1751
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Pelosi A, Alicata C, Tumino N, Ingegnere T, Loiacono F, Mingari MC, Moretta L, Vacca P. An Anti-inflammatory microRNA Signature Distinguishes Group 3 Innate Lymphoid Cells From Natural Killer Cells in Human Decidua. Front Immunol 2020; 11:133. [PMID: 32117280 PMCID: PMC7015979 DOI: 10.3389/fimmu.2020.00133] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/17/2020] [Indexed: 01/03/2023] Open
Abstract
Innate lymphoid cells (ILCs) are a heterogeneous subset of lymphocytes deeply implicated in the innate immune responses to different pathogens, in lymphoid organogenesis and in the maintenance of tissue homeostasis. Group 3 innate lymphoid cells (ILC3) have been detected in human decidua, where they play a role in the early inflammatory phase favoring implantation and tissue remodeling as well as in the subsequent regulatory phase preventing fetal rejection and supporting neoangiogenesis. A balance between inflammation and immune tolerance is required to maintain pregnancy, thus maternal immune system must be controlled by finely tuned mechanisms. microRNAs (miRNAs) are small non-coding RNAs with important regulatory roles in immune cells, but their function in decidual ILC3 (dILC3) and in decidual NK (dNK) cells is still undefined. Here, we examined the miRNome by microarray in these cells during the first trimester of pregnancy and compared with miRNA profiles of peripheral blood NK (pbNK) cells from pregnant women. We show that distinct miRNA profiles could clearly distinguish dILC3 from NK cells. Correlation analyses revealed that dNK and pbNK miRNome profiles are more similar to each other as compared to dILC3. In particular, we identified 302 and 279 mature miRNAs differentially expressed in dILC3 as compared to dNK and pbNK, respectively. The expression of miR-574-3p and the miR-99b/let-7e/miR-125a miRNA cluster resulted the most increased in dILC3. Remarkably, gene ontology analysis and pathway enrichments of miRNA targets revealed an involvement of these miRNAs in the promotion of anti-inflammatory responses. In agreement to this finding, we also found a higher expression of the anti-inflammatory miR-146a-5p in dILC3 with respect to NK cells. Overall, our data identified specific miRNA signatures distinguishing dILC3, dNK, and pbNK cells. Our data suggest the existence of a tight epigenetic control mediated by miRNAs in dILC3, potentially acting as a brake to prevent exaggerated inflammatory responses and to maintain the immune homeostasis in the early phases of pregnancy.
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Affiliation(s)
- Andrea Pelosi
- Immunology Research Area, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
| | - Claudia Alicata
- Immunology Research Area, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
| | - Nicola Tumino
- Immunology Research Area, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
| | - Tiziano Ingegnere
- Immunology Research Area, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
| | - Fabrizio Loiacono
- Immunology Operative Unit, Department of Integrated Oncological Therapies, IRCCS Policlinico San Martino Hospital, Genoa, Italy
| | - Maria Cristina Mingari
- Immunology Operative Unit, Department of Integrated Oncological Therapies, IRCCS Policlinico San Martino Hospital, Genoa, Italy.,Department of Experimental Medicine, School of Medical and Pharmaceutical Sciences, University of Genoa, Genoa, Italy.,Center of Excellence for Biomedical Research, University of Genoa, Genoa, Italy
| | - Lorenzo Moretta
- Immunology Research Area, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
| | - Paola Vacca
- Immunology Research Area, IRCCS Bambino Gesù Pediatric Hospital, Rome, Italy
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1752
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A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell Syst 2020; 10:133-155.e6. [PMID: 32027860 PMCID: PMC7042714 DOI: 10.1016/j.cels.2020.01.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/08/2019] [Accepted: 01/10/2020] [Indexed: 12/19/2022]
Abstract
Living systems integrate biochemical reactions that determine the functional state of each cell. Reactions are primarily mediated by proteins. In proteomic studies, these have been treated as independent entities, disregarding their higher-level organization into complexes that affects their activity and/or function and is thus of great interest for biological research. Here, we describe the implementation of an integrated technique to quantify cell-state-specific changes in the physical arrangement of protein complexes concurrently for thousands of proteins and hundreds of complexes. Applying this technique to a comparison of human cells in interphase and mitosis, we provide a systematic overview of mitotic proteome reorganization. The results recall key hallmarks of mitotic complex remodeling and suggest a model of nuclear pore complex disassembly, which we validate by orthogonal methods. To support the interpretation of quantitative SEC-SWATH-MS datasets, we extend the software CCprofiler and provide an interactive exploration tool, SECexplorer-cc. Global quantification of assembly state changes in the mitotic proteome Improved performance over thermostability measurement of proteome states Discovery of a mitotic disassembly intermediate of the nuclear pore complex Introduction of SECexplorer-cc, a publicly available online platform
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1753
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Robakis TK, Zhang S, Rasgon NL, Li T, Wang T, Roth MC, Humphreys KL, Gotlib IH, Ho M, Khechaduri A, Watson K, Roat-Shumway S, Budhan VV, Davis KN, Crowe SD, Ellie Williams K, Urban AE. Epigenetic signatures of attachment insecurity and childhood adversity provide evidence for role transition in the pathogenesis of perinatal depression. Transl Psychiatry 2020; 10:48. [PMID: 32066670 PMCID: PMC7026105 DOI: 10.1038/s41398-020-0703-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/05/2019] [Accepted: 12/08/2019] [Indexed: 11/16/2022] Open
Abstract
Early life adversity and insecure attachment style are known risk factors for perinatal depression. The biological pathways linking these experiences, however, have not yet been elucidated. We hypothesized that overlap in patterns of DNA methylation in association with each of these phenomena could identify genes and pathways of importance. Specifically, we wished to distinguish between allostatic-load and role-transition hypotheses of perinatal depression. We conducted a large-scale analysis of methylation patterns across 5 × 106 individual CG dinucleotides in 54 women participating in a longitudinal prospective study of perinatal depression, using clustering-based criteria for significance to control for multiple comparisons. We identified 1580 regions in which methylation density was associated with childhood adversity, 3 in which methylation density was associated with insecure attachment style, and 6 in which methylation density was associated with perinatal depression. Shorter telomeres were observed in association with childhood trauma but not with perinatal depression or attachment insecurity. A detailed analysis of methylation density in the oxytocin receptor gene revealed similar patterns of DNA methylation in association with perinatal depression and with insecure attachment style, while childhood trauma was associated with a distinct methylation pattern in this gene. Clinically, attachment style was strongly associated with depression only in pregnancy and the early postpartum, whereas the association of childhood adversity with depression was time-invariant. We concluded that the broad DNA methylation signature and reduced telomere length associated with childhood adversity could indicate increased allostatic load across multiple body systems, whereas perinatal depression and attachment insecurity may be narrower phenotypes with more limited DNA methylation signatures outside the CNS, and no apparent association with telomere length or, by extension, allostatic load. In contrast, the finding of matching DNA methylation patterns within the oxytocin receptor gene for perinatal depression and attachment insecurity is consistent with the theory that the perinatal period is a time of activation of existing attachment schemas for the purpose of structuring the mother-child relationship, and that such activation may occur in part through specific patterns of methylation of the oxytocin receptor gene.
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Affiliation(s)
- Thalia K Robakis
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA.
| | - Siming Zhang
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
- Stanford University Department of Genetics, Stanford, CA, USA
| | - Natalie L Rasgon
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | | | - Tao Wang
- AccuraScience, LLC, Johnston, IN, USA
| | - Marissa C Roth
- Vanderbilt University Department of Psychology, Nashville, TN, USA
| | | | - Ian H Gotlib
- Stanford University Department of Psychology, Stanford, CA, USA
| | - Marcus Ho
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | | | - Katherine Watson
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | - Siena Roat-Shumway
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | - Vena V Budhan
- Palo Alto University Graduate School of Psychology, Palo Alto, CA, USA
| | - Kasey N Davis
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | - Susan D Crowe
- Stanford University Department of Obstetrics & Gynecology, Stanford, CA, USA
| | | | - Alexander E Urban
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA.
- Stanford University Department of Genetics, Stanford, CA, USA.
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1754
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Metabolite therapy guided by liquid biopsy proteomics delays retinal neurodegeneration. EBioMedicine 2020; 52:102636. [PMID: 32028070 PMCID: PMC7005447 DOI: 10.1016/j.ebiom.2020.102636] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background Neurodegenerative diseases are incurable disorders caused by progressive neuronal cell death. Retinitis pigmentosa (RP) is a blinding neurodegenerative disease that results in photoreceptor death and progresses to the loss of the entire retinal network. We previously found that proteomic analysis of the adjacent vitreous served as way to indirectly biopsy the retina and identify changes in the retinal proteome. Methods We analyzed protein expression in liquid vitreous biopsies from autosomal recessive (ar)RP patients with PDE6A mutations and arRP mice with Pde6ɑ mutations. Proteomic analysis of retina and vitreous samples identified molecular pathways affected at the onset of photoreceptor death. Based on affected molecular pathways, arRP mice were treated with a ketogenic diet or metabolites involved in fatty-acid synthesis, oxidative phosphorylation, and the tricarboxylic acid (TCA) cycle. Findings Dietary supplementation of a single metabolite, ɑ-ketoglutarate, increased docosahexaeonic acid levels, provided neuroprotection, and enhanced visual function in arRP mice. A ketogenic diet delayed photoreceptor cell loss, while vitamin B supplementation had a limited effect. Finally, desorption electrospray ionization mass spectrometry imaging (DESI-MSI) on ɑ-ketoglutarate-treated mice revealed restoration of metabolites that correlated with our proteomic findings: uridine, dihydrouridine, and thymidine (pyrimidine and purine metabolism), glutamine and glutamate (glutamine/glutamate conversion), and succinic and aconitic acid (TCA cycle). Interpretation This study demonstrates that replenishing TCA cycle metabolites via oral supplementation prolongs retinal function and provides a neuroprotective effect on the photoreceptor cells and inner retinal network. Funding NIH grants [R01EY026682, R01EY024665, R01EY025225, R01EY024698, R21AG050437, P30EY026877, 5P30EY019007, R01EY018213, F30EYE027986, T32GM007337, 5P30CA013696], NSF grant CHE-1734082.
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1755
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Wheeler MA, Clark IC, Tjon EC, Li Z, Zandee SEJ, Couturier CP, Watson BR, Scalisi G, Alkwai S, Rothhammer V, Rotem A, Heyman JA, Thaploo S, Sanmarco LM, Ragoussis J, Weitz DA, Petrecca K, Moffitt JR, Becher B, Antel JP, Prat A, Quintana FJ. MAFG-driven astrocytes promote CNS inflammation. Nature 2020; 578:593-599. [PMID: 32051591 PMCID: PMC8049843 DOI: 10.1038/s41586-020-1999-0] [Citation(s) in RCA: 265] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/16/2019] [Indexed: 01/14/2023]
Abstract
Multiple sclerosis is a chronic inflammatory disease of the CNS1. Astrocytes contribute to the pathogenesis of multiple sclerosis2, but little is known about the heterogeneity of astrocytes and its regulation. Here we report the analysis of astrocytes in multiple sclerosis and its preclinical model experimental autoimmune encephalomyelitis (EAE) by single-cell RNA sequencing in combination with cell-specific Ribotag RNA profiling, assay for transposase-accessible chromatin with sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing (ChIP-seq), genome-wide analysis of DNA methylation and in vivo CRISPR-Cas9-based genetic perturbations. We identified astrocytes in EAE and multiple sclerosis that were characterized by decreased expression of NRF2 and increased expression of MAFG, which cooperates with MAT2α to promote DNA methylation and represses antioxidant and anti-inflammatory transcriptional programs. Granulocyte-macrophage colony-stimulating factor (GM-CSF) signalling in astrocytes drives the expression of MAFG and MAT2α and pro-inflammatory transcriptional modules, contributing to CNS pathology in EAE and, potentially, multiple sclerosis. Our results identify candidate therapeutic targets in multiple sclerosis.
