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Swahn H, Mertens J, Olmer M, Myers K, Mondala TS, Natarajan P, Head SR, Alvarez‐Garcia O, Lotz MK. Shared and Compartment-Specific Processes in Nucleus Pulposus and Annulus Fibrosus During Intervertebral Disc Degeneration. Adv Sci (Weinh) 2024; 11:e2309032. [PMID: 38403470 PMCID: PMC11077672 DOI: 10.1002/advs.202309032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/08/2024] [Indexed: 02/27/2024]
Abstract
Elucidating how cell populations promote onset and progression of intervertebral disc degeneration (IDD) has the potential to enable more precise therapeutic targeting of cells and mechanisms. Single-cell RNA-sequencing (scRNA-seq) is performed on surgically separated annulus fibrosus (AF) (19,978; 26,983 cells) and nucleus pulposus (NP) (20,884; 24,489 cells) from healthy and diseased human intervertebral discs (IVD). In both tissue types, depletion of cell subsets involved in maintenance of healthy IVD is observed, specifically the immature cell subsets - fibroblast progenitors and stem cells - indicative of an impairment of normal tissue self-renewal. Tissue-specific changes are also identified. In NP, several fibrotic populations are increased in degenerated IVD, indicating tissue-remodeling. In degenerated AF, a novel disease-associated subset is identified, which expresses disease-promoting genes. It is associated with pathogenic biological processes and the main gene regulatory networks include thrombospondin signaling and FOXO1 transcription factor. In NP and AF cells thrombospondin protein promoted expression of genes associated with TGFβ/fibrosis signaling, angiogenesis, and nervous system development. The data reveal new insights of both shared and tissue-specific changes in specific cell populations in AF and NP during IVD degeneration. These identified mechanisms and molecules are novel and more precise targets for IDD prevention and treatment.
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Affiliation(s)
- Hannah Swahn
- Department of Molecular and Cellular Biology & Department of Molecular MedicineScripps ResearchLa JollaCA92037USA
| | - Jasmin Mertens
- Department of Molecular and Cellular Biology & Department of Molecular MedicineScripps ResearchLa JollaCA92037USA
| | - Merissa Olmer
- Department of Molecular and Cellular Biology & Department of Molecular MedicineScripps ResearchLa JollaCA92037USA
| | - Kevin Myers
- Department of Molecular and Cellular Biology & Department of Molecular MedicineScripps ResearchLa JollaCA92037USA
| | - Tony S. Mondala
- Center for Computational Biology & Bioinformatics and Genomics CoreScripps ResearchLa JollaCA92037USA
| | - Padmaja Natarajan
- Center for Computational Biology & Bioinformatics and Genomics CoreScripps ResearchLa JollaCA92037USA
| | - Steven R. Head
- Center for Computational Biology & Bioinformatics and Genomics CoreScripps ResearchLa JollaCA92037USA
| | - Oscar Alvarez‐Garcia
- Department of Molecular and Cellular Biology & Department of Molecular MedicineScripps ResearchLa JollaCA92037USA
| | - Martin K. Lotz
- Department of Molecular and Cellular Biology & Department of Molecular MedicineScripps ResearchLa JollaCA92037USA
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Courties A, Olmer M, Myers K, Ordoukhanian P, Head SR, Natarajan P, Berenbaum F, Sellam J, Lotz MK. Human-specific duplicate CHRFAM7A gene is associated with more severe osteoarthritis and amplifies pain behaviours. Ann Rheum Dis 2023; 82:710-718. [PMID: 36627169 PMCID: PMC10101906 DOI: 10.1136/ard-2022-223470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023]
Abstract
OBJECTIVES CHRFAM7A is a uniquely human fusion gene that functions as a dominant negative regulator of alpha 7 acetylcholine nicotinic receptor (α7nAChR) in vitro. This study determined the impact of CHRFAM7A on α7nAChR agonist responses, osteoarthritis (OA) severity and pain behaviours and investigated mechanisms. METHODS Transgenic CHRFAM7A (TgCHRFAM7A) mice were used to determine the impact of CHRFAM7A on knee OA histology, pain severity in OA and other pain models, response to nAchR agonist and IL-1β. Mouse and human cells were used for mechanistic studies. RESULTS Transgenic (Tg) TgCHRFAM7A mice developed more severe structural damage and increased mechanical allodynia than wild type (WT) mice in the destabilisation of medial meniscus model of OA. This was associated with a decreased suppression of inflammation by α7nAchR agonist. TgCHRFAM7A mice displayed a higher basal sensitivity to pain stimuli and increased pain behaviour in the monoiodoacetate and formalin models. Dorsal root ganglia of TgCHRFAM7A mice showed increased macrophage infiltration and expression of the chemokine fractalkine and also had a compromised antinociceptive response to the α7nAchR agonist nicotine. Both native CHRNA7 and CHRFAM7A subunits were expressed in human joint tissues and the CHRFAM7A/CHRNA7 ratio was increased in OA cartilage. Human chondrocytes with two copies of CHRFAM7A had reduced anti-inflammatory responses to nicotine. CONCLUSION CHRFAM7A is an aggravating factor for OA-associated inflammation and tissue damage and a novel genetic risk factor and therapeutic target for pain.
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Affiliation(s)
- Alice Courties
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
- INSERM UMRS 938, Hôpital Saint-Antoine, Service de rhumatologie, AP-HP, Sorbonne Université, Paris, France
| | - Merissa Olmer
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Kevin Myers
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Phillip Ordoukhanian
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, California, USA
| | - Steven R Head
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, California, USA
| | - Padmaja Natarajan
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, California, USA
| | - Francis Berenbaum
- INSERM UMRS 938, Hôpital Saint-Antoine, Service de rhumatologie, AP-HP, Sorbonne Université, Paris, France
| | - Jérémie Sellam
- INSERM UMRS 938, Hôpital Saint-Antoine, Service de rhumatologie, AP-HP, Sorbonne Université, Paris, France
| | - Martin K Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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3
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Swahn H, Li K, Duffy T, Olmer M, D'Lima DD, Mondala TS, Natarajan P, Head SR, Lotz MK. Senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus. Ann Rheum Dis 2023; 82:403-415. [PMID: 36564153 PMCID: PMC10076001 DOI: 10.1136/ard-2022-223227] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [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: 08/12/2022] [Accepted: 11/08/2022] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Single-cell level analysis of articular cartilage and meniscus tissues from human healthy and osteoarthritis (OA) knees. METHODS Single-cell RNA sequencing (scRNA-seq) analyses were performed on articular cartilage and meniscus tissues from healthy (n=6, n=7) and OA (n=6, n=6) knees. Expression of genes of interest was validated using immunohistochemistry and RNA-seq and function was analysed by gene overexpression and depletion. RESULTS scRNA-seq analyses of human knee articular cartilage (70 972 cells) and meniscus (78 017 cells) identified a pathogenic subset that is shared between both tissues. This cell population is expanded in OA and has strong OA and senescence gene signatures. Further, this subset has critical roles in extracellular matrix (ECM) and tenascin signalling and is the dominant sender of signals to all other cartilage and meniscus clusters and a receiver of TGFβ signalling. Fibroblast activating protein (FAP) is also a dysregulated gene in this cluster and promotes ECM degradation. Regulons that are controlled by transcription factor ZEB1 are shared between the pathogenic subset in articular cartilage and meniscus. In meniscus and cartilage cells, FAP and ZEB1 promote expression of genes that contribute to OA pathogenesis, including senescence. CONCLUSIONS These single-cell studies identified a senescent pathogenic cell cluster that is present in cartilage and meniscus and has FAP and ZEB1 as main regulators which are novel and promising therapeutic targets for OA-associated pathways in both tissues.
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Affiliation(s)
- Hannah Swahn
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Kun Li
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Tomas Duffy
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Merissa Olmer
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Darryl D D'Lima
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
- Shiley Center for Orthopaedic Research and Education at Scripps Clinic, Scripps Health, La Jolla, California, USA
| | - Tony S Mondala
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jola, California, USA
| | - Padmaja Natarajan
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jola, California, USA
| | - Steven R Head
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jola, California, USA
| | - Martin K Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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4
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Hu Y, Li K, Swahn H, Ordoukhanian P, Head SR, Natarajan P, Woods AK, Joseph SB, Johnson KA, Lotz MK. Transcriptomic analyses of joint tissues during osteoarthritis development in a rat model reveal dysregulated mechanotransduction and extracellular matrix pathways. Osteoarthritis Cartilage 2023; 31:199-212. [PMID: 36354073 PMCID: PMC9892293 DOI: 10.1016/j.joca.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/20/2022] [Accepted: 10/03/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Transcriptomic changes in joint tissues during the development of osteoarthritis (OA) are of interest for the discovery of biomarkers and mechanisms of disease. The objective of this study was to use the rat medial meniscus transection (MMT) model to discover stage and tissue-specific transcriptomic changes. DESIGN Sham or MMT surgeries were performed in mature rats. Cartilage, menisci and synovium were scored for histopathological changes at 2, 4 and 6 weeks post-surgery and processed for RNA-sequencing. Differentially expressed genes (DEG) were used to identify pathways and mechanisms. Published transcriptomic datasets from animal models and human OA were used to confirm and extend present findings. RESULTS The total number of DEGs was already high at 2 weeks (723 in meniscus), followed by cartilage (259) and synovium (42) and declined to varying degrees in meniscus and synovium but increased in cartilage at 6 weeks. The most upregulated genes included tenascins. The 'response to mechanical stimulus' and extracellular matrix-related pathways were enriched in both cartilage and meniscus. Pathways that were enriched in synovium at 4 weeks indicate processes related to synovial hyperplasia and fibrosis. Synovium also showed upregulation of IL-11 and several MMPs. The mechanical stimulus pathway included upregulation of the mechanoreceptors PIEZO1, PIEZO2 and TRPV4 and nerve growth factor. Analysis of data from prior RNA-sequencing studies of animal models and human OA support these findings. CONCLUSION These results indicate several shared pathways that are affected during OA in cartilage and meniscus and support the role of mechanotransduction and other pathways in OA pathogenesis.
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Affiliation(s)
- Y Hu
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA; Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - K Li
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - H Swahn
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - P Ordoukhanian
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, CA, 92037, USA
| | - S R Head
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, CA, 92037, USA
| | - P Natarajan
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, CA, 92037, USA
| | - A K Woods
- Calibr, a Division of Scripps Research, La Jolla, CA, 92037, USA
| | - S B Joseph
- Calibr, a Division of Scripps Research, La Jolla, CA, 92037, USA
| | - K A Johnson
- Calibr, a Division of Scripps Research, La Jolla, CA, 92037, USA
| | - M K Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA.
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Nagy K, McBride R, Head SR, Ordoukhanian P, Law M. Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes. Methods Mol Biol 2023; 2578:63-81. [PMID: 36152281 DOI: 10.1007/978-1-0716-2732-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Understanding antibody specificity and defining response profiles to antigens continue to be essential to both vaccine research and therapeutic antibody development. Peptide scanning assays enable mapping of continuous epitopes in order to delineate antibody-antigen interactions beyond traditional immunoassay formats. We have developed a relatively low-cost method to generate peptide microarray slides for antibody binding studies that allow for interrogation of up to 1536 overlapping peptides derived from the target antigens on a single microslide. Using an IntavisAG MultiPep RS peptide synthesizer and a Digilab MicroGrid II 600 microarray printer robot, each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface. Interrogation of the surface can then be performed using polyclonal immune sera or monoclonal antibodies, and sensitive detection using an InnoScan 1100 AL scanner with fluorescent-conjugated secondary reagents maximizes conservation of reagents.
