiwan
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Rajan A, Eubanks E, Edwards S, Aronovich S, Rudek I, Wang F, Lanis A, Kaigler D. Cell survival and seeding efficiency for severe craniofacial reconstruction using stem cells: a proof-of-concept clinical study. Cytotherapy 2014. [DOI: 10.1016/j.jcyt.2014.01.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kelly RJ, Thomas A, Rajan A, Chun G, Lopez-Chavez A, Szabo E, Spencer S, Carter CA, Guha U, Khozin S, Poondru S, Van Sant C, Keating A, Steinberg SM, Figg W, Giaccone G. A phase I/II study of sepantronium bromide (YM155, survivin suppressor) with paclitaxel and carboplatin in patients with advanced non-small-cell lung cancer. Ann Oncol 2013; 24:2601-2606. [PMID: 23857959 DOI: 10.1093/annonc/mdt249] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND This phase I/II study examined the safety and efficacy of Sepantronium Bromide (S), a small-molecule selective survivin suppressant, administered in combination with carboplatin (C) and paclitaxel (P). PATIENTS AND METHODS Forty-one patients were treated on study. Twenty-two patients received escalating doses of S (3.6-12 mg/m(2)) and 19 with untreated stage IV non-small-cell lung cancer (NSCLC) were treated with the maximum tolerated dose of 10 mg/m(2) in combination with standard doses of C (AUC6) and P (200 mg/m(2)) for six cycles. S was administered as a continuous intravenous infusion (CIVI) over 72 h in 21-day treatment cycles. Study end points included safety and toxic effect, response rate, progression-free and overall survival (PFS and OS), as well as exploratory pharmacodynamic correlates. RESULTS Treatment with S was well tolerated, and toxic effects were mostly hematological in the phase II study. Two (11%) partial responses were observed with a median PFS of 5.7 months and median OS 16.1 months. Pharmacodynamic analysis did not demonstrate an association with response. CONCLUSION The combination of S (10 mg/m(2)/day 72-h CIVI) administered with C and P every 3 weeks exhibited a favorable safety profile but failed to demonstrate an improvement in response rate in advanced NSCLC. CLINICAL TRIAL NUMBER NCT01100931.
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Affiliation(s)
- R J Kelly
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins, Baltimore
| | - A Thomas
- Medical Oncology Branch, Center for Cancer Research
| | - A Rajan
- Medical Oncology Branch, Center for Cancer Research
| | - G Chun
- Medical Oncology Branch, Center for Cancer Research
| | | | - E Szabo
- Lung and Upper Aerodigestive Cancer Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda
| | - S Spencer
- Medical Oncology Branch, Center for Cancer Research
| | - C A Carter
- Medical Oncology, Walter Reed National Military Medical Center, Bethesda
| | - U Guha
- Medical Oncology Branch, Center for Cancer Research
| | - S Khozin
- Medical Oncology Branch, Center for Cancer Research
| | - S Poondru
- Astellas Pharma Global Development, Northbrook
| | - C Van Sant
- Astellas Pharma Global Development, Northbrook
| | - A Keating
- Astellas Pharma Global Development, Northbrook
| | - S M Steinberg
- Biostatistics and Data Management Section, Office of the Clinical Director, Center for Cancer Research, National Cancer Institute, Bethesda, USA
| | - W Figg
- Medical Oncology Branch, Center for Cancer Research
| | - G Giaccone
- Medical Oncology Branch, Center for Cancer Research.
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Rajan A, Bagai U, Chandel S. Effect of artesunate based combination therapy with homeopathic medicine china on liver and kidney of Plasmodium berghei infected mice. J Parasit Dis 2013; 37:62-7. [PMID: 24431543 PMCID: PMC3590377 DOI: 10.1007/s12639-012-0132-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 06/05/2012] [Indexed: 11/26/2022] Open
Abstract
Present study has been undertaken to evaluate antimalarial potential and safety of artesunate based combination therapy with homeopathic medicine china (ϕ/30 potency) against Plasmodium berghei (NK-65), a lethal rodent malaria parasite. In combination therapy, the oral administration of artesunate (100 mg/kg) + china ϕ/30 proved to be highly efficacious as it completely cleared the blood stage infection. During the follow up period up to day 28, no recrudescence was observed and the survival rate was 100 %. Combination did not disturb the normal functioning of liver and kidney, as evident from the normal activity of ALP (190.5 ± 0.2 and 174.2 ± 9.12 IU/l), level of bilirubin (0.6 ± 0.33 and 0.73 ± 0.1 mg/dl), urea (28 ± 0.51 and 29.1 ± 0.03 mg/dl) and creatinine (0.9 ± 0.62 and 1.1 ± 0.1 mg/dl) in serum of treated mice on day 7 and 28 respectively. Present study points to better efficacy of china as an alternative drug partner in combination to enhance antimalarial efficacy of artesunate without affecting the liver and kidney functions of P. berghei infected BALB/c mice.