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Affiliation(s)
- Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Iain C Clark
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Emily C Tjon
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie E J Zandee
- Neuroimmunology Unit, Centre de recherche du CHUM (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Charles P Couturier
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Brianna R Watson
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Giulia Scalisi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah Alkwai
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA
- Centre of Excellence for Biomedicine, Joint Centers of Excellence Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Veit Rothhammer
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Assaf Rotem
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - John A Heyman
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jiannis Ragoussis
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - David A Weitz
- Department of Physics, Harvard University, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Kevin Petrecca
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jeffrey R Moffitt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Jack P Antel
- Neuroimmunology Unit, Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Alexandre Prat
- Neuroimmunology Unit, Centre de recherche du CHUM (CRCHUM), Montreal, Quebec, Canada
- Department of Neuroscience, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Centre of Excellence for Biomedicine, Brigham and Women's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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1756
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Sanderson BJ, Park S, Jameel MI, Kraft JC, Thomashow MF, Schemske DW, Oakley CG. Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual. AMERICAN JOURNAL OF BOTANY 2020; 107:250-261. [PMID: 31762012 PMCID: PMC7065183 DOI: 10.1002/ajb2.1385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/14/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Italy and Sweden provides an essential foundation for uncovering the genotype-phenotype-fitness map for an adaptive response to a key environmental stress. METHODS We examined the consequences of a naturally occurring loss-of-function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing-tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing the Italian CBF2 allele, and two contained deletions created using CRISPR-Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression before and after cold acclimation. RESULTS Freezing tolerance was lower in the Italian (11%) compared to the Swedish (72%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified 10 genes for which all CBF2 LOF lines, and the IT ecotype had similar patterns of reduced cold responsive expression compared to the SW ecotype. CONCLUSIONS We identified 10 genes that are at least partially regulated by CBF2 that may contribute to the differences in cold-acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.
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Affiliation(s)
- Brian J. Sanderson
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Sunchung Park
- MSU‐DOE Plant Research Laboratory and the Plant Resilience InstituteMichigan State UniversityEast LansingMIUSA
- Present address:
USDA ARS SalinasCAUSA
| | - M. Inam Jameel
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
- Present address:
Department of GeneticsUniversity of GeorgiaAthensGAUSA
| | - Joshua C. Kraft
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Michael F. Thomashow
- MSU‐DOE Plant Research Laboratory and the Plant Resilience InstituteMichigan State UniversityEast LansingMIUSA
| | - Douglas W. Schemske
- Department of Plant Biology, and W. K. Kellogg Biological StationMichigan State UniversityEast LansingMIUSA
| | - Christopher G. Oakley
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
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1757
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Rocha LR, Nguyen Huu VA, Palomino La Torre C, Xu Q, Jabari M, Krawczyk M, Weinreb RN, Skowronska‐Krawczyk D. Early removal of senescent cells protects retinal ganglion cells loss in experimental ocular hypertension. Aging Cell 2020; 19:e13089. [PMID: 31867890 PMCID: PMC6996954 DOI: 10.1111/acel.13089] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 12/15/2022] Open
Abstract
Experimental ocular hypertension induces senescence of retinal ganglion cells (RGCs) that mimics events occurring in human glaucoma. Senescence-related chromatin remodeling leads to profound transcriptional changes including the upregulation of a subset of genes that encode multiple proteins collectively referred to as the senescence-associated secretory phenotype (SASP). Emerging evidence suggests that the presence of these proinflammatory and matrix-degrading molecules has deleterious effects in a variety of tissues. In the current study, we demonstrated in a transgenic mouse model that early removal of senescent cells induced upon elevated intraocular pressure (IOP) protects unaffected RGCs from senescence and apoptosis. Visual evoked potential (VEP) analysis demonstrated that remaining RGCs are functional and that the treatment protected visual functions. Finally, removal of endogenous senescent retinal cells after IOP elevation by a treatment with senolytic drug dasatinib prevented loss of retinal functions and cellular structure. Senolytic drugs may have the potential to mitigate the deleterious impact of elevated IOP on RGC survival in glaucoma and other optic neuropathies.
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Affiliation(s)
- Lorena Raquel Rocha
- Shiley Eye Institute Hamilton Glaucoma Center and Viterbi Family Department of Ophthalmology University of California, San Diego CA USA
| | - Viet Anh Nguyen Huu
- Shiley Eye Institute Hamilton Glaucoma Center and Viterbi Family Department of Ophthalmology University of California, San Diego CA USA
| | - Claudia Palomino La Torre
- Shiley Eye Institute Hamilton Glaucoma Center and Viterbi Family Department of Ophthalmology University of California, San Diego CA USA
| | - Qianlan Xu
- Shiley Eye Institute Hamilton Glaucoma Center and Viterbi Family Department of Ophthalmology University of California, San Diego CA USA
| | - Mary Jabari
- Shiley Eye Institute Hamilton Glaucoma Center and Viterbi Family Department of Ophthalmology University of California, San Diego CA USA
| | - Michal Krawczyk
- Shiley Eye Institute Hamilton Glaucoma Center and Viterbi Family Department of Ophthalmology University of California, San Diego CA USA
| | - Robert N. Weinreb
- Shiley Eye Institute Hamilton Glaucoma Center and Viterbi Family Department of Ophthalmology University of California, San Diego CA USA
| | - Dorota Skowronska‐Krawczyk
- Shiley Eye Institute Hamilton Glaucoma Center and Viterbi Family Department of Ophthalmology University of California, San Diego CA USA
- Richard C. Atkinson Lab for Regenerative Ophthalmology University of California, San Diego CA USA
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1758
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Baros SS, Blackburn JM, Soares NC. Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases. Mol Cell Proteomics 2020; 19:233-244. [PMID: 31839597 PMCID: PMC7000118 DOI: 10.1074/mcp.r119.001668] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Mycobacterial Ser/Thr protein kinases (STPKs) play a critical role in signal transduction pathways that ultimately determine mycobacterial growth and metabolic adaptation. Identification of key physiological substrates of these protein kinases is, therefore, crucial to better understand how Ser/Thr phosphorylation contributes to mycobacterial environmental adaptation, including response to stress, cell division, and host-pathogen interactions. Various substrate detection methods have been employed with limited success, with direct targets of STPKs remaining elusive. Recently developed mass spectrometry (MS)-based phosphoproteomic approaches have expanded the list of potential STPK substrate identifications, yet further investigation is required to define the most functionally significant phosphosites and their physiological importance. Prior to the application of MS workflows, for instance, GarA was the only known and validated physiological substrate for protein kinase G (PknG) from pathogenic mycobacteria. A subsequent list of at least 28 candidate PknG substrates has since been reported with the use of MS-based analyses. Herein, we integrate and critically review MS-generated datasets available on novel STPK substrates and report new functional and subcellular localization enrichment analyses on novel candidate protein kinase A (PknA), protein kinase B (PknB) and PknG substrates to deduce the possible physiological roles of these kinases. In addition, we assess substrate specificity patterns across different mycobacterial STPKs by analyzing reported sets of phosphopeptides, in order to determine whether novel motifs or consensus regions exist for mycobacterial Ser/Thr phosphorylation sites. This review focuses on MS-based techniques employed for STPK substrate identification in mycobacteria, while highlighting the advantages and challenges of the various applications.
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Affiliation(s)
- Seanantha S Baros
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa; Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates.
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1759
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MEIOSIN Directs the Switch from Mitosis to Meiosis in Mammalian Germ Cells. Dev Cell 2020; 52:429-445.e10. [DOI: 10.1016/j.devcel.2020.01.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/10/2019] [Accepted: 01/09/2020] [Indexed: 01/12/2023]
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1760
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Deol P, Kozlova E, Valdez M, Ho C, Yang EW, Richardson H, Gonzalez G, Truong E, Reid J, Valdez J, Deans JR, Martinez-Lomeli J, Evans JR, Jiang T, Sladek FM, Curras-Collazo MC. Dysregulation of Hypothalamic Gene Expression and the Oxytocinergic System by Soybean Oil Diets in Male Mice. Endocrinology 2020; 161:5698148. [PMID: 31912136 PMCID: PMC7041656 DOI: 10.1210/endocr/bqz044] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/04/2020] [Indexed: 01/04/2023]
Abstract
Soybean oil consumption has increased greatly in the past half-century and is linked to obesity and diabetes. To test the hypothesis that soybean oil diet alters hypothalamic gene expression in conjunction with metabolic phenotype, we performed RNA sequencing analysis using male mice fed isocaloric, high-fat diets based on conventional soybean oil (high in linoleic acid, LA), a genetically modified, low-LA soybean oil (Plenish), and coconut oil (high in saturated fat, containing no LA). The 2 soybean oil diets had similar but nonidentical effects on the hypothalamic transcriptome, whereas the coconut oil diet had a negligible effect compared to a low-fat control diet. Dysregulated genes were associated with inflammation, neuroendocrine, neurochemical, and insulin signaling. Oxt was the only gene with metabolic, inflammation, and neurological relevance upregulated by both soybean oil diets compared to both control diets. Oxytocin immunoreactivity in the supraoptic and paraventricular nuclei of the hypothalamus was reduced, whereas plasma oxytocin and hypothalamic Oxt were increased. These central and peripheral effects of soybean oil diets were correlated with glucose intolerance but not body weight. Alterations in hypothalamic Oxt and plasma oxytocin were not observed in the coconut oil diet enriched in stigmasterol, a phytosterol found in soybean oil. We postulate that neither stigmasterol nor LA is responsible for effects of soybean oil diets on oxytocin and that Oxt messenger RNA levels could be associated with the diabetic state. Given the ubiquitous presence of soybean oil in the American diet, its observed effects on hypothalamic gene expression could have important public health ramifications.
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Affiliation(s)
- Poonamjot Deol
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Elena Kozlova
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
| | - Matthew Valdez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
| | - Catherine Ho
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Ei-Wen Yang
- Department of Computer Science and Engineering, University of California Riverside, California
| | - Holly Richardson
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Gwendolyn Gonzalez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Edward Truong
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jack Reid
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Joseph Valdez
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jonathan R Deans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jose Martinez-Lomeli
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Jane R Evans
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California Riverside, California
| | - Frances M Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
| | - Margarita C Curras-Collazo
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, California
- Neuroscience Graduate Program, University of California, Riverside, California
- Correspondence: Margarita C. Curras-Collazo, PhD, FAPS, Department of Molecular, Cell and Systems Biology, University of California, 2110 Biological Sciences Building, Riverside, California 92521. E-mail:
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1761
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Leidal AM, Huang HH, Marsh T, Solvik T, Zhang D, Ye J, Kai F, Goldsmith J, Liu JY, Huang YH, Monkkonen T, Vlahakis A, Huang EJ, Goodarzi H, Yu L, Wiita AP, Debnath J. The LC3-conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles. Nat Cell Biol 2020; 22:187-199. [PMID: 31932738 PMCID: PMC7007875 DOI: 10.1038/s41556-019-0450-y] [Citation(s) in RCA: 280] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 12/03/2019] [Indexed: 12/11/2022]
Abstract
Traditionally viewed as an autodigestive pathway, autophagy also facilitates cellular secretion; however, the mechanisms underlying these processes remain unclear. Here, we demonstrate that components of the autophagy machinery specify secretion within extracellular vesicles (EVs). Using a proximity-dependent biotinylation proteomics strategy, we identify 200 putative targets of LC3-dependent secretion. This secretome consists of a highly interconnected network enriched in RNA-binding proteins (RBPs) and EV cargoes. Proteomic and RNA profiling of EVs identifies diverse RBPs and small non-coding RNAs requiring the LC3-conjugation machinery for packaging and secretion. Focusing on two RBPs, heterogeneous nuclear ribonucleoprotein K (HNRNPK) and scaffold-attachment factor B (SAFB), we demonstrate that these proteins interact with LC3 and are secreted within EVs enriched with lipidated LC3. Furthermore, their secretion requires the LC3-conjugation machinery, neutral sphingomyelinase 2 (nSMase2) and LC3-dependent recruitment of factor associated with nSMase2 activity (FAN). Hence, the LC3-conjugation pathway controls EV cargo loading and secretion.