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Affiliation(s)
- Kenna Nagy
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan McBride
- Genomics Core, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven R Head
- Genomics Core, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Mansun Law
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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Kawata M, Teramura T, Ordoukhanian P, Head SR, Natarajan P, Sundaresan A, Olmer M, Asahara H, Lotz MK. Krüppel-like factor-4 and Krüppel-like factor-2 are important regulators of joint tissue cells and protect against tissue destruction and inflammation in osteoarthritis. Ann Rheum Dis 2022; 81:annrheumdis-2021-221867. [PMID: 35534137 PMCID: PMC9643672 DOI: 10.1136/annrheumdis-2021-221867] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/24/2022] [Indexed: 12/16/2022]
Abstract
OBJECTIVES Analysing expression patterns of Krüppel-like factor (KLF) transcription factors in normal and osteoarthritis (OA) human cartilage, and determining functions and mechanisms of KLF4 and KLF2 in joint homoeostasis and OA pathogenesis. METHODS Experimental approaches included human joint tissues cells, transgenic mice and mouse OA model with viral KLF4 gene delivery to demonstrate therapeutic benefit in structure and pain improvement. Mechanistic studies applied global gene expression analysis and chromatin immunoprecipitation sequencing (ChIP-seq). RESULTS Several KLF genes were significantly decreased in OA cartilage. Among them, KLF4 and KLF2 were strong inducers of cartilage collagen genes and Proteoglycan-4. Cartilage-specific deletion of Klf2 in mature mice aggravated severity of experimental OA. Transduction of human chondrocytes with Adenovirus (Ad) expressing KLF4 or KLF2 enhanced expression of major cartilage extracellular matrix (ECM) genes and SRY-box transcription factor-9, and suppressed mediators of inflammation and ECM-degrading enzymes. Ad-KLF4 and Ad-KLF2 enhanced similar protective functions in meniscus cells and synoviocytes, and promoted chondrocytic differentiation of human mesenchymal stem cells. Viral KLF4 delivery into mouse knees reduced severity of OA-associated changes in cartilage, meniscus and synovium, and improved pain behaviours. ChIP-seq analysis suggested that KLF4 directly bound cartilage signature genes. Ras-related protein-1 signalling was the most enriched pathway in KLF4-transduced cells, and its signalling axis was involved in upregulating cartilage ECM genes by KLF4 and KLF2. CONCLUSIONS KLF4 and KLF2 may be central transcription factors that increase protective and regenerative functions in joint tissue cells, suggesting that KLF gene transfer or molecules upregulating KLFs are therapeutic candidates for OA.
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Affiliation(s)
- Manabu Kawata
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Takeshi Teramura
- Division of Cell Biology for Regenerative Medicine, Institute of Advanced Clinical Medicine, Kindai University, Osaka-Sayama, Osaka, Japan
| | - Philip Ordoukhanian
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, California, USA
| | - Steven R Head
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, California, USA
| | - Padmaja Natarajan
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, California, USA
| | - Aishwarya Sundaresan
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, California, USA
| | - Merissa Olmer
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Hiroshi Asahara
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Martin K Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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7
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Xu J, Duong K, Yang Z, Kaji K, Ou J, Head SR, Crynen G, Ordoukhanian P, Hanna L, Hanna A, Wang Y, Wang Z, Wang J. Real-time digital polymerase chain reaction (PCR) as a novel technology improves limit of detection for rare allele assays. Transl Lung Cancer Res 2021; 10:4336-4352. [PMID: 35070745 PMCID: PMC8743530 DOI: 10.21037/tlcr-21-728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022]
Abstract
Background Tumor heterogeneity may lead to false negative test results for tissue biopsy-based companion diagnostic tests. Real-time polymerase chain reaction (PCR) and digital PCR assays are used to detect rare alleles in cell-free circulating DNA for liquid biopsies; however, those tests lack strong sensitivity at low allele frequencies. We show here a novel real-time digital PCR instrument that utilizes cycle-based amplification curves to further improve the sensitivity and quantification accuracy of digital PCR. Methods The novel real-time digital PCR instrument was compared to an endpoint digital PCR system to determine the sensitivity and quantification accuracy of both instruments. Samples were all thermal cycled on the real-time digital PCR instrument but were analyzed on both endpoint and real-time digital PCR instruments to compare the performance without introducing other variables. Contrived samples for epidermal growth factor receptor (EGFR) exon 19 deletion, T790M, and L858R point mutations as well as human epidermal growth factor receptor 2 (HER2) amplification were tested. Different mutant allele frequencies and wildtype to mutant gene copy number ratios were tested for EGFR and HER2, respectively. Results By removing false positive datapoints using real-time amplification curves, real-time digital PCR improved sensitivity by lowering the baseline for wildtype samples. For EGFR 19del assay, samples with 2 or more fluorescein amidite (FAM) labeled positive wells are determined positive by real-time digital PCR, while a minimum of 5 FAM positive datapoints is needed by endpoint digital PCR. Improved limit of detection for EGFR 19del mutation was also observed. Real-time digital PCR also had better quantification accuracy and sensitivity, resulting in the mutant allele frequencies being closer to the expected values for all EGFR mutations, especially at very low allele frequencies. However, at high allele frequencies or for gene amplification assays, real-time digital PCR is comparable with endpoint digital PCR. Conclusions This novel technology with improved sensitivity is important and needed because it addresses current issues with liquid biopsy tests. Due to limited amounts of circulating tumor DNA (ctDNA) obtained for liquid biopsy tests, few copies of mutant alleles are expected. With the lower baseline of real-time digital PCR, false negative test results from tissue biopsy would be more effectively reduced, leading to more patients receiving the targeted therapy they need for better survival.
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Affiliation(s)
- Jiachen Xu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | - Steven R. Head
- Genomics Core Facility, Scripps Research, La Jolla, CA, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core Facility, Scripps Research, Jupiter, FL, USA
| | | | | | | | | | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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8
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Kenyon NS, Willman MA, Han D, Leeman RS, Rabassa A, Diaz WL, Geary JC, Poumian-Ruiz E, Griswold AJ, Van Booven DJ, Thompson R, Ordoukhanian P, Head SR, Kenyon NM, McHenry KG, Salomon DR, Bartholomew AM, Berman DM. Extended survival versus accelerated rejection of nonhuman primate islet allografts: Effect of mesenchymal stem cell source and timing. Am J Transplant 2021; 21:3524-3537. [PMID: 34008325 PMCID: PMC9034438 DOI: 10.1111/ajt.16693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/23/2021] [Accepted: 05/06/2021] [Indexed: 01/25/2023]
Abstract
Mesenchymal stem cells (MSC) have been shown to be immunomodulatory, tissue regenerative, and graft promoting; however, several questions remain with regard to ideal MSC source and timing of administration. In this study, we utilized a rigorous preclinical model of allogeneic islet cell transplantation, incorporating reduced immune suppression and near to complete mismatch of major histocompatibility antigens between the diabetic cynomolgus monkey recipient and the islet donor, to evaluate both the graft promoting impact of MSC source, that is, derived from the islet recipient, the islet donor or an unrelated third party as well as the impact of timing. Co-transplant of MSC and islets on post-operative day 0, followed by additional IV MSC infusions in the first posttransplant month, resulted in prolongation of rejection free and overall islet survival and superior metabolic control for animals treated with recipient as compared to donor or third-party MSC. Immunological analyses demonstrated that infusion of MSC from either source did not prevent alloantibody formation to the islet or MSC donor; however, treatment with recipient MSC resulted in significant downregulation of memory T cells, decreased anti-donor T cell proliferation, and a trend toward increased Tregulatory:Tconventional ratios.
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Affiliation(s)
- Norma S. Kenyon
- Diabetes Research Institute, University of Miami, Miami, Florida, USA,Department of Surgery, University of Miami, Miami, Florida, USA,Department of Microbiology and Immunology, University of Miami, Miami, Florida, USA,Department of Biomedical Engineering, University of Miami, Miami, Florida, USA
| | | | - Dongmei Han
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Rachel S. Leeman
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Alex Rabassa
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Waldo L. Diaz
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - James C. Geary
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Ena Poumian-Ruiz
- Diabetes Research Institute, University of Miami, Miami, Florida, USA
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA,The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Derek J. Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Ryan Thompson
- The Scripps Research Institute, La Jolla, California, USA
| | - Philip Ordoukhanian
- The Scripps Research Institute, La Jolla, California, USA,The Scripps Research Institute Genomics Core Facility, La Jolla, California, USA
| | - Steven R. Head
- The Scripps Research Institute, La Jolla, California, USA,The Scripps Research Institute Genomics Core Facility, La Jolla, California, USA
| | - Norman M. Kenyon
- Diabetes Research Institute, University of Miami, Miami, Florida, USA,Department of Surgery, University of Miami, Miami, Florida, USA
| | - Kenton G. McHenry
- National Center for Supercomputing Applications, University of Illinois, Urbana-Champaign, Chicago, Illinois, USA
| | | | | | - Dora M. Berman
- Diabetes Research Institute, University of Miami, Miami, Florida, USA,Department of Surgery, University of Miami, Miami, Florida, USA
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9
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Duong K, Ou J, Li Z, Lv Z, Dong H, Hu T, Zhang Y, Hanna A, Gordon S, Crynen G, Head SR, Ordoukhanian P, Wang Y. Increased sensitivity using real-time dPCR for detection of SARS-CoV-2. Biotechniques 2021; 70:7-20. [PMID: 33222514 PMCID: PMC7888512 DOI: 10.2144/btn-2020-0133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023] Open
Abstract
A real-time dPCR system was developed to improve the sensitivity, specificity and quantification accuracy of end point dPCR. We compared three technologies - real-time qPCR, end point dPCR and real-time dPCR - in the context of SARS-CoV-2. Some improvement in limit of detection was obtained with end point dPCR compared with real-time qPCR, and the limit of detection was further improved with the newly developed real-time dPCR technology through removal of false-positive signals. Real-time dPCR showed increased linear dynamic range compared with end point dPCR based on quantitation from amplification curves. Real-time dPCR can improve the performance of TaqMan assays beyond real-time qPCR and end point dPCR with better sensitivity and specificity, absolute quantification and a wider linear range of detection.
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Affiliation(s)
- Kyra Duong
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
| | - Jiajia Ou
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Zhaoliang Li
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Zhaoqing Lv
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Hao Dong
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Tao Hu
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Yunyun Zhang
- QuestGenomics, 12 E. Mozhou Rd, U-Park, Rm P308, Jiangning, Nanjing, Jiangsu, PR China
| | - Ava Hanna
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
| | - Skyler Gordon
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Gogce Crynen
- Bioinformatics Core Facility, Scripps Research, 120 Scripps Way, Jupiter, FL 33458, USA
| | - Steven R Head
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Phillip Ordoukhanian
- Genomics Core Facility, Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA, USA
| | - Yan Wang
- Gnomegen, 6440 Lusk Blvd, D207, San Diego, CA 92121, USA
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10
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Kurian SM, Gordon S, Barrick B, Dadlani MN, Fanelli B, Cornell JB, Head SR, Marsh CL, Case J. Feasibility and Comparison Study of Fecal Sample Collection Methods in Healthy Volunteers and Solid Organ Transplant Recipients Using 16S rRNA and Metagenomics Approaches. Biopreserv Biobank 2020; 18:425-440. [PMID: 32833508 DOI: 10.1089/bio.2020.0032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The human microbiome encompasses a variety of microorganisms that change dynamically and are in close contact with the body. The microbiome influences health and homeostasis, as well as the immune system, and any significant change in this equilibrium (dysbiosis) triggers both acute and chronic health conditions. Microbiome research has surged, in part, due to advanced sequencing technologies enabling rapid, accurate, and cost-effective identification of the microbiome. A major prerequisite for stool sample collection to study the gut microbiome in longitudinal prospective studies requires standardized protocols that can be easily replicated. However, there are still significant bottlenecks to stool specimen collection that contribute to low patient retention rates in microbiome studies. These barriers are further exacerbated in solid organ transplant recipients where diarrhea is estimated to occur in up to half the patient population. We sought to test two relatively easy sample collection methods (fecal swab and wipes) and compare them to the more cumbersome "gold" standard collection method (scoop) using two different sequencing technologies (16S ribosomal RNA sequencing and shotgun metagenomics). Our comparison of the collection methods shows that both the swabs and the wipes are comparable to the scoop method in terms of bacterial abundance and diversity. The swabs, however, were closer in representation to the scoop and were easier to collect and process compared to the wipes. Potential contamination of the swab and the wipe samples by abundant skin commensals was low in our analysis. Comparison of the two sequencing technologies showed that they were complementary, and that 16S sequencing provided enough coverage to detect and differentiate between bacterial species identified in the collected samples. Our pilot study demonstrates that alternative collection methods for stool sampling are a viable option in clinical applications, such as organ transplant studies. The use of these methods may result in better patient retention recruitment rates in serial microbiome studies.