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Affiliation(s)
- A. Rajan
- Department of Zoology, Parasitology Laboratory, Panjab University, Chandigarh, 160014 India
| | - U. Bagai
- Department of Zoology, Parasitology Laboratory, Panjab University, Chandigarh, 160014 India
| | - S. Chandel
- Department of Zoology, Parasitology Laboratory, Panjab University, Chandigarh, 160014 India
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Chen DS, Feltquate DM, Smothers F, Hoos A, Langermann S, Marshall S, May R, Fleming M, Hodi FS, Senderowicz A, Wiman KG, de Dosso S, Fiedler W, Gianni L, Cresta S, Schulze-Bergkamen HB, Gurrieri L, Salzberg M, Dietrich B, Danielczyk A, Baumeister H, Goletz S, Sessa C, Strumberg D, Schultheis B, Santel A, Gebhardt F, Meyer-Sabellek W, Keil O, Giese K, Kaufmann J, Maio M, Choy G, Covre A, Parisi G, Nicolay H, Fratta E, Fonsatti E, Sigalotti L, Coral S, Taverna P, Azab M, Deutsch E, Lepechoux C, Pignon JP, Tao YT, Rivera S, Bourgier BC, Angokai M, Bahleda R, Slimane K, Angevin E, Besse BB, Soria JC, Dragnev K, Beumer JH, Anyang B, Ma T, Galimberti F, Erkmen CP, Nugent W, Rigas J, Abraham K, Johnstone D, Memoli V, Dmitrovsky E, Voest EE, Siu L, Janku F, Soria JC, Tsimberidou A, Kurzrock R, Tabernero J, Rodon J, Berger R, Onn A, Batist G, Bresson C, Lazar V, Molenaar JJ, Koster J, Ebus M, Zwijnenburg DA, van Sluis P, Lamers F, Schild L, van der Ploeg I, Caron HN, Versteeg R, Pouyssegur J, Marchiq I, Chiche J, Roux D, Le Floch R, Critchlow SE, Wooster RF, Agresta S, Yen KE, Janne PA, Plummer ER, Trinchieri G, Ellis L, Chan SL, Yeo W, Chan AT, Mouliere F, El Messaoudi S, Gongora C, Lamy PJ, del Rio M, Lopez-Crapez E, Gillet B, Mathonnet M, Pezet D, Ychou M, Thierry AR, Ribrag V, Vainchenker W, Constantinescu S, Keilhack H, Umelo IA, Noeparast A, Chen G, Renard M, Geers C, Vansteenkiste J, Teugels E, de Greve J, Rixe O, Qi X, Chu Z, Celerier J, Leconte L, Minet N, Pakradouni J, Kaur B, Cuttitta F, Wagner AJ, Zhang YX, Sicinska E, Czaplinski JT, Remillard SP, Demetri GD, Weng S, Debussche L, Agoni L, Reddy EP, Guha C, Silence K, Thibault A, de Haard H, Dreier T, Ulrichts P, Moshir M, Gabriels S, Luo J, Carter C, Rajan A, Khozin S, Thomas A, Lopez-Chavez A, Brzezniak C, Doyle L, Keen C, Manu M, Raffeld M, Giaccone G, Lutzker S, Melief JM, Eckhardt SG, Trusolino L, Migliardi G, Zanella ER, Cottino F, Galimi F, Sassi F, Marsoni S, Comoglio PM, Bertotti A, Hidalgo M, Weroha SJ, Haluska P, Becker MA, Harrington SC, Goodman KM, Gonzalez SE, al Hilli M, Butler KA, Kalli KR, Oberg AL, Huijbers IJ, Bin Ali R, Pritchard C, Cozijnsen M, Proost N, Song JY, Krimpenfort P, Michalak E, Jonkers J, Berns A, Banerji U, Stewart A, Thavasu P, Banerjee S, Kaye SB. Lectures. Ann Oncol 2013. [DOI: 10.1093/annonc/mdt042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Carter C, Rajan A, Khozin S, Thomas A, Lopez-Chavez A, Brzezniak C, Doyle L, Keen C, Manu M, Raffeld M, Giaccone G. The Evaluation of Selumetinib a MEK-Inhibitor with and without the Addition of Erlotinib in KRAS Mutated Non-Small Cell Lung Cancer. Ann Oncol 2013. [DOI: 10.1093/annonc/mdt042.41] [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: 11/12/2022] Open
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Thomas A, Rajan A, Lopez-Chavez A, Wang Y, Giaccone G. From targets to targeted therapies and molecular profiling in non-small cell lung carcinoma. Ann Oncol 2013; 24:577-85. [PMID: 23131389 PMCID: PMC3574546 DOI: 10.1093/annonc/mds478] [Citation(s) in RCA: 55] [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: 07/17/2012] [Revised: 08/13/2012] [Accepted: 08/14/2012] [Indexed: 12/22/2022] Open
Abstract
Although tumor molecular-profile-directed therapy appears promising in early clinical studies, there are many practical challenges to its successful clinical application in non-small-cell lung cancer (NSCLC). These challenges may be broadly classified as those relating to tumor (heterogeneity), tissue (acquisition and processing), testing (assays for molecular profiling) and trials (clinical evaluation of molecular markers and drugs). Strategies to overcome these challenges include (i) understanding the biological basis of tumor heterogeneity and of carcinogenesis in the large subset of patients with no currently evident driver events; (ii) technological advances in minimally invasive acquisition of tumor and next-generation sequencing (NGS) which would enable single-platform analysis of molecular alterations in limited tissue at a reasonable turnaround time (TAT); (iii) deliberation in early stages of drug development as well as clinical trial design to identify, validate and assess the clinical utility of biomarkers in conjunction with drugs and (iv) collaboration to improve understanding of and accrual to trials enrolling patients with rare molecular alterations.