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Affiliation(s)
- Andrew M Leidal
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Hector H Huang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Timothy Marsh
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tina Solvik
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Dachuan Zhang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jordan Ye
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - FuiBoon Kai
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Juliet Goldsmith
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer Y Liu
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Yu-Hsin Huang
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Teresa Monkkonen
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Ariadne Vlahakis
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Huang
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, Department of Urology, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jayanta Debnath
- Department of Pathology and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
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1762
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Haywood ME, Cocciolo A, Porter KF, Dobrinskikh E, Slavov D, Graw SL, Reece TB, Ambardekar AV, Bristow MR, Mestroni L, Taylor MRG. Transcriptome signature of ventricular arrhythmia in dilated cardiomyopathy reveals increased fibrosis and activated TP53. J Mol Cell Cardiol 2020; 139:124-134. [PMID: 31958463 PMCID: PMC7144813 DOI: 10.1016/j.yjmcc.2019.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 12/19/2019] [Accepted: 12/29/2019] [Indexed: 12/21/2022]
Abstract
AIMS One-third of DCM patients experience ventricular tachycardia (VT), but a clear biological basis for this has not been established. The purpose of this study was to identify transcriptome signatures and enriched pathways in the hearts of dilated cardiomyopathy (DCM) patients with VT. METHODS AND RESULTS We used RNA-sequencing in explanted heart tissue from 49 samples: 19 DCM patients with VT, 16 DCM patients without VT, and 14 non-failing controls. We compared each DCM cohort to the controls and identified the genes that were differentially expressed in DCM patients with VT but not without VT. Differentially expressed genes were evaluated using pathway analysis, and pathways of interest were investigated by qRT-PCR validation, Western blot, and microscopy. There were 590 genes differentially expressed in DCM patients with VT that are not differentially expressed in patients without VT. These genes were enriched for genes in the TGFß1 and TP53 signaling pathways. Increased fibrosis and activated TP53 signaling was demonstrated in heart tissue of DCM patients with VT. CONCLUSIONS Our study supports that distinct biological mechanisms distinguish ventricular arrhythmia in DCM patients.
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Affiliation(s)
- Mary E Haywood
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA.
| | - Andrea Cocciolo
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA
| | - Kadijah F Porter
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
| | - Evgenia Dobrinskikh
- Division of Renal Diseases and Hypertension, Department of Medicine University of Colorado, Aurora, CO, USA.
| | - Dobromir Slavov
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
| | - Sharon L Graw
- Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
| | - T Brett Reece
- Department of Cardiothoracic Surgery, University of Colorado Hospital, Aurora, CO, USA.
| | - Amrut V Ambardekar
- Division of Cardiology, Department of Medicine, University of Colorado, Aurora, CO, USA.
| | - Michael R Bristow
- Division of Cardiology, Department of Medicine, University of Colorado, Aurora, CO, USA.
| | - Luisa Mestroni
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA; Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
| | - Matthew R G Taylor
- Human Medical Genetics and Genomics, University of Colorado, Aurora, CO, USA; Cardiovascular Institute and Adult Medical Genetics Program, University of Colorado, Aurora, CO, USA.
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1763
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Mapping proteome-wide targets of protein kinases in plant stress responses. Proc Natl Acad Sci U S A 2020; 117:3270-3280. [PMID: 31992638 DOI: 10.1073/pnas.1919901117] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein kinases are major regulatory components in almost all cellular processes in eukaryotic cells. By adding phosphate groups, protein kinases regulate the activity, localization, protein-protein interactions, and other features of their target proteins. It is known that protein kinases are central components in plant responses to environmental stresses such as drought, high salinity, cold, and pathogen attack. However, only a few targets of these protein kinases have been identified. Moreover, how these protein kinases regulate downstream biological processes and mediate stress responses is still largely unknown. In this study, we introduce a strategy based on isotope-labeled in vitro phosphorylation reactions using in vivo phosphorylated peptides as substrate pools and apply this strategy to identify putative substrates of nine protein kinases that function in plant abiotic and biotic stress responses. As a result, we identified more than 5,000 putative target sites of osmotic stress-activated SnRK2.4 and SnRK2.6, abscisic acid-activated protein kinases SnRK2.6 and casein kinase 1-like 2 (CKL2), elicitor-activated protein kinase CDPK11 and MPK6, cold-activated protein kinase MPK6, H2O2-activated protein kinase OXI1 and MPK6, and salt-induced protein kinase SOS1 and MPK6, as well as the low-potassium-activated protein kinase CIPK23. These results provide comprehensive information on the role of these protein kinases in the control of cellular activities and could be a valuable resource for further studies on the mechanisms underlying plant responses to environmental stresses.
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1764
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Liu B, Lindner P, Jirmo AC, Maus U, Illig T, DeLuca DS. A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. BMC Bioinformatics 2020; 21:28. [PMID: 31992182 PMCID: PMC6986093 DOI: 10.1186/s12859-020-3366-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite the significant contribution of transcriptomics to the fields of biological and biomedical research, interpreting long lists of significantly differentially expressed genes remains a challenging step in the analysis process. Gene set enrichment analysis is a standard approach for summarizing differentially expressed genes into pathways or other gene groupings. Here, we explore an alternative approach to utilizing gene sets from curated databases. We examine the method of deriving custom gene sets which may be relevant to a given experiment using reference data sets from previous transcriptomics studies. We call these data-derived gene sets, "gene signatures" for the biological process tested in the previous study. We focus on the feasibility of this approach in analyzing immune-related processes, which are complicated in their nature but play an important role in the medical research. RESULTS We evaluate several statistical approaches to detecting the activity of a gene signature in a target data set. We compare the performance of the data-derived gene signature approach with comparable GO term gene sets across all of the statistical tests. A total of 61 differential expression comparisons generated from 26 transcriptome experiments were included in the analysis. These experiments covered eight immunological processes in eight types of leukocytes. The data-derived signatures were used to detect the presence of immunological processes in the test data with modest accuracy (AUC = 0.67). The performance for GO and literature based gene sets was worse (AUC = 0.59). Both approaches were plagued by poor specificity. CONCLUSIONS When investigators seek to test specific hypotheses, the data-derived signature approach can perform as well, if not better than standard gene-set based approaches for immunological signatures. Furthermore, the data-derived signatures can be generated in the cases that well-defined gene sets are lacking from pathway databases and also offer the opportunity for defining signatures in a cell-type specific manner. However, neither the data-derived signatures nor standard gene-sets can be demonstrated to reliably provide negative predictions for negative cases. We conclude that the data-derived signature approach is a useful and sometimes necessary tool, but analysts should be weary of false positives.
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Affiliation(s)
- Bin Liu
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, Hannover, 30167 Germany
| | - Patrick Lindner
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, Hannover, 30167 Germany
| | - Adan Chari Jirmo
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Department of Pediatric Pneumology,Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625 Germany
| | - Ulrich Maus
- Division of Experimental Pneumology, Hannover Medical School, Feodor-Lynen-Straße 21, Hannover, 30625 Germany
| | - Thomas Illig
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Hannover Unified Biobank, Hannover Medical School, Feodor-Lynen-Straße, Hannover, 30625 Germany
| | - David S. DeLuca
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
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1765
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Lee DSM, Ghanem LR, Barash Y. Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations. Nat Commun 2020; 11:527. [PMID: 31988292 PMCID: PMC6985247 DOI: 10.1038/s41467-020-14404-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/03/2020] [Indexed: 11/17/2022] Open
Abstract
G-quadruplex (G4) sequences are abundant in untranslated regions (UTRs) of human messenger RNAs, but their functional importance remains unclear. By integrating multiple sources of genetic and genomic data, we show that putative G-quadruplex forming sequences (pG4) in 5' and 3' UTRs are selectively constrained, and enriched for cis-eQTLs and RNA-binding protein (RBP) interactions. Using over 15,000 whole-genome sequences, we find that negative selection acting on central guanines of UTR pG4s is comparable to that of missense variation in protein-coding sequences. At multiple GWAS-implicated SNPs within pG4 UTR sequences, we find robust allelic imbalance in gene expression across diverse tissue contexts in GTEx, suggesting that variants affecting G-quadruplex formation within UTRs may also contribute to phenotypic variation. Our results establish UTR G4s as important cis-regulatory elements and point to a link between disruption of UTR pG4 and disease.
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Affiliation(s)
- David S M Lee
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Louis R Ghanem
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Computer and Information Science, School of Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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1766
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Domingues AF, Kulkarni R, Giotopoulos G, Gupta S, Vinnenberg L, Arede L, Foerner E, Khalili M, Adao RR, Johns A, Tan S, Zeka K, Huntly BJ, Prabakaran S, Pina C. Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cells. eLife 2020; 9:e51754. [PMID: 31985402 PMCID: PMC7039681 DOI: 10.7554/elife.51754] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/24/2020] [Indexed: 12/21/2022] Open
Abstract
Acute Myeloid Leukemia (AML) is an aggressive hematological malignancy with abnormal progenitor self-renewal and defective white blood cell differentiation. Its pathogenesis comprises subversion of transcriptional regulation, through mutation and by hijacking normal chromatin regulation. Kat2a is a histone acetyltransferase central to promoter activity, that we recently associated with stability of pluripotency networks, and identified as a genetic vulnerability in AML. Through combined chromatin profiling and single-cell transcriptomics of a conditional knockout mouse, we demonstrate that Kat2a contributes to leukemia propagation through preservation of leukemia stem-like cells. Kat2a loss impacts transcription factor binding and reduces transcriptional burst frequency in a subset of gene promoters, generating enhanced variability of transcript levels. Destabilization of target programs shifts leukemia cell fate out of self-renewal into differentiation. We propose that control of transcriptional variability is central to leukemia stem-like cell propagation, and establish a paradigm exploitable in different tumors and distinct stages of cancer evolution.