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Affiliation(s)
- Sunil M Kurian
- Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.,Scripps Center for Organ Transplantation, La Jolla, California, USA
| | - Skyler Gordon
- Genomics Core, Scripps Research, La Jolla, California, USA
| | - Bethany Barrick
- Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.,Scripps Center for Organ Transplantation, La Jolla, California, USA
| | | | | | | | - Steven R Head
- Genomics Core, Scripps Research, La Jolla, California, USA
| | - Christopher L Marsh
- Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.,Scripps Center for Organ Transplantation, La Jolla, California, USA
| | - Jamie Case
- Scripps Clinic Bio-Repository and Bio-Informatics Core, La Jolla, California, USA.,Scripps Center for Organ Transplantation, La Jolla, California, USA
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11
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019. [PMID: 31285584 DOI: 10.1038/s41564-019-04904-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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12
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Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat Microbiol 2019; 4:1727-1736. [PMID: 31285584 DOI: 10.1101/527796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 05/22/2019] [Indexed: 05/26/2023]
Abstract
Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome.
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Affiliation(s)
- Robert A Edwards
- Department of Biology, San Diego State University, San Diego, CA, USA.
- The Viral Information Institute, San Diego State University, San Diego, CA, USA.
| | - Alejandro A Vega
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Holly M Norman
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Maria Ohaeri
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Kyle Levi
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | | | - Ondrej Cinek
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Katelyn McNair
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Kyle Bibby
- Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Patrick A de Jonge
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Christelle Desnues
- MEPHI, Aix-Marseille Université, IRD, AP-HM, CNRS, IHU Méditerranée Infection, Marseille, France
- Mediterranean Institute of Oceanography, Aix-Marseille Université, Université de Toulon, CNRS, IRD, UM 110, Marseille, France
| | - Samuel L Díaz Muñoz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alexander Kurilshikov
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Karla Mazankova
- Department of Pediatrics, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - David T McCarthy
- EPHM Lab, Civil Engineering Department, Monash University, Clayton, Victoria, Australia
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - German Tapia
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology & Environment, Universidad Mayor, Huechuraba, Chile
| | - Alexander V Tyakht
- Laboratory of Bioinformatics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Department of Informational Technologies, ITMO University, Saint Petersburg, Russia
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | | | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Abeer Alassaf
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Josefa Anton
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Abigail Asangba
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Emma K Billings
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Vito Adrian Cantu
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Jane M Carlton
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Daniel Cazares
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Tess Condeff
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Mike Cranfield
- Wildlife Health Center, University of California, Davis, Davis, CA, USA
| | - Daniel A Cuevas
- Computational Sciences Research Center, San Diego State University, San Diego, CA, USA
| | - Rodrigo De la Iglesia
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Przemyslaw Decewicz
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Michael P Doane
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Lukasz Dziewit
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Bashir Mukhtar Elwasila
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Center Groningen, Groningen, The Netherlands
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Elodie Ghedin
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Kristen M Gulino
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - John M Haggerty
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Rene S Hendriksen
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Elena N Ilina
- Department of Molecular Biology and Genetics, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL, USA
| | - Thomas C Jeffries
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Juan Jofre
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Randall E Junge
- Department of Animal Health, Columbus Zoo and Aquarium, Powell, OH, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Martin Kowalewski
- Department Estacion Biologica Corrientes, Institution Museo Arg. Cs. Naturales-CONICET, Corrientes, Argentina
| | - Deepak Kumaresan
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Steven R Leigh
- Department of Anthropology, University of Colorado, Boulder, CO, USA
| | - David Lipson
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Montserrat Llagostera
- Departament de Genètica i de Microbiologia, Universitat Autònoma De Barcelona, Barcelona, Spain
| | - Julia M Maritz
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Angela McCann
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Shahar Molshanski-Mor
- Clinical Microbiology & Immunology, Sackler school of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Silvia Monteiro
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - Benjamin Moreira-Grez
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Megan Morris
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Lawrence Mugisha
- CEHA, Kampala, Uganda
- COVAB, Makerere University, Kampala, Uganda
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona, Barcelona, Spain
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Nam-Phuong Nguyen
- Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Olivia D Nigro
- College of Natural and Computational Sciences, Hawai'i Pacific University, Kaneohe, HI, USA
| | - Anders S Nilsson
- Department of Molecular Biosciences, Stockholm University, Stockholm, Sweden
| | - Taylor O'Connell
- Biological and Medical Informatics Program, San Diego State University, San Diego, CA, USA
| | - Rasha Odeh
- Department of Pediatrics, School of Medicine, University of Jordan, Amman, Jordan
| | - Andrew Oliver
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Mariana Piuri
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Aaron J Prussin Ii
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Udi Qimron
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhe-Xue Quan
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Petra Rainetova
- Centre of Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | | | | | - Kim Reasor
- Department of Biology, San Diego State University, San Diego, CA, USA
| | | | - Alessandro Rossi
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands
- Department of Biology, University of Padova, Padova, Italy
| | - Ricardo Santos
- Laboratorio de Analises, Instituto Superior Tecnico, Universidade Lisboa, Lisboa, Portugal
| | - John Shimashita
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Elyse N Stachler
- Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lars C Stene
- Department of Child Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ronan Strain
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Rebecca Stumpf
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pedro J Torres
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alan Twaddle
- Center for Genomics and Systems Biology & Department of Biology, New York University, New York, NY, USA
| | - MaryAnn Ugochi Ibekwe
- Department of Pediatrics, Federal Teaching Hospital Abakaliki, Ebonyi State University, Abakaliki, Nigeria
| | - Nicolás Villagra
- Escuela de Tecnología Médica, Universidad Andres Bello, Santiago, Chile
| | - Stephen Wandro
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Bryan White
- Carl R. Woese Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy Whiteley
- UWA School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Katrine L Whiteson
- Department of Molecular Biology & Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Henrike Zschach
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Utrecht, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.
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Prussin AJ, Torres PJ, Shimashita J, Head SR, Bibby KJ, Kelley ST, Marr LC. Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center. Microbiome 2019; 7:53. [PMID: 30935423 PMCID: PMC6444849 DOI: 10.1186/s40168-019-0672-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children's daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects. RESULTS Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses. CONCLUSIONS This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Pedro J. Torres
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - John Shimashita
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Steven R. Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Kyle J. Bibby
- Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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14
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Saravanan C, Cao Z, Head SR, Panjwani N. Analysis of differential expression of glycosyltransferases in healing corneas by glycogene microarrays. Glycobiology 2018; 29:188-189. [PMID: 30508096 DOI: 10.1093/glycob/cwy076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 11/12/2022] Open
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15
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Zhou R, Cai Y, Li Z, Shen S, Sha M, Head SR, Wang Y. A digital PCR assay development to detect EGFR T790M mutation in NSCLC patients. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.flm.2018.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Sweeney JG, Liang J, Antonopoulos A, Giovannone N, Kang S, Mondala TS, Head SR, King SL, Tani Y, Brackett D, Dell A, Murphy GF, Haslam SM, Widlund HR, Dimitroff CJ. Loss of GCNT2/I-branched glycans enhances melanoma growth and survival. Nat Commun 2018; 9:3368. [PMID: 30135430 PMCID: PMC6105653 DOI: 10.1038/s41467-018-05795-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [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: 08/14/2017] [Accepted: 07/20/2018] [Indexed: 12/30/2022] Open
Abstract
Cancer cells often display altered cell-surface glycans compared to their nontransformed counterparts. However, functional contributions of glycans to cancer initiation and progression remain poorly understood. Here, from expression-based analyses across cancer lineages, we found that melanomas exhibit significant transcriptional changes in glycosylation-related genes. This gene signature revealed that, compared to normal melanocytes, melanomas downregulate I-branching glycosyltransferase, GCNT2, leading to a loss of cell-surface I-branched glycans. We found that GCNT2 inversely correlated with clinical progression and that loss of GCNT2 increased melanoma xenograft growth, promoted colony formation, and enhanced cell survival. Conversely, overexpression of GCNT2 decreased melanoma xenograft growth, inhibited colony formation, and increased cell death. More focused analyses revealed reduced signaling responses of two representative glycoprotein families modified by GCNT2, insulin-like growth factor receptor and integrins. Overall, these studies reveal how subtle changes in glycan structure can regulate several malignancy-associated pathways and alter melanoma signaling, growth, and survival.
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Affiliation(s)
- Jenna Geddes Sweeney
- 0000 0004 0378 8294grid.62560.37Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115 USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA 02115 USA
| | - Jennifer Liang
- 0000 0004 0378 8294grid.62560.37Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Aristotelis Antonopoulos
- 0000 0001 2113 8111grid.7445.2Imperial College London, Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, London, SW7 2AZ UK
| | - Nicholas Giovannone
- 0000 0004 0378 8294grid.62560.37Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115 USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA 02115 USA
| | - Shuli Kang
- 0000000122199231grid.214007.0The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Tony S. Mondala
- 0000000122199231grid.214007.0The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Steven R. Head
- 0000000122199231grid.214007.0The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Sandra L. King
- 0000 0004 0378 8294grid.62560.37Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Yoshihiko Tani
- 0000 0004 1762 2623grid.410775.0Japanese Red Cross Kinki Block Blood Center, 7-5-17 Saito Asagi, Ibaraki-shi, Osaka 567-0085 Japan
| | - Danielle Brackett
- 0000 0004 0378 8294grid.62560.37Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Anne Dell
- 0000 0001 2113 8111grid.7445.2Imperial College London, Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, London, SW7 2AZ UK
| | - George F. Murphy
- 000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA 02115 USA ,0000 0004 0378 8294grid.62560.37Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Stuart M. Haslam
- 0000 0001 2113 8111grid.7445.2Imperial College London, Division of Molecular Biosciences, Faculty of Natural Sciences, Biochemistry Building, London, SW7 2AZ UK
| | - Hans R. Widlund
- 0000 0004 0378 8294grid.62560.37Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115 USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA 02115 USA
| | - Charles J. Dimitroff
- 0000 0004 0378 8294grid.62560.37Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115 USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA 02115 USA
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Abstract
Background The Jurkat cell line has an extensive history as a model of T cell signaling. But at the turn of the 21st century, some expression irregularities were observed, raising doubts about how closely the cell line paralleled normal human T cells. While numerous expression deficiencies have been described in Jurkat, genetic explanations have only been provided for a handful of defects. Results Here, we report a comprehensive catolog of genomic variation in the Jurkat cell line based on whole-genome sequencing. With this list of all detectable, non-reference sequences, we prioritize potentially damaging mutations by mining public databases for functional effects. We confirm documented mutations in Jurkat and propose links from detrimental gene variants to observed expression abnormalities in the cell line. Conclusions The Jurkat cell line harbors many mutations that are associated with cancer and contribute to Jurkat’s unique characteristics. Genes with damaging mutations in the Jurkat cell line are involved in T-cell receptor signaling (PTEN, INPP5D, CTLA4, and SYK), maintenance of genome stability (TP53, BAX, and MSH2), and O-linked glycosylation (C1GALT1C1). This work ties together decades of molecular experiments and serves as a resource that will streamline both the interpretation of past research and the design of future Jurkat studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-4718-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louis Gioia
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA.
| | - Azeem Siddique
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Steven R Head
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Daniel R Salomon
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA
| | - Andrew I Su
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, 92037, USA
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Abstract
Many methods exist for examining CpG DNA methylation. However, many of these are qualitative, laborious to apply to a large number of genes simultaneously, or are not easy to target to specific regions of interest. Microdroplet PCR-based bisulfite sequencing allows for quantitative single base resolution analysis of investigator selected regions of interest. Following bisulfite conversion of genomic DNA, targeted microdroplet PCR is conducted with custom primer libraries. Samples are then fragmented, concatenated, and sequenced by high-throughput sequencing. The most recent technology allows for this method to be conducted with as little as 250 ng of bisulfite-converted DNA. The primary advantage of this method is the ability to hand-select the targeted regions covered by up to 10,000 amplicons of 500-600 bp. Moreover, the nature of microdroplet PCR virtually eliminates PCR bias and allows for the amplification of all targets simultaneously in a single tube.