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Affiliation(s)
- A. Thomas
- Medical Oncology Branch, National Cancer Institute, Bethesda
| | - A. Rajan
- Medical Oncology Branch, National Cancer Institute, Bethesda
| | - A. Lopez-Chavez
- Division of Hematology/Medical Oncology, Oregon Health and Science University, Portland, USA
| | - Y. Wang
- Medical Oncology Branch, National Cancer Institute, Bethesda
| | - G. Giaccone
- Medical Oncology Branch, National Cancer Institute, Bethesda
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Bagai U, Rajan A, Kaur S. Antimalarial potential of Nosode 30 and 200 against Plasmodium berghei infection in BALB/c mice. J Vector Borne Dis 2012; 49:72-77. [PMID: 22898477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND & OBJECTIVES Homeopathy is considered as an emerging area of alternative medicine which could be established for the global health care. One of the greatest objections to this science lies in its inability to explain the mechanism of action of the micro doses based on scientific experiments and proofs. The present study has been undertaken to screen in vivo antimalarial activity of Malaria Co Nosode 30 and Nosode 200 against Plasmodium berghei infection in BALB/c mice. METHODS Peter's 4-day test was used to evaluate the in vivo schizontocidal effect of Nosode 30 and Nosode 200. One month follow-up study was done to calculate the mean survival time of mice in each group. Biochemical analysis was carried out to assess the liver and kidney function tests using diagnostic kits. RESULTS Nosode 30 and 200 exhibited 87.02 and 37.97% chemosuppression on Day 7 and mean survival time (MST) of 18.5 ± 2.16 and 16.5 ± 1.37 days respectively, which were extremely statistically significant when compared to MST of infected control (8.55 ± 0.83 days). The safety of Nosode 30 was also confirmed by the comparable levels of ALP, SGOT, SGPT activities, concentration of bilirubin, urea and creatinine to CQ treated group. CONCLUSION Nosode 30 possesses considerable in vivo antiplasmodial activity against P. berghei infection as compared to Nosode 200 as evident from the chemosuppression obtained using Peter's 4-day test. Further, studies on the drug can be carried out to establish its antimalarial potential in monotherapy or in combination with other homeopathic drug formulations.
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Affiliation(s)
- U Bagai
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, India
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Rajan A, Bagai U. SEM studies on blood cells of Plasmodium berghei infected Balb/c mice treated with artesunate and homeopathic medicine China. J Parasit Dis 2011; 35:134-9. [PMID: 23024494 PMCID: PMC3235391 DOI: 10.1007/s12639-011-0059-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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: 05/04/2011] [Accepted: 07/12/2011] [Indexed: 11/25/2022] Open
Abstract
The therapeutic efficacy of antimalarial drugs and their effect on various organs in the form of surface morphological deformations can be analyzed using scanning electron microscopy (SEM). Present study has been undertaken on Plasmodium berghei (NK-65), a lethal rodent malaria parasite, to monitor the morphological changes in blood cells induced by the treatment with combination of artesunate and homeopathic medicine . Combination therapy of artesunate (100 mg/kg) and China ϕ was found to be highly effective in clearing the blood stage infection of Plasmodium berghei and it also enhanced the mean survival time (28 ± 0 days) of mice. Not much morphological changes were induced on WBCs and RBCs of mice treated with combination therapy but in treated groups the number of live PMN cells was more as observed in AO/EB staining. In normal mice the mononuclear cells were both smooth surfaced and layered surfaced, whereas, polymorphonuclear cells were having finger like projections. The combination of artesunate and China was found to be very effective and did not cause any alteration on the surface of blood cells as observed in SEM.
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Affiliation(s)
- A. Rajan
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014 India
| | - U. Bagai
- Parasitology Laboratory, Department of Zoology, Panjab University, Chandigarh, 160014 India
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50
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Kelly RJ, Rajan A, Chun G, Lopez-Chavez A, Giaccone G. A phase I study of paclitaxel, carboplatin, and YM155 (survivin suppressor) in subjects with solid tumors. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.3090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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