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Affiliation(s)
- Ana Filipa Domingues
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Rashmi Kulkarni
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - George Giotopoulos
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell InstituteCambridgeUnited Kingdom
| | - Shikha Gupta
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Laura Vinnenberg
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Liliana Arede
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Elena Foerner
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Mitra Khalili
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of Medical Genetics and Molecular Medicine, School of MedicineZanjan University of Medical Sciences (ZUMS)ZanjanIslamic Republic of Iran
| | - Rita Romano Adao
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
| | - Ayona Johns
- Division of Biosciences, College of Health and Life SciencesBrunel University LondonUxbridgeUnited Kingdom
| | - Shengjiang Tan
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
| | - Keti Zeka
- Department of HaematologyUniversity of Cambridge, NHS-BT Blood Donor CentreCambridgeUnited Kingdom
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Brian J Huntly
- Department of HaematologyUniversity of Cambridge, Cambridge Institute for Medical ResearchCambridgeUnited Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell InstituteCambridgeUnited Kingdom
| | - Sudhakaran Prabakaran
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- Department of BiologyIISERPuneIndia
| | - Cristina Pina
- Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
- Division of Biosciences, College of Health and Life SciencesBrunel University LondonUxbridgeUnited Kingdom
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1767
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Trem2 Deletion Reduces Late-Stage Amyloid Plaque Accumulation, Elevates the Aβ42:Aβ40 Ratio, and Exacerbates Axonal Dystrophy and Dendritic Spine Loss in the PS2APP Alzheimer's Mouse Model. J Neurosci 2020; 40:1956-1974. [PMID: 31980586 PMCID: PMC7046459 DOI: 10.1523/jneurosci.1871-19.2019] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/08/2019] [Accepted: 12/23/2019] [Indexed: 01/17/2023] Open
Abstract
TREM2 is an Alzheimer's disease (AD) risk gene expressed in microglia. To study the role of Trem2 in a mouse model of β-amyloidosis, we compared PS2APP transgenic mice versus PS2APP mice lacking Trem2 (PS2APP;Trem2ko) at ages ranging from 4 to 22 months. Microgliosis was impaired in PS2APP;Trem2ko mice, with Trem2-deficient microglia showing compromised expression of proliferation/Wnt-related genes and marked accumulation of ApoE. TREM2 is an Alzheimer's disease (AD) risk gene expressed in microglia. To study the role of Trem2 in a mouse model of β-amyloidosis, we compared PS2APP transgenic mice versus PS2APP mice lacking Trem2 (PS2APP;Trem2ko) at ages ranging from 4 to 22 months. Microgliosis was impaired in PS2APP;Trem2ko mice, with Trem2-deficient microglia showing compromised expression of proliferation/Wnt-related genes and marked accumulation of ApoE. Plaque abundance was elevated in PS2APP;Trem2ko females at 6–7 months; but by 12 or 19–22 months of age, it was notably diminished in female and male PS2APP;Trem2ko mice, respectively. Across all ages, plaque morphology was more diffuse in PS2APP;Trem2ko brains, and the Aβ42:Aβ40 ratio was elevated. The amount of soluble, fibrillar Aβ oligomers also increased in PS2APP;Trem2ko hippocampi. Associated with these changes, axonal dystrophy was exacerbated from 6 to 7 months onward in PS2APP;Trem2ko mice, notwithstanding the reduced plaque load at later ages. PS2APP;Trem2ko mice also exhibited more dendritic spine loss around plaque and more neurofilament light chain in CSF. Thus, aggravated neuritic dystrophy is a more consistent outcome of Trem2 deficiency than amyloid plaque load, suggesting that the microglial packing of Aβ into dense plaque is an important neuroprotective activity. SIGNIFICANCE STATEMENT Genetic studies indicate that TREM2 gene mutations confer increased Alzheimer's disease (AD) risk. We studied the effects of Trem2 deletion in the PS2APP mouse AD model, in which overproduction of Aβ peptide leads to amyloid plaque formation and associated neuritic dystrophy. Interestingly, neuritic dystrophies were intensified in the brains of Trem2-deficient mice, despite these mice displaying reduced plaque accumulation at later ages (12–22 months). Microglial clustering around plaques was impaired, plaques were more diffuse, and the Aβ42:Aβ40 ratio and amount of soluble, fibrillar Aβ oligomers were elevated in Trem2-deficient brains. These results suggest that the Trem2-dependent compaction of Aβ into dense plaques is a protective microglial activity, limiting the exposure of neurons to toxic Aβ species.
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1768
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Magri MS, Jiménez-Gancedo S, Bertrand S, Madgwick A, Escrivà H, Lemaire P, Gómez-Skarmeta JL. Assaying Chromatin Accessibility Using ATAC-Seq in Invertebrate Chordate Embryos. Front Cell Dev Biol 2020; 7:372. [PMID: 32039199 PMCID: PMC6992535 DOI: 10.3389/fcell.2019.00372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/16/2019] [Indexed: 01/30/2023] Open
Abstract
Cis-regulatory elements (CREs) are non-coding DNA regions involved in the spatio-temporal regulation of gene expression. Gene regulatory changes drive animal development and play major roles during evolution of animal body plans. Therefore, we believe that determining CREs at different developmental stages and across animal lineages is critical to understand how evolution operates through development. The Assay for Transposase-Accessible Chromatin followed by high-throughput sequencing (ATAC-seq) is a powerful technique for the study of CREs that takes advantage of Tn5 transposase activity. Starting from fewer than 105 cells, in a 1-day procedure, it is possible to detect, at a genome-wide level, CREs located in open chromatin regions with high resolution. Here, we describe a detailed step-by-step ATAC-seq protocol for invertebrate chordate marine embryos. We have successfully applied this technique to amphioxus and two species of tunicate embryos. We also show an easy workflow to analyze data generated with this technique. Moreover, we point out that this method and our bioinformatic pipeline are efficient to detect CREs associated with Wnt signaling pathway by simply using embryos treated with a drug that perturbs this pathway. This approach can be extended to other signaling pathways and also to embryo mutants for critical genes. Our results therefore demonstrate the power of ATAC-seq for the identification of CREs that play essential functions during animal development in a wide range of invertebrate or vertebrate animals.
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Affiliation(s)
- Marta Silvia Magri
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Sandra Jiménez-Gancedo
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Alicia Madgwick
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
| | - Hector Escrivà
- Sorbonne Université, CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Patrick Lemaire
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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1769
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Boraldi F, Lofaro FD, Costa S, Moscarelli P, Quaglino D. Rare Co-occurrence of Beta-Thalassemia and Pseudoxanthoma elasticum: Novel Biomolecular Findings. Front Med (Lausanne) 2020; 6:322. [PMID: 32039214 PMCID: PMC6989569 DOI: 10.3389/fmed.2019.00322] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/16/2019] [Indexed: 12/18/2022] Open
Abstract
A number of beta-thalassemia patients, independently from the type of beta-thalassemia (β0 or β+) and blood transfusion requirements, may develop, after puberty, dermal, cardiovascular, and ocular complications associated with an ectopic mineralization phenotype similar to that observed in another rare genetic disorder, namely, Pseudoxanthoma elasticum (PXE). To date, the causes of these alterations in beta-thalassemia patients are not known, but it has been suggested that they could be the consequence of oxidative stress-driven epigenetic regulatory mechanisms producing an ABCC6 down-regulation. Since, in the last years, several genes have been associated to the ectopic mineralization phenotype, this study, for the first time, applied, on beta-thalassemia patients with ectopic mineralization phenotype, a multigene testing strategy. Selection of genes to be analyzed was done on the basis of (i) their genetic involvement in calcification diseases or (ii) their role in calcium-phosphate equilibrium. Although, due to the rarity of these conditions, a limited number of patients was analyzed, the detection of pathogenic variants represents the proof of concept that PXE and beta-thalassemia traits co-occur on a genetic basis and that, in addition to causative mutations, functional polymorphisms may further influence connective tissue manifestations. The use of a multigene-based next-generation sequencing represents a useful time- and cost-effective approach, allowing to identify sequence variants that might improve prognostic assessment and better management of these patients, especially in the current era of precision medicine aiming to identify individual optimal care based on a unique personal profile.
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Affiliation(s)
- Federica Boraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Sonia Costa
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Pasquale Moscarelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daniela Quaglino
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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1770
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Kragh ML, Truelstrup Hansen L. Initial Transcriptomic Response and Adaption of Listeria monocytogenes to Desiccation on Food Grade Stainless Steel. Front Microbiol 2020; 10:3132. [PMID: 32038566 PMCID: PMC6987299 DOI: 10.3389/fmicb.2019.03132] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022] Open
Abstract
The foodborne pathogen Listeria monocytogenes survives exposure to a variety of stresses including desiccation in the food industry. Strand-specific RNA sequencing was applied to analyze changes in the transcriptomes of two strains of L. monocytogenes (Lm 568 and Lm 08-5578) during desiccation [15°C, 43% relative humidity (RH)] on food grade stainless steel surfaces over 48 h to simulate a weekend with no food production. Both strains showed similar survival during desiccation with a 1.8-2 Log CFU/cm2 reduction after 48 h. Analysis of differentially expressed (DE) genes (>twofold, adjusted p-value <0.05) revealed that the initial response to desiccation was established after 6 h and remained constant with few new genes being DE after 12, 24, and 48 h. A core of 81 up- and 73 down-regulated DE genes were identified as a shared, strain independent response to desiccation. Among common upregulated genes were energy and oxidative stress related genes e.g., qoxABCD (cytochrome aa3) pdhABC (pyruvate dehydrogenase complex) and mntABCH (manganese transporter). Common downregulated genes related to anaerobic growth, proteolysis and the two component systems lmo1172/lmo1173 and cheA/cheY, which are involved in cold growth and flagellin production, respectively. Both strains upregulated additional genes involved in combatting oxidative stress and reactive oxygen species (ROS), including sod (superoxide dismutase), kat (catalase), tpx (thiol peroxidase) and several thioredoxins including trxAB, lmo2390 and lmo2830. Osmotic stress related genes were also upregulated in both strains, including gbuABC (glycine betaine transporter) and several chaperones clpC, cspA, and groE. Significant strain differences were also detected with the food outbreak strain Lm 08-5578 differentially expressing 1.9 × more genes (726) compared to Lm 568 (410). Unique to Lm 08-5578 was a significant upregulation of the expression of the alternative transcription factor σB and its regulon. A number of long antisense transcripts (lasRNA) were upregulated during desiccation including anti0605, anti0936, anti1846, and anti0777, with the latter controlling flagellum biosynthesis and possibly the downregulation of motility genes observed in both strains. This exploration of the transcriptomes of desiccated L. monocytogenes provides further understanding of how this bacterium encounters and survives the stress faced when exposed to dry conditions in the food industry.
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1771
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Attwood MM, Schiöth HB. Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. Front Cell Dev Biol 2020; 7:386. [PMID: 32039202 PMCID: PMC6987440 DOI: 10.3389/fcell.2019.00386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/19/2019] [Indexed: 11/13/2022] Open
Abstract
As the structure and functions of proteins are correlated, investigating groups of proteins with the same gross structure may provide important insights about their functional roles. Trispanins, proteins that contain three alpha-helical transmembrane (3TM) regions, have not been previously studied considering their transmembrane features. Our comprehensive identification and classification using bioinformatic methods describe 152 3TM proteins. These proteins are frequently involved in membrane biosynthesis and lipid biogenesis, protein trafficking, catabolic processes, and in particular signal transduction due to the large ionotropic glutamate receptor family. Proteins that localize to intracellular compartments are overrepresented in the dataset in comparison to the entire human transmembrane proteome, and nearly 45% localize specifically to the endoplasmic reticulum (ER). Furthermore, nearly 20% of the trispanins function in lipid metabolic processes and transport, which are also overrepresented. Nearly one-third of trispanins are identified as being targeted by drugs and/or being associated with diseases. A high number of 3TMs have unknown functions and based on this analysis we speculate on the functional involvement of uncharacterized trispanins in relationship to disease or important cellular activities. This first overall study of trispanins provides a unique analysis of a diverse group of membrane proteins.
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Affiliation(s)
- Misty M. Attwood
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B. Schiöth
- Functional Pharmacology, Department of Neuroscience, Uppsala University, Uppsala, Sweden
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow, Russia
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1772
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Silvestro S, Chiricosta L, Gugliandolo A, Pizzicannella J, Diomede F, Bramanti P, Trubiani O, Mazzon E. Extracellular Vesicles Derived from Human Gingival Mesenchymal Stem Cells: A Transcriptomic Analysis. Genes (Basel) 2020; 11:genes11020118. [PMID: 31973135 PMCID: PMC7073771 DOI: 10.3390/genes11020118] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/08/2020] [Accepted: 01/18/2020] [Indexed: 02/06/2023] Open
Abstract
Human gingival mesenchymal stem cells (hGMSCs) have outstanding characteristics of proliferation and are able to differentiate into osteogenic, chondrogenic, adipogenic, and neurogenic cell lineages. The extracellular vesicles (EVs) secreted by hGMSCs contain proteins, lipids, mRNA and microRNA have emerged as important mediators of cell-to-cell communication. In this study, we analyzed the transcriptome of hGMSCs-derived EVs using Next Generation Sequencing (NGS). The functional evaluation of the transcriptome highlighted 26 structural protein classes and the presence of "non-coding RNAs". Our results showed that EVs contain several growth factors such as Transforming Growth Factor-β (TGF-β), Fibroblast Growth Factor (FGF), and Vascular Endothelial Growth Factors (VEGF) implicated in osteoblast differentiation and in angiogenetic process. Furthermore, the transcriptomic analysis showed the presence of glial cell-derived neurotrophic factor (GDNF) family ligands and neurotrophins involved in neuronal development. The NGS analysis also identified the presence of several interleukins among which some with anti-inflammatory action. Moreover, the transcriptome profile of EVs contained members of the Wnt family, involved in several biological processes, such as cellular proliferation and tissue regeneration. In conclusion, the huge amount of growth factors included in the hGMSCs-derived EVs could make them a big resource in regenerative medicine.