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Affiliation(s)
- H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Traver Hart
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada, M5G 1L6
| | - Steven R Head
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Ali Torkamani
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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Buzby JS, Williams SA, Schaffer L, Head SR, Nugent DJ. Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome. Cancer Genet 2017; 211:9-17. [PMID: 28279309 DOI: 10.1016/j.cancergen.2017.01.001] [Citation(s) in RCA: 2] [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: 07/21/2016] [Revised: 12/14/2016] [Accepted: 01/06/2017] [Indexed: 01/01/2023]
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder where an oncogenic TP53 germline mutation is passed from parent to child. Tumor protein p53 is a key tumor suppressor regulating cell cycle arrest in response to DNA damage. Paradoxically, some mutant TP53 carriers remain unaffected, while their children develop cancer within the first few years of life. To address this paradox, response to UV stress was compared in dermal fibroblasts (dFb) from an affected LFS patient vs. their unaffected carrier parent. UV induction of CDKN1A/p21, a regulatory target of p53, in LFS patient dFb was significantly reduced compared to the unaffected parent. UV exposure also induced significantly greater p53[Ser15]-phosphorylation in LFS patient dFb, a reported property of some mutant p53 variants. Taken together, these results suggested that unaffected parental dFb may express an increased proportion of wild-type vs. mutant p53. Indeed, a significantly increased ratio of wild-type to mutant TP53 allele-specific expression in the unaffected parent dFb was confirmed by RT-PCR-RFLP and RNA-seq analysis. Hence, allele-specific expression of wild-type TP53 may allow an unaffected parent to mount a response to genotoxic stress more characteristic of homozygous wild-type TP53 individuals than their affected offspring, providing protection from the oncogenesis associated with LFS.
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Affiliation(s)
- Jeffrey S Buzby
- Hematology Research and Advanced Diagnostics Laboratories, CHOC Children's Hospital of Orange County, Orange, CA, USA.
| | - Shirley A Williams
- Hematology Research and Advanced Diagnostics Laboratories, CHOC Children's Hospital of Orange County, Orange, CA, USA
| | - Lana Schaffer
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven R Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Diane J Nugent
- Hematology Research and Advanced Diagnostics Laboratories, CHOC Children's Hospital of Orange County, Orange, CA, USA; Division of Hematology, CHOC Children's Hospital of Orange County, Orange, CA, USA; Division of Pediatric Hematology, School of Medicine, University of California at Irvine, Orange, CA, USA
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20
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Jin HY, Oda H, Chen P, Yang C, Zhou X, Kang SG, Valentine E, Kefauver JM, Liao L, Zhang Y, Gonzalez-Martin A, Shepherd J, Morgan GJ, Mondala TS, Head SR, Kim PH, Xiao N, Fu G, Liu WH, Han J, Williamson JR, Xiao C. Differential Sensitivity of Target Genes to Translational Repression by miR-17~92. PLoS Genet 2017; 13:e1006623. [PMID: 28241004 PMCID: PMC5348049 DOI: 10.1371/journal.pgen.1006623] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/13/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are thought to exert their functions by modulating the expression of hundreds of target genes and each to a small degree, but it remains unclear how small changes in hundreds of target genes are translated into the specific function of a miRNA. Here, we conducted an integrated analysis of transcriptome and translatome of primary B cells from mutant mice expressing miR-17~92 at three different levels to address this issue. We found that target genes exhibit differential sensitivity to miRNA suppression and that only a small fraction of target genes are actually suppressed by a given concentration of miRNA under physiological conditions. Transgenic expression and deletion of the same miRNA gene regulate largely distinct sets of target genes. miR-17~92 controls target gene expression mainly through translational repression and 5’UTR plays an important role in regulating target gene sensitivity to miRNA suppression. These findings provide molecular insights into a model in which miRNAs exert their specific functions through a small number of key target genes. MicroRNAs (miRNAs) are small RNAs encoded by our genome. Each miRNA binds hundreds of target mRNAs and performs specific functions. It is thought that miRNAs exert their function by reducing the expression of all these target genes and each to a small degree. However, these target genes often have very diverse functions. It has been unclear how small changes in hundreds of target genes with diverse functions are translated into the specific function of a miRNA. Here we take advantage of recent technical advances to globally examine the mRNA and protein levels of 868 target genes regulated by miR-17~92, the first oncogenic miRNA, in mutant mice with transgenic overexpression or deletion of this miRNA gene. We show that miR-17~92 regulates target gene expression mainly at the protein level, with little effect on mRNA. Surprisingly, only a small fraction of target genes respond to miR-17~92 expression changes. Further studies show that the sensitivity of target genes to miR-17~92 is determined by a non-coding region of target mRNA. Our findings demonstrate that not every target gene is equal, and suggest that the function of a miRNA is mediated by a small number of key target genes.
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Affiliation(s)
- Hyun Yong Jin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Hiroyo Oda
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pengda Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Chao Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiaojuan Zhou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Seung Goo Kang
- Division of Biomedical Convergence/Institute of Bioscience & Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Elizabeth Valentine
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jennifer M. Kefauver
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lujian Liao
- Shanghai Key Laboratory of Regulatory Biology, Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), School of Life Sciences, East China Normal University, Shanghai, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Alicia Gonzalez-Martin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jovan Shepherd
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
| | - Gareth J. Morgan
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tony S. Mondala
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pyeung-Hyeun Kim
- Department of Molecular Bioscience/Institute of Bioscience & Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Nengming Xiao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Guo Fu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiahuai Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Changchun Xiao
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian, China
- * E-mail:
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Sweeney JG, Liang J, Giovannone N, Schaffer L, Head SR, Antonopoulos A, Haslam SM, Widlund HR, Dimitroff CJ. “I”-branched Carbohydrates Negatively Regulate Galectin-3-binding and Melanoma Malignancy. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.144.17] [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] [Indexed: 01/03/2023]
Abstract
Abstract
Malignant transformation is often associated with aberrant glycosylation of cell surface proteins. Commonly observed changes in glycan structures include increased presence of sialic acid, altered expression of mucins, and abnormal branching of N-glycans. Increasing evidence supports the idea that the presence of certain glycans correlate with cancer progression by affecting tumor cell invasiveness, ability to bind pro-tumorigenic galectins, and by promoting metastasis to distant organs. Taking this relationship into consideration, we conducted MALDI-TOF mass spectrometry on cell surface glycans as well as glycomic gene profiling from normal human epidermal melanocytes (NHEM) and human metastatic melanoma (MM) cells. We found that a defining feature between NHEMs and MMs was the relative level of “I”-branched and “i”-linear poly-N-acetyllactosamines on N-glycans. While NHEM predominantly expressed “I”-branched structures, MMs expressed “i”-linear modified N-glycans. Furthermore, glycomic gene profiling and confirmatory RT-qPCR data showed that the “I”-branching β1,6 N-acetylglucosaminyltransferase 2, GCNT2, is decreased in MM compared with NHEMs. With regards to its role in malignancy, we found that GCNT2 functioned as a negative regulator of galectin-3 (Gal-3) binding. GCNT2 overexpression in human MM cells inhibited Gal-3 mediated ERK1/2 phosphorylation and significantly reduced primary tumor growth. While GCNT2 knockdown in human MM cells promoted Gal-3 mediated ERK1/2 phosphorylation and significantly enhanced primary tumor growth. These findings highlight new glycobiological insights into melanoma development, implicating GCNT2 as a negative regulator of Gal-3 binding and melanoma malignancy.
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Carney K, Chang YMR, Wilson S, Calnan C, Reddy PS, Chan WY, Gilmartin T, Hernandez G, Schaffer L, Head SR, Morley J, de Mestre A, Affleck K, Garden OA. Regulatory T-cell-intrinsic amphiregulin is dispensable for suppressive function. J Allergy Clin Immunol 2016; 137:1907-1909. [PMID: 27040371 PMCID: PMC4889774 DOI: 10.1016/j.jaci.2016.01.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/15/2015] [Accepted: 01/15/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Katharine Carney
- Department of Clinical Science and Services, Immune Regulation Laboratory, Royal Veterinary College, London, United Kingdom
| | - Yu-Mei Ruby Chang
- Research Support Office, Royal Veterinary College, London, United Kingdom
| | - Stephen Wilson
- GlaxoSmithKline, Platform Technology and Science R&D, Stevenage, Hertfordshire, United Kingdom
| | - Clare Calnan
- Department of Clinical Science and Services, Immune Regulation Laboratory, Royal Veterinary College, London, United Kingdom
| | - Pala S Reddy
- Department of Clinical Science and Services, Immune Regulation Laboratory, Royal Veterinary College, London, United Kingdom
| | - Win-Yan Chan
- Department of Clinical Science and Services, Immune Regulation Laboratory, Royal Veterinary College, London, United Kingdom
| | | | | | | | | | - Joanne Morley
- GlaxoSmithKline, Respiratory R&D, Stevenage, Hertfordshire, United Kingdom
| | - Amanda de Mestre
- Department of Comparative Biomedical Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire, United Kingdom
| | - Karen Affleck
- GlaxoSmithKline, Respiratory R&D, Stevenage, Hertfordshire, United Kingdom
| | - Oliver A Garden
- Department of Clinical Science and Services, Immune Regulation Laboratory, Royal Veterinary College, London, United Kingdom.
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Whisenant TC, Peralta ER, Aarreberg LD, Gao NJ, Head SR, Ordoukhanian P, Williamson JR, Salomon DR. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells. PLoS One 2015; 10:e0144409. [PMID: 26641092 PMCID: PMC4671683 DOI: 10.1371/journal.pone.0144409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 10/16/2015] [Indexed: 12/22/2022] Open
Abstract
Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. We immunoprecipitated U2AF2 to identify what mRNA transcripts were bound as a function of activation by TCR crosslinking and costimulation. In parallel, mass spectrometry revealed the proteins incorporated into the U2AF2-centered RNA/protein interactome. Molecules that retained interaction with the U2AF2 complex after RNAse treatment were designated as "central" interactome members (CIMs). Mass spectrometry also identified a second class of activation-induced proteins, "peripheral" interactome members (PIMs), that bound to the same transcripts but were not in physical association with U2AF2 or its partners. siRNA knockdown of two CIMs and two PIMs caused changes in activation marker expression, cytokine secretion, and gene expression that were unique to each protein and mapped to pathways associated with key aspects of T cell activation. While knocking down the PIM, SYNCRIP, impacts a limited but immunologically important set of U2AF2-bound transcripts, knockdown of U2AF1 significantly impairs assembly of the majority of protein and mRNA components in the activation-induced interactome. These results demonstrated that CIMs and PIMs, either directly or indirectly through RNA, assembled into activation-induced U2AF2 complexes and play roles in post-transcriptional regulation of genes related to cytokine secretion. These data suggest an additional layer of regulation mediated by the activation-induced assembly of RNA splicing interactomes that is important for understanding T cell activation.
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Affiliation(s)
- Thomas C. Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Eigen R. Peralta
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lauren D. Aarreberg
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Nina J. Gao
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Phillip Ordoukhanian
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jamie R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Daniel R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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24
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Jin HY, Gonzalez-Martin A, Miletic AV, Lai M, Knight S, Sabouri-Ghomi M, Head SR, Macauley MS, Rickert RC, Xiao C. Transfection of microRNA Mimics Should Be Used with Caution. Front Genet 2015; 6:340. [PMID: 26697058 PMCID: PMC4667072 DOI: 10.3389/fgene.2015.00340] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/12/2015] [Indexed: 12/19/2022] Open
Abstract
Transient transfection of chemically synthesized microRNA (miRNA) mimics is being used extensively to study the functions and mechanisms of endogenous miRNAs. However, it remains unclear whether transfected miRNAs behave similarly to endogenous miRNAs. Here we show that transient transfection of miRNA mimics into HeLa cells by a commonly used method led to the accumulation of high molecular weight RNA species and a few hundred fold increase in mature miRNA levels. In contrast, expression of the same miRNAs through lentiviral infection or plasmid transfection of HeLa cells, transgenic expression in primary lymphocytes, and endogenous overexpression in lymphoma and leukemia cell lines did not lead to the appearance of high molecular weight RNA species. The increase of mature miRNA levels in these cells was below 10-fold, which was sufficient to suppress target gene expression and to drive lymphoma development in mice. Moreover, transient transfection of miRNA mimics at high concentrations caused non-specific alterations in gene expression, while at low concentrations achieved expression levels comparable to other methods but failed to efficiently suppress target gene expression. Small RNA deep sequencing analysis revealed that the guide strands of miRNA mimics were frequently mutated, while unnatural passenger strands of some miRNA mimics accumulated to high levels. The high molecular weight RNA species were a heterogeneous mixture of several classes of RNA species generated by concatemerization, 5'- and 3'-end tailing of miRNA mimics. We speculate that the supraphysiological levels of mature miRNAs and these artifactual RNA species led to non-specific changes in gene expression. Our results have important implications for the design and interpretation of experiments primarily employing transient transfection of miRNA mimics.