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Affiliation(s)
- Serena Silvestro
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (S.S.); (L.C.); (A.G.); (P.B.)
| | - Luigi Chiricosta
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (S.S.); (L.C.); (A.G.); (P.B.)
| | - Agnese Gugliandolo
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (S.S.); (L.C.); (A.G.); (P.B.)
| | | | - Francesca Diomede
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” Chieti-Pescara, 66100 Chieti, Italy; (F.D.); (O.T.)
| | - Placido Bramanti
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (S.S.); (L.C.); (A.G.); (P.B.)
| | - Oriana Trubiani
- Department of Medical, Oral and Biotechnological Sciences, University “G. d’Annunzio” Chieti-Pescara, 66100 Chieti, Italy; (F.D.); (O.T.)
| | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, 98124 Messina, Italy; (S.S.); (L.C.); (A.G.); (P.B.)
- Correspondence: ; Tel.: +39-090-60-12-8172
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1773
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Prusinkiewicz MA, Gameiro SF, Ghasemi F, Dodge MJ, Zeng PYF, Maekebay H, Barrett JW, Nichols AC, Mymryk JS. Survival-Associated Metabolic Genes in Human Papillomavirus-Positive Head and Neck Cancers. Cancers (Basel) 2020; 12:E253. [PMID: 31968678 PMCID: PMC7017314 DOI: 10.3390/cancers12010253] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/12/2020] [Accepted: 01/16/2020] [Indexed: 12/12/2022] Open
Abstract
Human papillomavirus (HPV) causes an increasing number of head and neck squamous cell carcinomas (HNSCCs). Altered metabolism contributes to patient prognosis, but the impact of HPV status on HNSCC metabolism remains relatively uncharacterized. We hypothesize that metabolism-related gene expression differences unique to HPV-positive HNSCC influences patient survival. The Cancer Genome Atlas RNA-seq data from primary HNSCC patient samples were categorized as 73 HPV-positive, 442 HPV-negative, and 43 normal-adjacent control tissues. We analyzed 229 metabolic genes and identified numerous differentially expressed genes between HPV-positive and negative HNSCC patients. HPV-positive carcinomas exhibited lower expression levels of genes involved in glycolysis and higher levels of genes involved in the tricarboxylic acid cycle, oxidative phosphorylation, and β-oxidation than the HPV-negative carcinomas. Importantly, reduced expression of the metabolism-related genes SDHC, COX7A1, COX16, COX17, ELOVL6, GOT2, and SLC16A2 were correlated with improved patient survival only in the HPV-positive group. This work suggests that specific transcriptional alterations in metabolic genes may serve as predictive biomarkers of patient outcome and identifies potential targets for novel therapeutic intervention in HPV-positive head and neck cancers.
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Affiliation(s)
- Martin A. Prusinkiewicz
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Steven F. Gameiro
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Farhad Ghasemi
- Department of Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Mackenzie J. Dodge
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - Peter Y. F. Zeng
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
| | - Hanna Maekebay
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
| | - John W. Barrett
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
| | - Anthony C. Nichols
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
- Department of Oncology, The University of Western Ontario, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6C 2R5, Canada
| | - Joe S. Mymryk
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON N6A 3K7, Canada
- Department of Otolaryngology, Head & Neck Surgery, The University of Western Ontario, London, ON N6A 3K7, Canada; (P.Y.F.Z.)
- Department of Oncology, The University of Western Ontario, London, ON N6A 3K7, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, ON N6C 2R5, Canada
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1774
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Dutta P, Saha S, Pai S, Kumar A. A Protein Interaction Information-based Generative Model for Enhancing Gene Clustering. Sci Rep 2020; 10:665. [PMID: 31959782 PMCID: PMC6971242 DOI: 10.1038/s41598-020-57437-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 12/20/2019] [Indexed: 11/18/2022] Open
Abstract
In the field of computational bioinformatics, identifying a set of genes which are responsible for a particular cellular mechanism, is very much essential for tasks such as medical diagnosis or disease gene identification. Accurately grouping (clustering) the genes is one of the important tasks in understanding the functionalities of the disease genes. In this regard, ensemble clustering becomes a promising approach to combine different clustering solutions to generate almost accurate gene partitioning. Recently, researchers have used generative model as a smart ensemble method to produce the right consensus solution. In the current paper, we develop a protein-protein interaction-based generative model that can efficiently perform a gene clustering. Utilizing protein interaction information as the generative model's latent variable enables enhance the generative model's efficiency in inferring final probabilistic labels. The proposed generative model utilizes different weak supervision sources rather utilizing any ground truth information. For weak supervision sources, we use a multi-objective optimization based clustering technique together with the world's largest gene ontology based knowledge-base named Gene Ontology Consortium(GOC). These weakly supervised labels are supplied to a generative model that eventually assigns all genes to probabilistic labels. The comparative study with respect to silhouette score, Biological Homogeneity Index (BHI) and Biological Stability Index (BSI) proves that the proposed generative model outperforms than other state-of-the-art techniques.
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Affiliation(s)
- Pratik Dutta
- Department of Computer Science and Engineering, Indian Institute of Technology Patna, Bihta, 801103, India.
| | - Sriparna Saha
- Department of Computer Science and Engineering, Indian Institute of Technology Patna, Bihta, 801103, India
| | - Sanket Pai
- Department of Chemical Science and Technology, Indian Institute of Technology Patna, Bihta, 801103, India
| | - Aviral Kumar
- Department of Chemical Science and Technology, Indian Institute of Technology Patna, Bihta, 801103, India
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1775
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Baschal EE, Larson ED, Bootpetch Roberts TC, Pathak S, Frank G, Handley E, Dinwiddie J, Moloney M, Yoon PJ, Gubbels SP, Scholes MA, Cass SP, Jenkins HA, Frank DN, Yang IV, Schwartz DA, Ramakrishnan VR, Santos-Cortez RLP. Identification of Novel Genes and Biological Pathways That Overlap in Infectious and Nonallergic Diseases of the Upper and Lower Airways Using Network Analyses. Front Genet 2020; 10:1352. [PMID: 32010199 PMCID: PMC6979043 DOI: 10.3389/fgene.2019.01352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
Previous genetic studies on susceptibility to otitis media and airway infections have focused on immune pathways acting within the local mucosal epithelium, and outside of allergic rhinitis and asthma, limited studies exist on the overlaps at the gene, pathway or network level between the upper and lower airways. In this report, we compared [1] pathways identified from network analysis using genes derived from published genome-wide family-based and association studies for otitis media, sinusitis, and lung phenotypes, to [2] pathways identified using differentially expressed genes from RNA-sequence data from lower airway, sinus, and middle ear tissues, in particular cholesteatoma tissue compared to middle ear mucosa. For otitis media, a large number of genes (n = 1,806) were identified as differentially expressed between cholesteatoma and middle ear mucosa, which in turn led to the identification of 68 pathways that are enriched in cholesteatoma. Two differentially expressed genes CR1 and SAA1 overlap in middle ear, sinus, and lower airway samples and are potentially novel genes for otitis media susceptibility. In addition, 56 genes were differentially expressed in both tissues from the middle ear and either sinus or lower airways. Pathways that are common in upper and lower airway diseases, whether from published DNA studies or from our RNA-sequencing analyses, include chromatin organization/remodeling, endocytosis, immune system process, protein folding, and viral process. Taken together, our findings from genetic susceptibility and differential tissue expression studies support the hypothesis that the unified airway theory wherein the upper and lower respiratory tracts act as an integrated unit also applies to infectious and nonallergic airway epithelial disease. Our results may be used as reference for identification of genes or pathways that are relevant to upper and lower airways, whether common across sites, or unique to each disease.
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Affiliation(s)
- Erin E Baschal
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Eric D Larson
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Tori C Bootpetch Roberts
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shivani Pathak
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Gretchen Frank
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Elyse Handley
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Jordyn Dinwiddie
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Molly Moloney
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J Yoon
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Samuel P Gubbels
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A Scholes
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pediatric Otolaryngology, Children's Hospital Colorado, Aurora, CO, United States
| | - Stephen P Cass
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A Jenkins
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Daniel N Frank
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Ivana V Yang
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Vijay R Ramakrishnan
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Regie Lyn P Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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1776
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Unterholzner J, Gryglewski G, Philippe C, Seiger R, Pichler V, Godbersen GM, Berroterán-Infante N, Murgaš M, Hahn A, Wadsak W, Mitterhauser M, Kasper S, Lanzenberger R. Topologically Guided Prioritization of Candidate Gene Transcripts Coexpressed with the 5-HT1A Receptor by Combining In Vivo PET and Allen Human Brain Atlas Data. Cereb Cortex 2020; 30:3771-3780. [PMID: 31989157 PMCID: PMC7232988 DOI: 10.1093/cercor/bhz341] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
The serotonin-1A receptor (5-HT1AR) represents a viable target in the treatment of disorders of the brain. However, development of psychiatric drugs continues to be hindered by the relative inaccessibility of brain tissue. Although the efficacy of drugs selective for the 5-HT1AR has not been proven, research continues to focus on drugs that influence this receptor subtype. To further knowledge on this topic, we investigated the topological coexpression patterns of the 5-HT1AR. We calculated Spearman’s rho for the correlation of positron emission tomography-binding potentials (BPND) of the 5-HT1AR assessed in 30 healthy subjects using the tracer [carbonyl-11C]WAY-100635 and predicted whole-brain mRNA expression of 18 686 genes. After applying a threshold of r > 0.3 in a leave-one-out cross-validation of the prediction of mRNA expression, genes with ρ ≥ 0.7 were considered to be relevant. In cortical regions, 199 genes showed high correlation with the BPND of the 5-HT1AR, in subcortical regions 194 genes. Using our approach, we could consolidate the role of BDNF and implicate new genes (AnxA8, NeuroD2) in serotonergic functioning. Despite its explorative nature, the analysis can be seen as a gene prioritization approach to reduce the number of genes potentially connected to 5-HT1AR functioning and guide future in vitro studies.
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Affiliation(s)
- Jakob Unterholzner
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Gregor Gryglewski
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Cecile Philippe
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Rene Seiger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Verena Pichler
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Godber M Godbersen
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Neydher Berroterán-Infante
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Matej Murgaš
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Andreas Hahn
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Wolfgang Wadsak
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.,Centre for Biomarker Research in Medicine (CBmed), Stiftingtalstrasse 5, 8010, Graz, Austria
| | - Markus Mitterhauser
- Division of Nuclear Medicine, Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.,Ludwig Boltzmann Institute Applied Diagnostics, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Siegfried Kasper
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Rupert Lanzenberger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
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1777
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Rosa N, Campos B, Esteves AC, Duarte AS, Correia MJ, Silva RM, Barros M. Tracking the functional meaning of the human oral-microbiome protein-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 121:199-235. [PMID: 32312422 DOI: 10.1016/bs.apcsb.2019.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The interactome - the network of protein-protein interactions (PPIs) within a cell or organism - is technically difficult to assess. Bioinformatic tools can, not only, identify potential PPIs that can be later experimentally validated, but also be used to assign functional meaning to PPIs. Saliva's potential as a non-invasive diagnostic fluid is currently being explored by several research groups. But, in order to fully attain its potential, it is necessary to achieve the full characterization of the mechanisms that take place within this ecosystem. The onset of omics technologies, and specifically of proteomics, delivered a huge set of data that is largely underexplored. Quantitative information relative to proteins within a given context (for example a given disease) can be used by computational algorithms to generate information regarding PPIs. These PPIs can be further analyzed concerning their functional meaning and used to identify potential biomarkers, therapeutic targets, defense and pathogenicity mechanisms. We describe a computational pipeline that can be used to identify and analyze PPIs between human and microbial proteins. The pipeline was tested within the scenario of human PPIs of systemic (Zika Virus infection) and of oral conditions (Periodontal disease) and also in the context of microbial interactions (Candida-Streptococcus) and showed to successfully predict functionally relevant PPIs. The pipeline can be applied to different scientific areas, such as pharmacological research, since a functional meaningful PPI network can provide insights on potential drug targets, and even new uses for existing drugs on the market.
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Affiliation(s)
- Nuno Rosa
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Bruno Campos
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Cristina Esteves
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Ana Sofia Duarte
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Maria José Correia
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Raquel M Silva
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
| | - Marlene Barros
- Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
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1778
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Jean-Quartier C, Jeanquartier F, Holzinger A. Open Data for Differential Network Analysis in Glioma. Int J Mol Sci 2020; 21:E547. [PMID: 31952211 PMCID: PMC7013918 DOI: 10.3390/ijms21020547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/29/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022] Open
Abstract
The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. By using selected exemplary tools and open-access resources for cancer research and differential network analysis, we highlight disturbed signaling components in brain cancer subtypes of glioma.
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1779
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Evaluation of SCD, ACACA and FASN Mutations: Effects on Pork Quality and Other Production Traits in Pigs Selected Based on RNA-Seq Results. Animals (Basel) 2020; 10:ani10010123. [PMID: 31940936 PMCID: PMC7023423 DOI: 10.3390/ani10010123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary This study aimed to evaluate mutations within three candidate genes (SCD, ACACA, FASN) for their effects on fattening and slaughter characteristics, as well as meat quality traits, including intramuscular fat (IMF) level in pork. They were selected within differentially expressed genes activated in response to variable backfat content obtained using the RNA sequencing method. The RNA-seq analysis identifies mutations/SNPs located in the mRNA and could be a useful tool for prediction of genetic markers in farm animals. The results showed that selection for FASN A allele in Polish Large White pigs could lead to improved meat quality traits such as water exudation and meat colour. However, analysed polymorphisms showed only slight effects on fat metabolism and IMF content. Abstract In recent years, pig producers have struggled with the problem of low intramuscular fat levels in pork, which impacts palatability and ultimately meat quality. Reduced levels of intramuscular fat are likely the result of breeding objectives aimed at increasing lean meat content. In this study, three mutations within candidate genes for fat content (SCD, ACACA, and FASN) were selected, based on RNA-seq results and the relationship between polymorphisms in genes related to lipid metabolism, fattening and slaughter characteristics, as well as pork quality, including IMF level, were evaluated to identify selection markers. Moreover, their impact on gene expression was also examined. The PCR–RFLP (polymerase cha- in reaction – restriction fragments length) method was used to establish genotypes and effect sizes of potential genetic markers were estimated using a GLM model. It was identified that a FASN missense variant was positively associated with the expression level of this gene, which suggested its linkage with a mutation having a regulatory function. The association study indicated that the FASN missense variant may play a role in the determination of feed conversion and meat colour. In turn, a mutation in the ACACA gene showed a relationship with IMF content in the Puławska breed where the differences reached as much as 20%. We suggest considering all three mutations in further studies based on different pig populations due to the crucial role of SCD, ACACA, and FASN genes in lipid metabolism.
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1780
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Sheih A, Voillet V, Hanafi LA, DeBerg HA, Yajima M, Hawkins R, Gersuk V, Riddell SR, Maloney DG, Wohlfahrt ME, Pande D, Enstrom MR, Kiem HP, Adair JE, Gottardo R, Linsley PS, Turtle CJ. Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy. Nat Commun 2020; 11:219. [PMID: 31924795 PMCID: PMC6954177 DOI: 10.1038/s41467-019-13880-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 12/04/2019] [Indexed: 12/21/2022] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has produced remarkable anti-tumor responses in patients with B-cell malignancies. However, clonal kinetics and transcriptional programs that regulate the fate of CAR-T cells after infusion remain poorly understood. Here we perform TCRB sequencing, integration site analysis, and single-cell RNA sequencing (scRNA-seq) to profile CD8+ CAR-T cells from infusion products (IPs) and blood of patients undergoing CD19 CAR-T immunotherapy. TCRB sequencing shows that clonal diversity of CAR-T cells is highest in the IPs and declines following infusion. We observe clones that display distinct patterns of clonal kinetics, making variable contributions to the CAR-T cell pool after infusion. Although integration site does not appear to be a key driver of clonal kinetics, scRNA-seq demonstrates that clones that expand after infusion mainly originate from infused clusters with higher expression of cytotoxicity and proliferation genes. Thus, we uncover transcriptional programs associated with CAR-T cell behavior after infusion.
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Affiliation(s)
- Alyssa Sheih
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Laïla-Aïcha Hanafi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Hannah A DeBerg
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, 98101, USA
| | - Masanao Yajima
- Department of Mathematics and Statistics, Boston University, Boston, Massachusetts, 02215, USA
| | - Reed Hawkins
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Vivian Gersuk
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, 98101, USA
| | - Stanley R Riddell
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - David G Maloney
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Martin E Wohlfahrt
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Dnyanada Pande
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Mark R Enstrom
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Jennifer E Adair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Raphaël Gottardo
- Vaccine and Infectious Disease Division and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA
| | - Peter S Linsley
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, 98101, USA
| | - Cameron J Turtle
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA.
- Department of Medicine, University of Washington, Seattle, Washington, USA.
- Integrated Immunotherapy Research Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109, USA.
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1781
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Hales EN, Esparza C, Peng S, Dahlgren AR, Peterson JM, Miller AD, Finno CJ. Genome-Wide Association Study and Subsequent Exclusion of ATCAY as a Candidate Gene Involved in Equine Neuroaxonal Dystrophy Using Two Animal Models. Genes (Basel) 2020; 11:E82. [PMID: 31936863 PMCID: PMC7016928 DOI: 10.3390/genes11010082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/01/2020] [Accepted: 01/04/2020] [Indexed: 12/12/2022] Open
Abstract
Equine neuroaxonal dystrophy/equine degenerative myeloencephalopathy (eNAD/EDM) is an inherited neurodegenerative disorder of unknown etiology. Clinical signs of neurological deficits develop within the first year of life in vitamin E (vitE) deficient horses. A genome-wide association study (GWAS) was carried out using 670,000 SNP markers in 27 case and 42 control Quarter Horses. Two markers, encompassing a 2.5 Mb region on ECA7, were associated with the phenotype (p = 2.05 × 10-7 and 4.72 × 10-6). Within this region, caytaxin (ATCAY) was identified as a candidate gene due to its known role in Cayman Ataxia and ataxic/dystonic phenotypes in mouse models. Whole-genome sequence data in four eNAD/EDM and five unaffected horses identified 199 associated variants within the ECA7 region. MassARRAY® genotyping was performed on these variants within the GWAS population. The three variants within ATCAY were not concordant with the disease phenotype. No difference in expression or alternative splicing was identified using qRT-PCR in brainstem across the ATCAY transcript. Atcayji-hes mice were then used to conduct functional analysis in a second animal model. Histologic lesions were not identified in the central nervous system of Atcayji-hes mice. Additionally, supplementation of homozygous Atcayji-hes mice with 600 IU/day of dl-α-tocopheryl acetate (vitE) during gestation, lactation, and adulthood did not improve the phenotype. ATCAY has therefore been excluded as a candidate gene for eNAD/EDM.
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Affiliation(s)
- Erin N Hales
- Department of Population, Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA 95616, USA; (E.N.H.); (C.E.); (S.P.); (A.R.D.); (J.M.P.)
| | - Christina Esparza
- Department of Population, Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA 95616, USA; (E.N.H.); (C.E.); (S.P.); (A.R.D.); (J.M.P.)
| | - Sichong Peng
- Department of Population, Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA 95616, USA; (E.N.H.); (C.E.); (S.P.); (A.R.D.); (J.M.P.)
| | - Anna R Dahlgren
- Department of Population, Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA 95616, USA; (E.N.H.); (C.E.); (S.P.); (A.R.D.); (J.M.P.)
| | - Janel M Peterson
- Department of Population, Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA 95616, USA; (E.N.H.); (C.E.); (S.P.); (A.R.D.); (J.M.P.)
| | - Andrew D Miller
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA;
| | - Carrie J Finno
- Department of Population, Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA 95616, USA; (E.N.H.); (C.E.); (S.P.); (A.R.D.); (J.M.P.)
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1782
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Bhati M, Kadri NK, Crysnanto D, Pausch H. Assessing genomic diversity and signatures of selection in Original Braunvieh cattle using whole-genome sequencing data. BMC Genomics 2020; 21:27. [PMID: 31914939 PMCID: PMC6950892 DOI: 10.1186/s12864-020-6446-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/31/2019] [Indexed: 02/07/2023] Open
Abstract
Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10− 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.
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Affiliation(s)
- Meenu Bhati
- Animal Genomics, ETH Zürich, Zürich, Switzerland.
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1783
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Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. Advances and Applications in the Quest for Orthologs. Mol Biol Evol 2020; 36:2157-2164. [PMID: 31241141 PMCID: PMC6759064 DOI: 10.1093/molbev/msz150] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
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Affiliation(s)
- Natasha Glover
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Department of Genetics, Evolution & Environment, University College London, London, United Kingdom.,Department of Computer Science, University College London, London, United Kingdom
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Centre (BIK-F), Frankfurt, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany.,Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität u Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Maria-Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Cécile Pereira
- Eura Nova, Marseille, France.,Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL
| | - Alan Sousa da Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Yan Wang
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA
| | - Erik Sonnhammer
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA
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1784
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Huang J, Wang C, Li X, Fang X, Huang N, Wang Y, Ma H, Wang Y, Copenhaver GP. Conservation and Divergence in the Meiocyte sRNAomes of Arabidopsis, Soybean, and Cucumber. PLANT PHYSIOLOGY 2020; 182:301-317. [PMID: 31719152 PMCID: PMC6945826 DOI: 10.1104/pp.19.00807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/22/2019] [Indexed: 05/15/2023]
Abstract
Meiosis is a critical process for sexual reproduction. During meiosis, genetic information on homologous chromosomes is shuffled through meiotic recombination to produce gametes with novel allelic combinations. Meiosis and recombination are orchestrated by several mechanisms including regulation by small RNAs (sRNAs). Our previous work in Arabidopsis (Arabidopsis thaliana) meiocytes showed that meiocyte-specific sRNAs (ms-sRNAs) have distinct characteristics, including positive association with the coding region of genes that are transcriptionally upregulated during meiosis. Here, we characterized the ms-sRNAs in two important crops, soybean (Glycine max) and cucumber (Cucumis sativus). Ms-sRNAs in soybean have the same features as those in Arabidopsis, suggesting that they may play a conserved role in eudicots. We also investigated the profiles of microRNAs (miRNAs) and phased secondary small interfering RNAs in the meiocytes of all three species. Two conserved miRNAs, miR390 and miR167, are highly abundant in the meiocytes of all three species. In addition, we identified three novel cucumber miRNAs. Intriguingly, our data show that the previously identified phased secondary small interfering RNA pathway involving soybean-specific miR4392 is more abundant in meiocytes. These results showcase the conservation and divergence of ms-sRNAs in flowering plants, and broaden our understanding of sRNA function in crop species.
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Affiliation(s)
- Jiyue Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
- University of North Carolina at Chapel Hill Department of Biology and the Integrative Program for Biological and Genome Sciences, Genome Science Building, Chapel Hill, North Carolina 27599-3280
| | - Cong Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiang Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaolong Fang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ning Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, Pennsylvania 16802
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Gregory P Copenhaver
- University of North Carolina at Chapel Hill Department of Biology and the Integrative Program for Biological and Genome Sciences, Genome Science Building, Chapel Hill, North Carolina 27599-3280
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599
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1785
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Behr M, Neutelings G, El Jaziri M, Baucher M. You Want it Sweeter: How Glycosylation Affects Plant Response to Oxidative Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:571399. [PMID: 33042189 PMCID: PMC7525049 DOI: 10.3389/fpls.2020.571399] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/01/2020] [Indexed: 05/02/2023]
Abstract
Oxidative stress is a cellular threat which puts at risk the productivity of most of crops valorized by humankind in terms of food, feed, biomaterial, or bioenergy. It is therefore of crucial importance to understand the mechanisms by which plants mitigate the deleterious effects of oxidizing agents. Glycosylation of antioxidant molecules and phytohormones modifies their chemical properties as well as their cellular and histological repartition. This review emphasizes the mechanisms and the outcomes of this conjugation reaction on plant ability to face growing conditions favoring oxidative stress, in mirror with the activity of deglycosylating enzymes. Pioneer evidence bridging flavonoid, glycosylation, and redox homeostasis paved the way for numerous functional analyses of UDP-glycosyltransferases (UGTs), such as the identification of their substrates and their role to circumvent oxidative stress resulting from various environmental challenges. (De)glycosylation appears as a simple chemical reaction regulating the biosynthesis and/or the activity of a myriad of specialized metabolites partaking in response to pathogen and abiotic stresses. This outcome underlies the possibility to valorize UGTs potential to upgrade plant adaptation and fitness in a rising context of sub-optimal growing conditions subsequent to climate change.