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Affiliation(s)
- Hyun Yong Jin
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA ; Kellogg School of Science and Technology, The Scripps Research Institute La Jolla, CA, USA
| | - Alicia Gonzalez-Martin
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
| | - Ana V Miletic
- Program on Immunity and Pathogenesis, Sanford-Burnham Medical Research Institute La Jolla, CA, USA
| | - Maoyi Lai
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
| | - Sarah Knight
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA ; Department of Cell and Molecular Biology, The Scripps Research Institute La Jolla, CA, USA ; Department of Chemical Physiology, The Scripps Research Institute La Jolla, CA, USA
| | - Mohsen Sabouri-Ghomi
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
| | - Steven R Head
- Next Generation Sequencing Core, The Scripps Research Institute La Jolla, CA, USA
| | - Matthew S Macauley
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA ; Department of Cell and Molecular Biology, The Scripps Research Institute La Jolla, CA, USA ; Department of Chemical Physiology, The Scripps Research Institute La Jolla, CA, USA
| | - Robert C Rickert
- Program on Immunity and Pathogenesis, Sanford-Burnham Medical Research Institute La Jolla, CA, USA
| | - Changchun Xiao
- Department of Immunology and Microbial Science, The Scripps Research Institute La Jolla, CA, USA
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25
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Routh A, Head SR, Ordoukhanian P, Johnson JE. ClickSeq: Fragmentation-Free Next-Generation Sequencing via Click Ligation of Adaptors to Stochastically Terminated 3'-Azido cDNAs. J Mol Biol 2015; 427:2610-6. [PMID: 26116762 DOI: 10.1016/j.jmb.2015.06.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 10/23/2022]
Abstract
We present a simple method called "ClickSeq" for NGS (next-generation sequencing) library synthesis that uses click chemistry rather than enzymatic reactions for the ligation of Illumina sequencing adaptors. In ClickSeq, randomly primed reverse transcription reactions are supplemented with azido-2',3'-dideoxynucleotides that randomly terminate DNA synthesis and release 3'-azido-blocked cDNA fragments in a process akin to dideoxy-Sanger sequencing. Purified fragments are "click ligated" via copper-catalyzed alkyne-azide cycloaddition to DNA oligos modified with a 5'-alkyne group. This generates ssDNA molecules containing an unnatural triazole-linked DNA backbone that is sufficiently biocompatible for PCR amplification to generate a cDNA library for RNAseq. Here, we analyze viral RNAs and mRNA to demonstrate that ClickSeq produces unbiased NGS libraries with low error rates comparable to standard methods. Importantly, ClickSeq is robust against common artifacts of NGS such as chimera formation and artifactual recombination with fewer than 3 aberrant events detected per million reads.
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Affiliation(s)
- Andrew Routh
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Steven R Head
- The Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Phillip Ordoukhanian
- The Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Head SR, Mondala T, Gelbart T, Ordoukhanian P, Chappel R, Hernandez G, Salomon DR. RNA purification and expression analysis using microarrays and RNA deep sequencing. Methods Mol Biol 2014; 1034:385-403. [PMID: 23775753 DOI: 10.1007/978-1-62703-493-7_25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Transcriptome analysis or global gene expression profiling is a powerful tool for discovery as well as -understanding biological mechanisms in health and disease. We present in this chapter a description of methods used to isolate mRNA from cells and tissues that has been optimized for preservation of RNA quality using clinical materials and implemented successfully in several large, multicenter studies by the authors. In addition, two methods, gene expression microarrays and RNAseq, are described for mRNA profiling of cells and tissues from clinical or laboratory sources.
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Affiliation(s)
- Steven R Head
- Microarray and Next Generation Sequencing Core Facility, The Scripps Research Institute, La Jolla, CA, USA
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27
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Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, Zhang D, Han T, Yang CS, Cunningham TJ, Head SR, Duester G, Dong PDS, Rana TM. An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 2014; 53:1005-19. [PMID: 24530304 DOI: 10.1016/j.molcel.2014.01.021] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/03/2013] [Accepted: 01/10/2014] [Indexed: 11/29/2022]
Abstract
Here, we generated a genome-scale shRNA library targeting long intergenic noncoding RNAs (lincRNAs) in the mouse. We performed an unbiased loss-of-function study in mouse embryonic stem cells (mESCs) and identified 20 lincRNAs involved in the maintenance of pluripotency. Among these, TUNA (Tcl1 Upstream Neuron-Associated lincRNA, or megamind) was required for pluripotency and formed a complex with three RNA-binding proteins (RBPs). The TUNA-RBP complex was detected at the promoters of Nanog, Sox2, and Fgf4, and knockdown of TUNA or the individual RBPs inhibited neural differentiation of mESCs. TUNA showed striking evolutionary conservation of both sequence- and CNS-restricted expression in vertebrates. Accordingly, knockdown of tuna in zebrafish caused impaired locomotor function, and TUNA expression in the brains of Huntington's disease patients was significantly associated with disease grade. Our results suggest that the lincRNA TUNA plays a vital role in pluripotency and neural differentiation of ESCs and is associated with neurological function of adult vertebrates.
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Affiliation(s)
- Nianwei Lin
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kung-Yen Chang
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Zhonghan Li
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Keith Gates
- Program for Genetic Disease, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Zacharia A Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jason Dang
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Danhua Zhang
- Program for Genetic Disease, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tianxu Han
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Chao-Shun Yang
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Thomas J Cunningham
- Program for Development and Aging, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Steven R Head
- The Scripps Research Institute, Microarray and NGS Core Facility, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Gregg Duester
- Program for Development and Aging, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - P Duc Si Dong
- Program for Genetic Disease, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tariq M Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA; Department of Pediatrics, Rady Children's Hospital San Diego and University of California San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA.
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Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 2014; 56:61-4, 66, 68, passim. [PMID: 24502796 DOI: 10.2144/000114133] [Citation(s) in RCA: 334] [Impact Index Per Article: 33.4] [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: 01/14/2014] [Accepted: 01/21/2014] [Indexed: 01/03/2023] Open
Abstract
High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries from DNA and RNA sources. Factors such as the quantity and physical characteristics of the RNA or DNA source material as well as the desired application (i.e., genome sequencing, targeted sequencing, RNA-seq, ChIP-seq, RIP-seq, and methylation) are addressed in the context of preparing high quality sequencing libraries. In addition, the current methods for preparing NGS libraries from single cells are also discussed.
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Affiliation(s)
- Steven R Head
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA
| | - H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Thomas Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S. Technical variations in low-input RNA-seq methodologies. Sci Rep 2014; 4:3678. [PMID: 24419370 PMCID: PMC3890974 DOI: 10.1038/srep03678] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [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: 09/12/2013] [Accepted: 12/13/2013] [Indexed: 12/16/2022] Open
Abstract
Recent advances in RNA-seq methodologies from limiting amounts of mRNA have facilitated the characterization of rare cell-types in various biological systems. So far, however, technical variations in these methods have not been adequately characterized, vis-à-vis sensitivity, starting with reduced levels of mRNA. Here, we generated sequencing libraries from limiting amounts of mRNA using three amplification-based methods, viz. Smart-seq, DP-seq and CEL-seq, and demonstrated significant technical variations in these libraries. Reduction in mRNA levels led to inefficient amplification of the majority of low to moderately expressed transcripts. Furthermore, noise in primer hybridization and/or enzyme incorporation was magnified during the amplification step resulting in significant distortions in fold changes of the transcripts. Consequently, the majority of the differentially expressed transcripts identified were either high-expressed and/or exhibited high fold changes. High technical variations ultimately masked subtle biological differences mandating the development of improved amplification-based strategies for quantitative transcriptomics from limiting amounts of mRNA.
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Affiliation(s)
- Vipul Bhargava
- Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, California, USA
| | - Steven R Head
- Next Generation Sequencing Core Facility, The Scripps Research Institute, La Jolla, California, USA
| | - Phillip Ordoukhanian
- Next Generation Sequencing Core Facility, The Scripps Research Institute, La Jolla, California, USA
| | - Mark Mercola
- 1] Department of Bioengineering, University of California at San Diego, La Jolla, California, USA [2] Sanford-Burnham Medical Research Institute, La Jolla, California, USA
| | - Shankar Subramaniam
- 1] Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, California, USA [2] Department of Bioengineering, University of California at San Diego, La Jolla, California, USA [3] Departments of Cellular and Molecular Medicine and Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, USA
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Soetaert SSA, Van Neste CMF, Vandewoestyne ML, Head SR, Goossens A, Van Nieuwerburgh FCW, Deforce DLD. Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua. BMC Plant Biol 2013; 13:220. [PMID: 24359620 PMCID: PMC3878173 DOI: 10.1186/1471-2229-13-220] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 12/12/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND The medicinal plant Artemisia annua is covered with filamentous trichomes and glandular, artemisinin producing trichomes. A high artemisinin supply is needed at a reduced cost for treating malaria. Artemisinin production in bioreactors can be facilitated if a better insight is obtained in the biosynthesis of artemisinin and other metabolites. Therefore, metabolic activities of glandular and filamentous trichomes were investigated at the transcriptome level. RESULTS By laser pressure catapulting, glandular and filamentous trichomes as well as apical and sub-apical cells from glandular trichomes were collected and their transcriptome was sequenced using Illumina RNA-Seq. A de novo transcriptome was assembled (Trinity) and studied with a differential expression analysis (edgeR).A comparison of the transcriptome from glandular and filamentous trichomes shows that MEP, MVA, most terpene and lipid biosynthesis pathways are significantly upregulated in glandular trichomes. Conversely, some transcripts coding for specific sesquiterpenoid and triterpenoid enzymes such as 8-epi-cedrol synthase and an uncharacterized oxidosqualene cyclase were significantly upregulated in filamentous trichomes. All known artemisinin biosynthesis genes are upregulated in glandular trichomes and were detected in both the apical and sub-apical cells of the glandular trichomes. No significant differential expression could be observed between the apical and sub-apical cells. CONCLUSIONS Our results underscore the vast metabolic capacities of A. annua glandular trichomes but nonetheless point to the existence of specific terpene metabolic pathways in the filamentous trichomes. Candidate genes that might be involved in artemisinin biosynthesis are proposed based on their putative function and their differential expression level.
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Affiliation(s)
- Sandra SA Soetaert
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Christophe MF Van Neste
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Mado L Vandewoestyne
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Steven R Head
- Next Generation Sequencing Core, The Scripps Research Institute, 10550N. Torrey Pines Rd, La Jolla, CA 92037 United States of America
| | - Alain Goossens
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Filip CW Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Dieter LD Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
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31
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Ruwona TB, Mcbride R, Chappel R, Head SR, Ordoukhanian P, Burton DR, Law M. Optimization of peptide arrays for studying antibodies to hepatitis C virus continuous epitopes. J Immunol Methods 2013; 402:35-42. [PMID: 24269751 DOI: 10.1016/j.jim.2013.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/22/2013] [Accepted: 11/12/2013] [Indexed: 02/02/2023]
Abstract
Accurate and in-depth mapping of antibody responses is of great value in vaccine and antibody research. Using hepatitis C virus (HCV) as a model, we developed an affordable and high-throughput microarray-based assay for mapping antibody specificities to continuous antibody epitopes of HCV at high resolution. Important parameters in the chemistry for conjugating peptides/antigens to the array surface, the array layout, fluorophore choice and the methods for data analysis were investigated. Microscopic glass slide pre-coated with N-Hydroxysuccinimide (NHS)-ester (Slide H) was the preferred surface for conjugation of aminooxy-tagged peptides. This combination provides a simple chemical means to orient the peptides to the conjugation surface via an orthogonal covalent linkage at the N- or C-terminus of each peptide. The addition of polyvinyl alcohol to printing buffer gave uniform spot morphology and improved sensitivity and specificity of binding signals. Libraries of overlapping peptides covering the HCV E1 and E2 glycoprotein polypeptides (15-mer, 10 amino acids overlap) of 6 major HCV genotypes and the entire polypeptide sequence of the prototypic strain H77 were synthesized and printed in quadruplets in the assays. The utility of the peptide arrays was confirmed using HCV monoclonal antibodies (mAbs) specific to known continuous epitopes and immune sera of rabbits immunized with HCV antigens. The methods developed here can be easily adapted to studying antibody responses to antigens relevant in vaccine and autoimmune research.