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Affiliation(s)
- Marc Behr
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Gosselies, Belgium
| | - Godfrey Neutelings
- UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, Université de Lille, CNRS, Lille, France
| | - Mondher El Jaziri
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Gosselies, Belgium
| | - Marie Baucher
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Gosselies, Belgium
- *Correspondence: Marie Baucher,
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1786
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Abeler-Dörner L, Laing AG, Lorenc A, Ushakov DS, Clare S, Speak AO, Duque-Correa MA, White JK, Ramirez-Solis R, Saran N, Bull KR, Morón B, Iwasaki J, Barton PR, Caetano S, Hng KI, Cambridge E, Forman S, Crockford TL, Griffiths M, Kane L, Harcourt K, Brandt C, Notley G, Babalola KO, Warren J, Mason JC, Meeniga A, Karp NA, Melvin D, Cawthorne E, Weinrick B, Rahim A, Drissler S, Meskas J, Yue A, Lux M, Song-Zhao GX, Chan A, Ballesteros Reviriego C, Abeler J, Wilson H, Przemska-Kosicka A, Edmans M, Strevens N, Pasztorek M, Meehan TF, Powrie F, Brinkman R, Dougan G, Jacobs W, Lloyd CM, Cornall RJ, Maloy KJ, Grencis RK, Griffiths GM, Adams DJ, Hayday AC. High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation. Nat Immunol 2020; 21:86-100. [PMID: 31844327 PMCID: PMC7338221 DOI: 10.1038/s41590-019-0549-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/29/2019] [Indexed: 01/28/2023]
Abstract
By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation (http://www.immunophenotype.org). Specifically, high-throughput phenotyping of 530 unique mouse gene knockouts identified 140 monogenic 'hits', of which most had no previous immunologic association. Furthermore, hits were collectively enriched in genes for which humans show poor tolerance to loss of function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with each other and with specific physiologic traits. Such linkages limit freedom of movement for individual immune parameters, thereby imposing genetically regulated 'immunologic structures', the integrity of which was associated with immunocompetence. Hence, we provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.
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Affiliation(s)
| | - Adam G Laing
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | - Anna Lorenc
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | - Dmitry S Ushakov
- Department of Immunobiology, King's College London, London, UK
- The Francis Crick Institute, London, UK
| | | | | | | | | | | | - Namita Saran
- Department of Immunobiology, King's College London, London, UK
| | | | - Belén Morón
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jua Iwasaki
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Philippa R Barton
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - Susana Caetano
- Department of Immunobiology, King's College London, London, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Keng I Hng
- Department of Immunobiology, King's College London, London, UK
| | | | - Simon Forman
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | | | | | | | | | | | - Kolawole O Babalola
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Jonathan Warren
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Jeremy C Mason
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Amrutha Meeniga
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Natasha A Karp
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge, UK
| | | | | | - Brian Weinrick
- Department of Microbiology and Immunology, Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Albina Rahim
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Justin Meskas
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Alice Yue
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Markus Lux
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Anna Chan
- Department of Immunobiology, King's College London, London, UK
| | | | | | | | | | - Matthew Edmans
- MRC Human Immunology Unit, University of Oxford, Oxford, UK
| | | | - Markus Pasztorek
- Department of Immunobiology, King's College London, London, UK
- Department of Biomedical Science, University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Terrence F Meehan
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, UK
| | - Fiona Powrie
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Ryan Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
- Department of Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | | | - William Jacobs
- Department of Microbiology and Immunology, Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Clare M Lloyd
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Kevin J Maloy
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Richard K Grencis
- Lydia Becker Institute of Immunology and Inflammation, Wellcome Trust Centre for Cell Matrix Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Gillian M Griffiths
- Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | | | - Adrian C Hayday
- Department of Immunobiology, King's College London, London, UK.
- The Francis Crick Institute, London, UK.
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1787
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Somjee R, Mitrea DM, Kriwacki RW. Exploring Relationships between the Density of Charged Tracts within Disordered Regions and Phase Separation. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020; 25:207-218. [PMID: 31797598 PMCID: PMC6939312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Biomolecular condensates form through a process termed phase separation and play diverse roles throughout the cell. Proteins that undergo phase separation often have disordered regions that can engage in weak, multivalent interactions; however, our understanding of the sequence grammar that defines which proteins phase separate is far from complete. Here, we show that proteins that display a high density of charged tracts within intrinsically disordered regions are likely to be constituents of electrostatically organized biomolecular condensates. We scored the human proteome using an algorithm termed ABTdensity that quantifies the density of charged tracts and observed that proteins with more charged tracts are enriched in particular Gene Ontology annotations and, based upon analysis of interaction networks, cluster into distinct biomolecular condensates. These results suggest that electrostatically-driven, multivalent interactions involving charged tracts within disordered regions serve to organize certain biomolecular condensates through phase separation.
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Affiliation(s)
- Ramiz Somjee
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
- Department of Chemistry, Rhodes College, 2000 North Parkway, Memphis, Tennessee 38112, USA,
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1788
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Califar B, Sng NJ, Zupanska A, Paul AL, Ferl RJ. Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:239. [PMID: 32194611 PMCID: PMC7064724 DOI: 10.3389/fpls.2020.00239] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 02/17/2020] [Indexed: 05/03/2023]
Abstract
The observation that plant roots skew in microgravity recently refuted the long-held conviction that skewing was a gravity-dependent phenomenon. Further, spaceflight root skewing suggests that specific root morphologies and cell wall remodeling systems may be important aspects of spaceflight physiological adaptation. However, connections between skewing, cell wall modification and spaceflight physiology are currently based on inferences rather than direct tests. Therefore, the Advanced Plant Experiments-03-2 (APEX-03-2) spaceflight study was designed to elucidate the contribution of two skewing- and cell wall-associated genes in Arabidopsis to root behavior and gene expression patterns in spaceflight, to assess whether interruptions of different skewing pathways affect the overall spaceflight-associated process. SPIRAL1 is a skewing-related protein implicated in directional cell expansion, and functions by regulating cortical microtubule dynamics. SKU5 is skewing-related glycosylphosphatidylinositol-anchored protein of the plasma membrane and cell wall implicated in stress response signaling. These two genes function in different cellular pathways that affect skewing on the Earth, and enable a test of the relevance of skewing pathways to spaceflight physiological adaptation. In this study, both sku5 and spr1 mutants showed different skewing behavior and markedly different patterns of gene expression in the spaceflight environment. The spr1 mutant showed fewer differentially expressed genes than its Col-0 wild-type, whereas sku5 showed considerably more than its WS wild-type. Developmental age played a substantial role in spaceflight acclimation in all genotypes, but particularly in sku5 plants, where spaceflight 4d seedlings had almost 10-times as many highly differentially expressed genes as the 8d seedlings. These differences demonstrated that the two skewing pathways represented by SKU5 and SPR1 have unique and opposite contributions to physiological adaptation to spaceflight. The spr1 response is less intense than wild type, suggesting that the loss of SPR1 positively impacts spaceflight adaptation. Conversely, the intensity of the sku5 responses suggests that the loss of SKU5 initiates a much more complex, deeper and more stress related response to spaceflight. This suggests that proper SKU5 function is important to spaceflight adaptation.
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Affiliation(s)
- Brandon Califar
- Horticultural Sciences, University of Florida, Gainesville, FL, United States
- The Genetics Institute, University of Florida, Gainesville, FL, United States
- Program in Genetics and Genomics, University of Florida, Gainesville, FL, United States
| | - Natasha J. Sng
- Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Agata Zupanska
- Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Anna-Lisa Paul
- Horticultural Sciences, University of Florida, Gainesville, FL, United States
- The Genetics Institute, University of Florida, Gainesville, FL, United States
- Program in Genetics and Genomics, University of Florida, Gainesville, FL, United States
- Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, United States
- Interdisciplinary Center for Biotechnology and Research, University of Florida, Gainesville, FL, United States
- *Correspondence: Anna-Lisa Paul,
| | - Robert J. Ferl
- Horticultural Sciences, University of Florida, Gainesville, FL, United States
- The Genetics Institute, University of Florida, Gainesville, FL, United States
- Program in Genetics and Genomics, University of Florida, Gainesville, FL, United States
- Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, United States
- Robert J. Ferl,
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1789
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Palmisano A, Krushkal J, Li MC, Fang J, Sonkin D, Wright G, Yee L, Zhao Y, McShane L. Bioinformatics Tools and Resources for Cancer Immunotherapy Study. Methods Mol Biol 2020; 2055:649-678. [PMID: 31502173 DOI: 10.1007/978-1-4939-9773-2_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In recent years, cancer immunotherapy has emerged as a highly promising approach to treat patients with cancer, as the patient's own immune system is harnessed to attack cancer cells. However, the application of these approaches is still limited to a minority of patients with cancer and it is difficult to predict which patients will derive the greatest clinical benefit.One of the challenges faced by the biomedical community in the search of more effective biomarkers is the fact that translational research efforts involve collecting and accessing data at many different levels: from the type of material examined (e.g., cell line, animal models, clinical samples) to multiple data type (e.g., pharmacodynamic markers, genetic sequencing data) to the scale of a study (e.g., small preclinical study, moderate retrospective study on stored specimen sets, clinical trials with large cohorts).This chapter reviews several publicly available bioinformatics tools and data resources for high throughput molecular analyses applied to a range of data types, including those generated from microarray, whole-exome sequencing (WES), RNA-seq, DNA copy number, and DNA methylation assays, that are extensively used for integrative multidimensional data analysis and visualization.
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Affiliation(s)
- Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ming-Chung Li
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianwen Fang
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - George Wright
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura Yee
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Lisa McShane
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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1790
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Akekawatchai C, Roytrakul S, Phaonakrop N, Jaresitthikunchai J, Jitrapakdee S. Proteomic Analysis of the Anoikis-Resistant Human Breast Cancer Cell Lines. Methods Mol Biol 2020; 2138:185-193. [PMID: 32219748 DOI: 10.1007/978-1-0716-0471-7_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Acquisition of anoikis resistance is a prerequisite for cancer metastasis and invasion, which are major causes of death from cancer. The molecular mechanisms underlying antianoikis properties in cancer cells are still largely unclear. Here, we describe a protocol for preparation of anoikis-resistant cultured nonmetastatic MCF-7 and metastatic MDA-MB-231 cell lines. The anoikis-resistant cultures were prepared by plating cells in the poly-2-hydroxyethyl methacrylate coated plates and cultured for 24 h. The viability of cells in the cultures was determined using trypan blue staining and annexin V cell death assay, while protein profiles associated with anoikis-resistance in both cells and conditioned media were analyzed by proteomics.
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Affiliation(s)
- Chareeporn Akekawatchai
- Faculty of Allied Health Sciences, Department of Medical Technology, Thammasat University, Pathumtani, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumtani, Thailand
| | - Narumon Phaonakrop
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumtani, Thailand
| | - Janthima Jaresitthikunchai
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumtani, Thailand
| | - Sarawut Jitrapakdee
- Faculty of Science, Department of Biochemistry, Mahidol University, Bangkok, Thailand.