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Affiliation(s)
- Tinashe B Ruwona
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Ryan Mcbride
- Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, United States
| | - Rebecca Chappel
- Center for Protein and Nucleic Acids Research, The Scripps Research Institute, La Jolla, CA, United States
| | - Steven R Head
- Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, United States
| | - Phillip Ordoukhanian
- Center for Protein and Nucleic Acids Research, The Scripps Research Institute, La Jolla, CA, United States
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Mansun Law
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.
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Aggelis V, Craven RA, Peng J, Harnden P, Schaffer L, Hernandez GE, Head SR, Maher ER, Tonge R, Selby PJ, Banks RE. VHL-dependent regulation of a β-dystroglycan glycoform and glycogene expression in renal cancer. Int J Oncol 2013; 43:1368-76. [PMID: 23970118 PMCID: PMC3823392 DOI: 10.3892/ijo.2013.2066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 06/26/2013] [Accepted: 07/30/2013] [Indexed: 12/27/2022] Open
Abstract
Identification of novel biomarkers and targets in renal cell carcinoma (RCC) remains a priority and one cellular compartment that is a rich potential source of such molecules is the plasma membrane. A shotgun proteomic analysis of cell surface proteins enriched by cell surface biotinylation and avidin affinity chromatography was explored using the UMRC2- renal cancer cell line, which lacks von Hippel-Lindau (VHL) tumour suppressor gene function, to determine whether proteins of interest could be detected. Of the 814 proteins identified ~22% were plasma membrane or membrane-associated, including several with known associations with cancer. This included β-dystroglycan, the transmembrane subunit of the DAG1 gene product. VHL-dependent changes in the form of β-dystroglycan were detected in UMRC2-/+VHL transfectants. Deglycosylation experiments showed that this was due to differential sialylation. Analysis of normal kidney cortex and conventional RCC tissues showed that a similar change also occurred in vivo. Investigation of the expression of genes involved in glycosylation in UMRC2-/+VHL cells using a focussed microarray highlighted a number of enzymes involved in sialylation; upregulation of bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) was validated in UMRC2- cells compared with their +VHL counterparts and also found in conventional RCC tissue. These results implicate VHL in the regulation of glycosylation and raise interesting questions regarding the extent and importance of such changes in RCC.
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Affiliation(s)
- Vassilis Aggelis
- Cancer Research UK Centre, Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds LS9 7TF, UK
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Dosanjh A, Robison E, Mondala T, Head SR, Salomon DR, Kurian SM. Genomic meta-analysis of growth factor and integrin pathways in chronic kidney transplant injury. BMC Genomics 2013; 14:275. [PMID: 23617750 PMCID: PMC3644490 DOI: 10.1186/1471-2164-14-275] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [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: 10/18/2012] [Accepted: 04/18/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Chronic Allograft Nephropathy (CAN) is a clinical entity of progressive kidney transplant injury. The defining histology is tubular atrophy with interstitial fibrosis (IFTA). Using a meta-analysis of microarrays from 84 kidney transplant biopsies, we revealed growth factor and integrin adhesion molecule pathways differentially expressed and correlated with histological progression. A bioinformatics approach mining independent datasets leverages new and existing data to identify correlative changes in integrin and growth factor signaling pathways. RESULTS Analysis of CAN/IFTA Banff grades showed that hepatocyte growth factor (HGF), and epidermal growth factor (EGF) pathways are significantly differentially expressed in all classes of CAN/IFTA. MAPK-dependent pathways were also significant. However, the TGFβ pathways, albeit present, failed to differentiate CAN/IFTA progression. The integrin subunits β8, αv, αμ and β5 are differentially expressed, but β1, β6 and α6 specifically correlate with progression of chronic injury. Results were validated using our published proteomic profiling of CAN/IFTA. CONCLUSIONS CAN/IFTA with chronic kidney injury is characterized by expression of distinct growth factors and specific integrin adhesion molecules as well as their canonical signaling pathways. Drug target mapping suggests several novel candidates for the next generation of therapeutics to prevent or treat progressive transplant dysfunction with interstitial fibrosis.
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Affiliation(s)
- Amrita Dosanjh
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Verma-Gaur J, Torkamani A, Schaffer L, Head SR, Schork NJ, Feeney AJ. Noncoding transcription within the Igh distal V(H) region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells. Proc Natl Acad Sci U S A 2012; 109:17004-9. [PMID: 23027941 PMCID: PMC3479473 DOI: 10.1073/pnas.1208398109] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Noncoding sense and antisense germ-line transcription within the Ig heavy chain locus precedes V(D)J recombination and has been proposed to be associated with Igh locus accessibility, although its precise role remains elusive. However, no global analysis of germ-line transcription throughout the Igh locus has been done. Therefore, we performed directional RNA-seq, demonstrating the locations and extent of both sense and antisense transcription throughout the Igh locus. Surprisingly, the majority of antisense transcripts are localized around two Pax5-activated intergenic repeat (PAIR) elements in the distal IghV region. Importantly, long-distance loops measured by chromosome conformation capture (3C) are observed between these two active PAIR promoters and Eμ, the start site of Iμ germ-line transcription, in a lineage- and stage-specific manner, even though this antisense transcription is Eμ-independent. YY1(-/-) pro-B cells are greatly impaired in distal V(H) gene rearrangement and Igh locus compaction, and we demonstrate that YY1 deficiency greatly reduces antisense transcription and PAIR-Eμ interactions. ChIP-seq shows high level YY1 binding only at Eμ, but low levels near some antisense promoters. PAIR-Eμ interactions are not disrupted by DRB, which blocks transcription elongation without disrupting transcription factories once they are established, but the looping is reduced after heat-shock treatment, which disrupts transcription factories. We propose that transcription-mediated interactions, most likely at transcription factories, initially compact the Igh locus, bringing distal V(H) genes close to the DJ(H) rearrangement which is adjacent to Eμ. Therefore, we hypothesize that one key role of noncoding germ-line transcription is to facilitate locus compaction, allowing distal V(H) genes to undergo efficient rearrangement.
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Affiliation(s)
- Jiyoti Verma-Gaur
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Ali Torkamani
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, and The Scripps Translational Science Institute, La Jolla, CA 92037; and
| | - Lana Schaffer
- Next Generation Sequencing Core Facility, The Scripps Research Institute, La Jolla, CA 92037
| | - Steven R. Head
- Next Generation Sequencing Core Facility, The Scripps Research Institute, La Jolla, CA 92037
| | - Nicholas J. Schork
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, and The Scripps Translational Science Institute, La Jolla, CA 92037; and
| | - Ann J. Feeney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
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35
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Gouveia R, Schaffer L, Papp S, Grammel N, Kandzia S, Head SR, Kleene R, Schachner M, Conradt HS, Costa J. Expression of glycogenes in differentiating human NT2N neurons. Downregulation of fucosyltransferase 9 leads to decreased Lewis(x) levels and impaired neurite outgrowth. Biochim Biophys Acta Gen Subj 2012; 1820:2007-19. [PMID: 23000574 DOI: 10.1016/j.bbagen.2012.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 09/07/2012] [Accepted: 09/10/2012] [Indexed: 12/12/2022]
Abstract
BACKGROUND Several glycan structures are functionally relevant in biological events associated with differentiation and regeneration which occur in the central nervous system. Here we have analysed the glycogene expression and glycosylation patterns during human NT2N neuron differentiation. We have further studied the impact of downregulating fucosyltransferase 9 (FUT9) on neurite outgrowth. METHODS The expression of glycogenes in human NT2N neurons differentiating from teratocarcinoma NTERA-2/cl.D1 cells has been analysed using the GlycoV4 GeneChip expression microarray. Changes in glycosylation have been monitored by immunoblot, immunofluorescence microscopy, HPLC and MALDI-TOF MS. Peptide mass fingerprinting and immunoprecipitation have been used for protein identification. FUT9 was downregulated using silencing RNA. RESULTS AND CONCLUSIONS One hundred twelve mRNA transcripts showed statistically significant up-regulation, including the genes coding for proteins involved in the synthesis of the Lewis(x) motif (FUT9), polysialic acid (ST8SIA2 and ST8SIA4) and HNK-1 (B3GAT2). Accordingly, increased levels of the corresponding carbohydrate epitopes have been observed. The Lewis(x) structure was found in a carrier glycoprotein that was identified as the CRA-a isoform of human neural cell adhesion molecule 1. Downregulation of FUT9 caused significant decreases in the levels of Lewis(x), as well as GAP-43, a marker of neurite outgrowth. Concomitantly, a reduction in neurite formation and outgrowth has been observed that was reversed by FUT9 overexpression. GENERAL SIGNIFICANCE These results provided information about the regulation of glycogenes during neuron differentiation and they showed that the Lewis(x) motif plays a functional role in neurite outgrowth from human neurons.
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Affiliation(s)
- Ricardo Gouveia
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Oeiras, Portugal
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Gomes J, Magalhães A, Carvalho AS, Hernandez GE, Papp SL, Head SR, Michel V, David L, Gärtner F, Touati E, Reis CA. Glycophenotypic alterations induced by Pteridium aquilinum in mice gastric mucosa: synergistic effect with Helicobacter pylori infection. PLoS One 2012; 7:e38353. [PMID: 22719879 PMCID: PMC3374793 DOI: 10.1371/journal.pone.0038353] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 05/08/2012] [Indexed: 01/13/2023] Open
Abstract
The bracken fern Pteridium aquilinum is a plant known to be carcinogenic to animals. Epidemiological studies have shown an association between bracken fern exposure and gastric cancer development in humans. The biological effects of exposure to this plant within the gastric carcinogenesis process are not fully understood. In the present work, effects in the gastric mucosa of mice treated with Pteridium aquilinum were evaluated, as well as molecular mechanisms underlying the synergistic role with Helicobacter pylori infection. Our results showed that exposure to Pteridium aquilinum induces histomorphological modifications including increased expression of acidic glycoconjugates in the gastric mucosa. The transcriptome analysis of gastric mucosa showed that upon exposure to Pteridium aquilinum several glycosyltransferase genes were differently expressed, including Galntl4, C1galt1 and St3gal2, that are mainly involved in the biosynthesis of simple mucin-type carbohydrate antigens. Concomitant treatment with Pteridium aquilinum and infection with Helicobacter pylori also resulted in differently expressed glycosyltransferase genes underlying the biosynthesis of terminal sialylated Lewis antigens, including Sialyl-Lewisx. These results disclose the molecular basis for the altered pattern of glycan structures observed in the mice gastric mucosa. The gene transcription alterations and the induced glycophenotypic changes observed in the gastric mucosa contribute for the understanding of the molecular mechanisms underlying the role of Pteridium aquilinum in the gastric carcinogenesis process.
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Affiliation(s)
- Joana Gomes
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Universidade do Porto, Porto, Portugal
- Institut Pasteur, Unité de Pathogenèse de Helicobacter, Paris, France
| | - Ana Magalhães
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Universidade do Porto, Porto, Portugal
| | - Ana S. Carvalho
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Universidade do Porto, Porto, Portugal
| | | | - Suzanne L. Papp
- The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- The Scripps Research Institute, La Jolla, California, United States of America
| | - Valérie Michel
- Institut Pasteur, Unité de Pathogenèse de Helicobacter, Paris, France
| | - Leonor David
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Universidade do Porto, Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Fátima Gärtner
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Eliette Touati
- Institut Pasteur, Unité de Pathogenèse de Helicobacter, Paris, France
| | - Celso A. Reis
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Universidade do Porto, Porto, Portugal
- Faculdade de Medicina, Universidade do Porto, Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- * E-mail:
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Van Nieuwerburgh F, Thompson RC, Ledesma J, Deforce D, Gaasterland T, Ordoukhanian P, Head SR. Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. Nucleic Acids Res 2011; 40:e24. [PMID: 22127871 PMCID: PMC3273786 DOI: 10.1093/nar/gkr1000] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3–5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae. We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome.
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Affiliation(s)
- Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
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38
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Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, Schaffer L, Deforce D, Salomon DR, Head SR, Ordoukhanian P. Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS One 2011; 6:e26969. [PMID: 22046424 PMCID: PMC3203936 DOI: 10.1371/journal.pone.0026969] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/06/2011] [Indexed: 01/29/2023] Open
Abstract
Here we demonstrate a method for unbiased multiplexed deep sequencing of RNA and DNA libraries using a novel, efficient and adaptable barcoding strategy called Post Amplification Ligation-Mediated (PALM). PALM barcoding is performed as the very last step of library preparation, eliminating a potential barcode-induced bias and allowing the flexibility to synthesize as many barcodes as needed. We sequenced PALM barcoded micro RNA (miRNA) and DNA reference samples and evaluated the quantitative barcode-induced bias in comparison to the same reference samples prepared using the Illumina TruSeq barcoding strategy. The Illumina TruSeq small RNA strategy introduces the barcode during the PCR step using differentially barcoded primers, while the TruSeq DNA strategy introduces the barcode before the PCR step by ligation of differentially barcoded adaptors. Results show virtually no bias between the differentially barcoded miRNA and DNA samples, both for the PALM and the TruSeq sample preparation methods. We also multiplexed miRNA reference samples using a pre-PCR barcode ligation. This barcoding strategy results in significant bias.
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Tang B, Di Lena P, Schaffer L, Head SR, Baldi P, Thomas EA. Genome-wide identification of Bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling. PLoS One 2011; 6:e23691. [PMID: 21912641 PMCID: PMC3164671 DOI: 10.1371/journal.pone.0023691] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [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: 05/17/2011] [Accepted: 07/22/2011] [Indexed: 01/01/2023] Open
Abstract
B-cell leukemia/lymphoma 11B (Bcl11b) is a transcription factor showing predominant expression in the striatum. To date, there are no known gene targets of Bcl11b in the nervous system. Here, we define targets for Bcl11b in striatal cells by performing chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) in combination with genome-wide expression profiling. Transcriptome-wide analysis revealed that 694 genes were significantly altered in striatal cells over-expressing Bcl11b, including genes showing striatal-enriched expression similar to Bcl11b. ChIP-seq analysis demonstrated that Bcl11b bound a mixture of coding and non-coding sequences that were within 10 kb of the transcription start site of an annotated gene. Integrating all ChIP-seq hits with the microarray expression data, 248 direct targets of Bcl11b were identified. Functional analysis on the integrated gene target list identified several zinc-finger encoding genes as Bcl11b targets, and further revealed a significant association of Bcl11b to brain-derived neurotrophic factor/neurotrophin signaling. Analysis of ChIP-seq binding regions revealed significant consensus DNA binding motifs for Bcl11b. These data implicate Bcl11b as a novel regulator of the BDNF signaling pathway, which is disrupted in many neurological disorders. Specific targeting of the Bcl11b-DNA interaction could represent a novel therapeutic approach to lowering BDNF signaling specifically in striatal cells.
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Affiliation(s)
- Bin Tang
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pietro Di Lena
- Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
| | - Lana Schaffer
- Department of Shared Research Services, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- Department of Shared Research Services, The Scripps Research Institute, La Jolla, California, United States of America
| | - Pierre Baldi
- Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
| | - Elizabeth A. Thomas
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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40
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Grigoryev YA, Kurian SM, Hart T, Nakorchevsky AA, Chen C, Campbell D, Head SR, Yates JR, Salomon DR. MicroRNA regulation of molecular networks mapped by global microRNA, mRNA, and protein expression in activated T lymphocytes. J Immunol 2011; 187:2233-43. [PMID: 21788445 DOI: 10.4049/jimmunol.1101233] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) regulate specific immune mechanisms, but their genome-wide regulation of T lymphocyte activation is largely unknown. We performed a multidimensional functional genomics analysis to integrate genome-wide differential mRNA, miRNA, and protein expression as a function of human T lymphocyte activation and time. We surveyed expression of 420 human miRNAs in parallel with genome-wide mRNA expression. We identified a unique signature of 71 differentially expressed miRNAs, 57 of which were previously not known as regulators of immune activation. The majority of miRNAs are upregulated, mRNA expression of these target genes is downregulated, and this is a function of binding multiple miRNAs (combinatorial targeting). Our data reveal that consideration of this complex signature, rather than single miRNAs, is necessary to construct a full picture of miRNA-mediated regulation. Molecular network mapping of miRNA targets revealed the regulation of activation-induced immune signaling. In contrast, pathways populated by genes that are not miRNA targets are enriched for metabolism and biosynthesis. Finally, we specifically validated miR-155 (known) and miR-221 (novel in T lymphocytes) using locked nucleic acid inhibitors. Inhibition of these two highly upregulated miRNAs in CD4(+) T cells was shown to increase proliferation by removing suppression of four target genes linked to proliferation and survival. Thus, multiple lines of evidence link top functional networks directly to T lymphocyte immunity, underlining the value of mapping global gene, protein, and miRNA expression.
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Affiliation(s)
- Yevgeniy A Grigoryev
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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Komori HK, LaMere SA, Torkamani A, Hart GT, Kotsopoulos S, Warner J, Samuels ML, Olson J, Head SR, Ordoukhanian P, Lee PL, Link DR, Salomon DR. Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res 2011; 21:1738-45. [PMID: 21757609 DOI: 10.1101/gr.116863.110] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytosine methylation of DNA CpG dinucleotides in gene promoters is an epigenetic modification that regulates gene transcription. While many methods exist to interrogate methylation states, few current methods offer large-scale, targeted, single CpG resolution. We report an approach combining bisulfite treatment followed by microdroplet PCR with next-generation sequencing to assay the methylation state of 50 genes in the regions 1 kb upstream of and downstream from their transcription start sites. This method yielded 96% coverage of the targeted CpGs and demonstrated high correlation between CpG island (CGI) DNA methylation and transcriptional regulation. The method was scaled to interrogate the methylation status of 77,674 CpGs in the promoter regions of 2100 genes in primary CD4 T cells. The 2100 gene library yielded 97% coverage of all targeted CpGs and 99% of the target amplicons.
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Affiliation(s)
- H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
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Flaherty BL, Van Nieuwerburgh F, Head SR, Golden JW. Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation. BMC Genomics 2011; 12:332. [PMID: 21711558 PMCID: PMC3141674 DOI: 10.1186/1471-2164-12-332] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [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: 02/18/2011] [Accepted: 06/28/2011] [Indexed: 11/13/2022] Open
Abstract
Background Cyanobacteria are potential sources of renewable chemicals and biofuels and serve as model organisms for bacterial photosynthesis, nitrogen fixation, and responses to environmental changes. Anabaena (Nostoc) sp. strain PCC 7120 (hereafter Anabaena) is a multicellular filamentous cyanobacterium that can "fix" atmospheric nitrogen into ammonia when grown in the absence of a source of combined nitrogen. Because the nitrogenase enzyme is oxygen sensitive, Anabaena forms specialized cells called heterocysts that create a microoxic environment for nitrogen fixation. We have employed directional RNA-seq to map the Anabaena transcriptome during vegetative cell growth and in response to combined-nitrogen deprivation, which induces filaments to undergo heterocyst development. Our data provide an unprecedented view of transcriptional changes in Anabaena filaments during the induction of heterocyst development and transition to diazotrophic growth. Results Using the Illumina short read platform and a directional RNA-seq protocol, we obtained deep sequencing data for RNA extracted from filaments at 0, 6, 12, and 21 hours after the removal of combined nitrogen. The RNA-seq data provided information on transcript abundance and boundaries for the entire transcriptome. From these data, we detected novel antisense transcripts within the UTRs (untranslated regions) and coding regions of key genes involved in heterocyst development, suggesting that antisense RNAs may be important regulators of the nitrogen response. In addition, many 5' UTRs were longer than anticipated, sometimes extending into upstream open reading frames (ORFs), and operons often showed complex structure and regulation. Finally, many genes that had not been previously identified as being involved in heterocyst development showed regulation, providing new candidates for future studies in this model organism. Conclusions Directional RNA-seq data were obtained that provide comprehensive mapping of transcript boundaries and abundance for all transcribed RNAs in Anabaena filaments during the response to nitrogen deprivation. We have identified genes and noncoding RNAs that are transcriptionally regulated during heterocyst development. These data provide detailed information on the Anabaena transcriptome as filaments undergo heterocyst development and begin nitrogen fixation.
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Affiliation(s)
- Britt L Flaherty
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093-0116, USA
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Chang LM, Maheshwari P, Werth S, Schaffer L, Head SR, Kovarik C, Werth VP. Identification and molecular analysis of glycosaminoglycans in cutaneous lupus erythematosus and dermatomyositis. J Histochem Cytochem 2011; 59:336-45. [PMID: 21378287 DOI: 10.1369/0022155410398000] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Glycosaminoglycans (GAGs), also known histologically as dermal mucin, accumulate in several inflammatory skin conditions. Because different GAG species have distinct immunologic effects, the authors examined two GAGs, hyaluronan (HA) and chondroitin sulfate (CS), using specific stains in cutaneous lupus erythematosus (CLE) and dermatomyositis (DM). In the dermis of one CLE subtype, tumid LE (TLE), they found only increased HA, but both HA and CS were significantly elevated in another CLE subtype, discoid LE (DLE). DM lesional dermis accumulated mainly CS but not HA. The authors then used glycomic gene expression microarrays to assess the expression of HA- and CS-related genes in CLE skin. Real-time quantitative PCR confirmed significantly increased expression of HAS2, CHSY1, and C4ST1 in the combined groups of CLE lesions (n = 8) compared to healthy controls (n = 4). Thus, the increase in HA in CLE presumably results from upregulation of HAS2, whereas CHSY1 and C4ST1 appear to contribute to increased CS. Based on their known immunomodulatory effects in other systems, HA and CS may thus participate in the pathophysiology of these inflammatory skin conditions.
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Affiliation(s)
- Laura M Chang
- Philadelphia VA Medical Center, Philadelphia, Pennsylvania, USA
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Rozenzhak S, Mejía-Ramírez E, Williams JS, Schaffer L, Hammond JA, Head SR, Russell P. Rad3 decorates critical chromosomal domains with gammaH2A to protect genome integrity during S-Phase in fission yeast. PLoS Genet 2010; 6:e1001032. [PMID: 20661445 PMCID: PMC2908685 DOI: 10.1371/journal.pgen.1001032] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [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: 04/08/2010] [Accepted: 06/17/2010] [Indexed: 01/24/2023] Open
Abstract
Schizosaccharomyces pombe Rad3 checkpoint kinase and its human ortholog ATR are essential for maintaining genome integrity in cells treated with genotoxins that damage DNA or arrest replication forks. Rad3 and ATR also function during unperturbed growth, although the events triggering their activation and their critical functions are largely unknown. Here, we use ChIP-on-chip analysis to map genomic loci decorated by phosphorylated histone H2A (γH2A), a Rad3 substrate that establishes a chromatin-based recruitment platform for Crb2 and Brc1 DNA repair/checkpoint proteins. Unexpectedly, γH2A marks a diverse array of genomic features during S-phase, including natural replication fork barriers and a fork breakage site, retrotransposons, heterochromatin in the centromeres and telomeres, and ribosomal RNA (rDNA) repeats. γH2A formation at the centromeres and telomeres is associated with heterochromatin establishment by Clr4 histone methyltransferase. We show that γH2A domains recruit Brc1, a factor involved in repair of damaged replication forks. Brc1 C-terminal BRCT domain binding to γH2A is crucial in the absence of Rqh1Sgs1, a RecQ DNA helicase required for rDNA maintenance whose human homologs are mutated in patients with Werner, Bloom, and Rothmund–Thomson syndromes that are characterized by cancer-predisposition or accelerated aging. We conclude that Rad3 phosphorylates histone H2A to mobilize Brc1 to critical genomic domains during S-phase, and this pathway functions in parallel with Rqh1 DNA helicase in maintaining genome integrity. Eukaryotic genomes, which range in size from ∼107 to ∼1011 base pairs, are replicated with nearly absolute fidelity every cell cycle. This amazing feat happens despite the frequent stalling or collapse of replication forks. The checkpoint kinase ATR is activated by replication fork stalling and phosphorylates histone H2A in nucleosomes surrounding damaged DNA. As the genomic regions triggering ATR activation are largely unknown, we used a whole-genome microarray to map chromosomal domains enriched with phospho-H2A during DNA replication in fission yeast. This analysis identified specific sites, including natural replication fork barriers in ribosomal DNA repeats, retrotransposon elements, and most surprisingly, all heterochromatin regions. Phospho-H2A binds the genome maintenance protein Brc1, and our genetic studies reveal that this molecular pathway becomes crucial in the absence of Rqh1, a conserved DNA helicase that is linked to cancer predisposition. As the fission yeast and human genomes share many similarities, our study reveals genomic landmarks that could similarly trigger ATR activation in human cells and shows that phospho-H2A and Brc1 are a critical part of the network that maintains genome integrity during DNA replication.
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Affiliation(s)
- Sophie Rozenzhak
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Eva Mejía-Ramírez
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jessica S. Williams
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Lana Schaffer
- DNA Array Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jennifer A. Hammond
- DNA Array Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Steven R. Head
- DNA Array Core Facility, The Scripps Research Institute, La Jolla, California, United States of America
| | - Paul Russell
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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Moutaftsi M, Tscharke DC, Vaughan K, Koelle DM, Stern L, Calvo-Calle M, Ennis F, Terajima M, Sutter G, Crotty S, Drexler I, Franchini G, Yewdell JW, Head SR, Blum J, Peters B, Sette A. Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol 2010; 5:221-39. [PMID: 20143946 DOI: 10.2217/fmb.09.110] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Vaccinia virus (VACV) was used as the vaccine strain to eradicate smallpox. VACV is still administered to healthcare workers or researchers who are at risk of contracting the virus, and to military personnel. Thus, VACV represents a weapon against outbreaks, both natural (e.g., monkeypox) or man-made (bioterror). This virus is also used as a vector for experimental vaccine development (cancer/infectious disease). As a prototypic poxvirus, VACV is a model system for studying host-pathogen interactions. Until recently, little was known about the targets of host immune responses, which was likely owing to VACVs large genome (>200 open reading frames). However, the last few years have witnessed an explosion of data, and VACV has quickly become a useful model to study adaptive immune responses. This review summarizes and highlights key findings based on identification of VACV antigens targeted by the immune system (CD4, CD8 and antibodies) and the complex interplay between responses.
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Affiliation(s)
- Magdalini Moutaftsi
- Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.
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Abstract
Glycans are vital elements of living organisms and are involved in recognition, communication, cell growth and development, motility, and other significant processes. The interactions of glycans with the proteins that bind them provide valuable information about protein interaction and specificity. By printing glycans on microarrays, investigators are able to effectively determine the binding specificity of certain proteins with an extremely efficient and precise result. Such chips are performed by standard robotic microarray printing. Incubating the slides with various GBP-containing substances not only reveals clear receptor preferences of the proteins, but also detects minute differences in structure specificity.
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Affiliation(s)
- Julia Busch
- DNA Array Core Facility, The Scripps Research Institute, La Jolla, CA, USA
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Robison EH, Mondala TS, Williams AR, Head SR, Salomon DR, Kurian SM. Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study. BMC Genomics 2009; 10:617. [PMID: 20017944 PMCID: PMC2811129 DOI: 10.1186/1471-2164-10-617] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [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: 08/26/2009] [Accepted: 12/17/2009] [Indexed: 11/10/2022] Open
Abstract
Background Whole genome gene expression profiling has revolutionized research in the past decade especially with the advent of microarrays. Recently, there have been significant improvements in whole blood RNA isolation techniques which, through stabilization of RNA at the time of sample collection, avoid bias and artifacts introduced during sample handling. Despite these improvements, current human whole blood RNA stabilization/isolation kits are limited by the requirement of a venous blood sample of at least 2.5 mL. While fingerstick blood collection has been used for many different assays, there has yet to be a kit developed to isolate high quality RNA for use in gene expression studies from such small human samples. The clinical and field testing advantages of obtaining reliable and reproducible gene expression data from a fingerstick are many; it is less invasive, time saving, more mobile, and eliminates the need of a trained phlebotomist. Furthermore, this method could also be employed in small animal studies, i.e. mice, where larger sample collections often require sacrificing the animal. In this study, we offer a rapid and simple method to extract sufficient amounts of high quality total RNA from approximately 70 μl of whole blood collected via a fingerstick using a modified protocol of the commercially available Qiagen PAXgene RNA Blood Kit. Results From two sets of fingerstick collections, about 70 uL whole blood collected via finger lancet and capillary tube, we recovered an average of 252.6 ng total RNA with an average RIN of 9.3. The post-amplification yields for 50 ng of total RNA averaged at 7.0 ug cDNA. The cDNA hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips had an average % Present call of 52.5%. Both fingerstick collections were highly correlated with r2 values ranging from 0.94 to 0.97. Similarly both fingerstick collections were highly correlated to the venous collection with r2 values ranging from 0.88 to 0.96 for fingerstick collection 1 and 0.94 to 0.96 for fingerstick collection 2. Conclusions Our comparisons of RNA quality and gene expression data of the fingerstick method with traditionally processed sample workflows demonstrate excellent RNA quality from the capillary collection as well as very high correlations of gene expression data.
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Affiliation(s)
- Elizabeth H Robison
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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48
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Saravanan C, Cao Z, Head SR, Panjwani N. Detection of differentially expressed wound-healing-related glycogenes in galectin-3-deficient mice. Invest Ophthalmol Vis Sci 2009; 50:5690-6. [PMID: 19643959 PMCID: PMC3005591 DOI: 10.1167/iovs.08-3359] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PURPOSE A prior study showed that exogenous galectin-3 (Gal-3) stimulates re-epithelialization of corneal wounds in wild-type (Gal-3(+/+)) mice but, surprisingly, not in galectin-3-deficient (Gal-3(-/-)) mice. In an effort to understand why the injured corneas of Gal-3(-/-) mice are unresponsive to exogenous Gal-3, the present study was designed to determine whether genes encoding the enzymes that regulate the synthesis of glycan ligands of Gal-3 are differentially expressed in Gal-3(-/-) corneas compared with the Gal-3(+/+) corneas. METHODS Glycogene microarray technology was used to identify differentially expressed glycosyltransferases in healing Gal-3(+/+) and Gal-3(-/-) corneas. RESULTS Of approximately 2000 glycogenes on the array, the expression of 8 was upregulated and that of 14 was downregulated more than 1.3-fold in healing Gal-3(-/-) corneas. A galactosyltransferase, beta3GalT5, which has the ability to synthesize Gal-3 ligands was markedly downregulated in healing Gal-3(-/-) corneas. The genes for polypeptide galactosaminyltransferases (ppGalNAcT-3 and -7) that are known to initiate O-linked glycosylation and N-aspartyl-beta-glucosaminidase, which participates in the removal of N-glycans, were found to be upregulated in healing Gal-3(-/-) corneas. Microarray data were validated by qRT-PCR. CONCLUSIONS Based on the known functions of the differentially expressed glycogenes, it appears that the glycan structures on glycoproteins and glycolipids, synthesized as a result of the differential glycogene expression pattern in healing Gal-3(-/-) corneas may lead to the downregulation of specific counterreceptors for Gal-3. This may explain, at least in part, why, unlike healing Gal-3(+/+) corneas, the healing Gal-3(-/-) corneas are unresponsive to the stimulatory effect of exogenous Gal-3 on re-epithelialization of corneal wounds.
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Affiliation(s)
- Chandrassegar Saravanan
- Department of Ophthalmology and The New England Eye Center, Tufts University School of Medicine, Boston, Massachusetts
- Program in Cell, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts
| | - Zhiyi Cao
- Department of Ophthalmology and The New England Eye Center, Tufts University School of Medicine, Boston, Massachusetts
| | - Steven R. Head
- DNA Array Core Facility, The Scripps Research Institute, La Jolla, California
| | - Noorjahan Panjwani
- Department of Ophthalmology and The New England Eye Center, Tufts University School of Medicine, Boston, Massachusetts
- Program in Cell, Molecular and Developmental Biology, Tufts University School of Medicine, Boston, Massachusetts
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Kunicki TJ, Williams SA, Salomon DR, Harrison P, Crisler P, Nakagawa P, Mondala TS, Head SR, Nugent DJ. Genetics of platelet reactivity in normal, healthy individuals. J Thromb Haemost 2009; 7:2116-22. [PMID: 19740098 DOI: 10.1111/j.1538-7836.2009.03610.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
BACKGROUND The Platelet Function Analyzer-100 (PFA-100) is widely used to measure platelet reactivity in whole blood under high shear. OBJECTIVE To characterize the genetic component of platelet reactivity among normal individuals, using the PFA-100. METHODS We compared baseline platelet reactivity with sex, age, platelet count, hematocrit, plasma von Willebrand factor antigen (VWF:Ag), and alleles of seven candidate genes: integrin subunits alpha2 (ITGA2) and beta3 (ITGB3), platelet glycoproteins GPIbalpha (GP1BA) and GPVI (GP6), purinogenic receptors (P2RY1 and P2RY12) and cyclooxygenase-1 (COX1). RESULTS Based on linear and logistic regression models, we report an inverse correlation between baseline closure time (CT) initiated by collagen plus epinephrine (CEPI) and plasma VWF:Ag level, ITGA2 807T and P2RY1 893C, and an inverse correlation between baseline CT initiated by collagen plus adenosine diphosphate (CADP) and P2RY1 893C or GP1BA -5C. CONCLUSIONS These results indicate that genetic polymorphisms in ITGA2 and P2RY1 combine with plasma VWF:Ag levels to modulate baseline platelet reactivity in response to collagen plus EPI, while genetic differences in P2RY1 and GP1BA significantly effect platelet responses to collagen plus ADP. Our results demonstrate that the PFA-100 can be used to evaluate the effects of genetic predictors of platelet function.
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Affiliation(s)
- T J Kunicki
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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50
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Saravanan C, Cao Z, Head SR, Panjwani N. Analysis of differential expression of glycosyltransferases in healing corneas by glycogene microarrays. Glycobiology 2009; 20:13-23. [PMID: 19736239 DOI: 10.1093/glycob/cwp133] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
It is generally accepted that the glycans on the cell surface and extracellular matrix proteins play a pivotal role in the events that mediate re-epithelialization of wounds. Yet, the global alteration in the structure and composition of glycans, specifically occurring during corneal wound closure remains unknown. In this study, GLYCOv2 glycogene microarray technology was used for the first time to identify the differentially expressed glycosylation-related genes in healing mouse corneas. Of approximately 2000 glycogenes on the array, the expression of 11 glycosytransferase and glycosidase enzymes was upregulated and that of 19 was downregulated more than 1.5-fold in healing corneas compared with the normal, uninjured corneas. Among them, notably, glycosyltransferases, beta3GalT5, T-synthase, and GnTIVb, were all found to be induced in the corneas in response to injury, whereas, GnTIII and many sialyltransferases were downregulated. Interestingly, it appears that the glycan structures on glycoproteins and glycolipids, expressed in healing corneas as a result of differential regulation of these glycosyltransferases, may serve as specific counter-receptors for galectin-3, a carbohydrate-binding protein, known to play a key role in re-epithelialization of corneal wounds. Additionally, many glycogenes including a proteoglycan, glypican-3, cell adhesion proteins dectin-1 and -2, and mincle, and mucin 1 were identified for the first time to be differentially regulated during corneal wound healing. Results of glycogene microarray data were confirmed by qRT-PCR and lectin blot analyses. The differentially expressed glycogenes identified in the present study have not previously been investigated in the context of wound healing and represent novel factors for investigating the role of carbohydrate-mediated recognition in corneal wound healing.
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Affiliation(s)
- Chandrassegar Saravanan
- Program in Cell, Molecular and Developmental Biology, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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