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1791
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Gromova O, Torshin I, Semenov V, Putilina M, Chuchalin A. Direct and indirect neurological manifestations of COVID-19. Zh Nevrol Psikhiatr Im S S Korsakova 2020; 120:11-21. [DOI: 10.17116/jnevro202012011111] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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1792
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Neocleous V, Fanis P, Toumba M, Tanteles GA, Schiza M, Cinarli F, Nicolaides NC, Oulas A, Spyrou GM, Mantzoros CS, Vlachakis D, Skordis N, Phylactou LA. GnRH Deficient Patients With Congenital Hypogonadotropic Hypogonadism: Novel Genetic Findings in ANOS1, RNF216, WDR11, FGFR1, CHD7, and POLR3A Genes in a Case Series and Review of the Literature. Front Endocrinol (Lausanne) 2020; 11:626. [PMID: 32982993 PMCID: PMC7485345 DOI: 10.3389/fendo.2020.00626] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Congenital hypogonadotropic hypogonadism (CHH) is a rare genetic disease caused by Gonadotropin-Releasing Hormone (GnRH) deficiency. So far a limited number of variants in several genes have been associated with the pathogenesis of the disease. In this original research and review manuscript the retrospective analysis of known variants in ANOS1 (KAL1), RNF216, WDR11, FGFR1, CHD7, and POLR3A genes is described, along with novel variants identified in patients with CHH by the present study. Methods: Seven GnRH deficient unrelated Cypriot patients underwent whole exome sequencing (WES) by Next Generation Sequencing (NGS). The identified novel variants were initially examined by in silico computational algorithms and structural analysis of their predicted pathogenicity at the protein level was confirmed. Results: In four non-related GnRH males, a novel X-linked pathogenic variant in ANOS1 gene, two novel autosomal dominant (AD) probably pathogenic variants in WDR11 and FGFR1 genes and one rare AD probably pathogenic variant in CHD7 gene were identified. A rare autosomal recessive (AR) variant in the SRA1 gene was identified in homozygosity in a female patient, whilst two other male patients were also, respectively, found to carry novel or previously reported rare pathogenic variants in more than one genes; FGFR1/POLR3A and SRA1/RNF216. Conclusion: This report embraces the description of novel and previously reported rare pathogenic variants in a series of genes known to be implicated in the biological development of CHH. Notably, patients with CHH can harbor pathogenic rare variants in more than one gene which raises the hypothesis of locus-locus interactions providing evidence for digenic inheritance. The identification of such aberrations by NGS can be very informative for the management and future planning of these patients.
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Affiliation(s)
- Vassos Neocleous
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pavlos Fanis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Meropi Toumba
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Pediatric Endocrine Clinic, IASIS Hospital, Paphos, Cyprus
| | - George A. Tanteles
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Clinical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Melpo Schiza
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Feride Cinarli
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nicolas C. Nicolaides
- Division of Endocrinology, Diabetes and Metabolism, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, “Aghia Sophia” Childrens Hospital, Athens, Greece
- Division of Endocrinology and Metabolism, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Anastasis Oulas
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Bioinformatics ERA Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George M. Spyrou
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Bioinformatics ERA Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Christos S. Mantzoros
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Section of Endocrinology, Diabetes and Metabolism, Boston VA Healthcare System, Boston, MA, United States
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
- Lab of Molecular Endocrinology, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Nicos Skordis
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Division of Pediatric Endocrinology, Paedi Center for Specialized Pediatrics, Nicosia, Cyprus
- St George's, University of London Medical School at the University of Nicosia, Nicosia, Cyprus
- *Correspondence: Nicos Skordis
| | - Leonidas A. Phylactou
- Department of Molecular Genetics, Function and Therapy, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Leonidas A. Phylactou
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1793
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Gorr MW, Sriram K, Chinn AM, Muthusamy A, Insel PA. Transcriptomic profiles reveal differences between the right and left ventricle in normoxia and hypoxia. Physiol Rep 2020; 8:e14344. [PMID: 31960631 PMCID: PMC6971333 DOI: 10.14814/phy2.14344] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chronic hypoxia from diseases in the lung, such as pulmonary hypertension, pulmonary fibrosis, and chronic obstructive pulmonary disease, can increase pulmonary vascular resistance, resulting in hypertrophy and dysfunction of the right ventricle (RV). In order to obtain insight into RV biology and perhaps uncover potentially novel therapeutic approaches for RV dysfunction, we performed RNA-sequencing (RNA-seq) of RV and LV tissue from rats in normal ambient conditions or subjected to hypoxia (10% O2 ) for 2 weeks. Gene ontology and pathway analysis of the RV and LV revealed multiple transcriptomic differences, in particular increased expression in the RV of genes related to immune function in both normoxia and hypoxia. Immune cell profiling by flow cytometry of cardiac digests revealed that in both conditions, the RV had a larger percentage than the LV of double-positive CD45+ /CD11b/c+ cells (which are predominantly macrophages and dendritic cells). Analysis of gene expression changes under hypoxic conditions identified multiple pathways that may contribute to hypoxia-induced changes in the RV, including increased expression of genes related to cell mitosis/proliferation and decreased expression of genes related to metabolic processes. Together, the findings indicate that the RV differs from the LV with respect to content of immune cells and expression of certain genes, thus suggesting the two ventricles differ in aspects of pathophysiology and in potential therapeutic targets for RV dysfunction.
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Affiliation(s)
- Matthew W. Gorr
- Dorothy M. Davis Heart and Lung Research InstituteCollege of MedicineThe Ohio State UniversityColumbusOHUSA
- College of NursingThe Ohio State UniversityColumbusOHUSA
| | - Krishna Sriram
- Department of PharmacologyUniversity of California San DiegoLa JollaCAUSA
| | - Amy M. Chinn
- Department of PharmacologyUniversity of California San DiegoLa JollaCAUSA
| | - Abinaya Muthusamy
- Department of PharmacologyUniversity of California San DiegoLa JollaCAUSA
| | - Paul A. Insel
- Department of PharmacologyUniversity of California San DiegoLa JollaCAUSA
- Department of MedicineUniversity of California San DiegoLa JollaCAUSA
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1794
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Groen K, Maltby VE, Scott RJ, Tajouri L, Lechner‐Scott J. Erythrocyte microRNAs show biomarker potential and implicate multiple sclerosis susceptibility genes. Clin Transl Med 2020; 10:74-90. [PMID: 32508012 PMCID: PMC7240864 DOI: 10.1002/ctm2.22] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Multiple sclerosis is a demyelinating autoimmune disease, for which there is no blood-borne biomarker. Erythrocytes may provide a source of such biomarkers as they contain microRNAs. MicroRNAs regulate protein translation through complementary binding to messenger RNA. As erythrocytes are transcriptionally inactive, their microRNA profiles may be less susceptible to variation. The aim of this study was to assess the biomarker potential of erythrocyte microRNAs for multiple sclerosis and assess the potential contribution of erythrocyte-derived extracellular vesicle microRNAs to pathology. METHODS Erythrocytes were isolated from whole blood by density gradient centrifugation. Erythrocyte microRNAs of a discovery cohort (23 multiple sclerosis patients and 22 healthy controls) were sequenced. Increased expression of miR-183 cluster microRNAs (hsa-miR-96-5p, hsa-miR-182-5p and hsa-miR-183-5p) was validated in an independent cohort of 42 patients and 45 healthy and pathological (migraine) controls. Erythrocyte-derived extracellular vesicles were created ex vivo and their microRNAs were sequenced. Targets of microRNAs were predicted using miRDIP. RESULTS Hsa-miR-182-5p and hsa-miR-183-5p were able to discriminate relapsing multiple sclerosis patients from migraine patients and/or healthy controls with 89-94% accuracy and around 90% specificity. Hsa-miR-182-5p and hsa-miR-183-5p expression correlated with measures of physical disability and hsa-miR-96-5p expression correlated with measures of cognitive disability in multiple sclerosis. Erythrocytes were found to selectively package microRNAs into extracellular vesicles and 34 microRNAs were found to be differentially packaged between healthy controls and multiple sclerosis patients. Several gene targets of differentially expressed and packaged erythrocyte microRNAs overlapped with multiple sclerosis susceptibility genes. Gene enrichment analysis indicated involvement in nervous system development and histone H3-K27 demethylation. CONCLUSIONS Erythrocyte miR-183 cluster members may be developed into specific multiple sclerosis biomarkers that could assist with diagnosis and disability monitoring. Erythrocyte and their extracellular microRNAs were shown to target multiple sclerosis susceptibility genes and may be contributing to the pathophysiology via previously identified routes.
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Affiliation(s)
- Kira Groen
- School of Medicine and Public HealthUniversity of NewcastleCallaghanNew South WalesAustralia
- Centre for Brain and Mental Health ResearchHunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
| | - Vicki E. Maltby
- School of Medicine and Public HealthUniversity of NewcastleCallaghanNew South WalesAustralia
- Centre for Brain and Mental Health ResearchHunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- Department of NeurologyJohn Hunter HospitalNew Lambton HeightsNew South WalesAustralia
| | - Rodney J. Scott
- CancerHunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- Division of Molecular MedicinePathology NorthJohn Hunter HospitalNew Lambton HeightsNew South WalesAustralia
- School of Biomedical Sciences and PharmacyUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Lotti Tajouri
- Faculty of Health Sciences and MedicineBond UniversityRobinaQueenslandAustralia
- Dubai Police Scientific CouncilDubaiUnited Arab Emirates
| | - Jeannette Lechner‐Scott
- School of Medicine and Public HealthUniversity of NewcastleCallaghanNew South WalesAustralia
- Centre for Brain and Mental Health ResearchHunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- Department of NeurologyJohn Hunter HospitalNew Lambton HeightsNew South WalesAustralia
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1795
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Kelahmetoglu Y, Jannig PR, Cervenka I, Koch LG, Britton SL, Zhou J, Wang H, Robinson MM, Nair KS, Ruas JL. Comparative Analysis of Skeletal Muscle Transcriptional Signatures Associated With Aerobic Exercise Capacity or Response to Training in Humans and Rats. Front Endocrinol (Lausanne) 2020; 11:591476. [PMID: 33193103 PMCID: PMC7649134 DOI: 10.3389/fendo.2020.591476] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022] Open
Abstract
Increasing exercise capacity promotes healthy aging and is strongly associated with lower mortality rates. In this study, we analyzed skeletal muscle transcriptomics coupled to exercise performance in humans and rats to dissect the inherent and response components of aerobic exercise capacity. Using rat models selected for intrinsic and acquired aerobic capacity, we determined that the high aerobic capacity muscle transcriptome is associated with pathways for tissue oxygenation and vascularization. Conversely, the low capacity muscle transcriptome indicated immune response and metabolic dysfunction. Low response to training was associated with an inflammatory signature and revealed a potential link to circadian rhythm. Next, we applied bioinformatics tools to predict potential secreted factors (myokines). The predicted secretome profile for exercise capacity highlighted circulatory factors involved in lipid metabolism and the exercise response secretome was associated with extracellular matrix remodelling. Lastly, we utilized human muscle mitochondrial respiration and transcriptomics data to explore molecular mediators of exercise capacity and response across species. Human transcriptome comparison highlighted epigenetic mechanisms linked to exercise capacity and the damage repair for response. Overall, our findings from this cross-species transcriptome analysis of exercise capacity and response establish a foundation for future studies on the mechanisms that link exercise and health.
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Affiliation(s)
- Yildiz Kelahmetoglu
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum. Karolinska Institute, Stockholm, Sweden
| | - Paulo R. Jannig
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum. Karolinska Institute, Stockholm, Sweden
| | - Igor Cervenka
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum. Karolinska Institute, Stockholm, Sweden
| | - Lauren G. Koch
- Department of Physiology and Pharmacology, The University of Toledo College of Medicine and Life Sciences, Toledo, OH, United States
| | - Steven L. Britton
- Department of Anesthesiology, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Jiajia Zhou
- Li Ka Shing Institute of Health Sciences, Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Li Ka Shing Institute of Health Sciences, Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew M. Robinson
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, United States
- Department of Integrative Physiology, Division of Endocrinology, Diabetes and Nutrition, Mayo Clinic, Rochester, MN, United States
| | - K Sreekumaran Nair
- Department of Integrative Physiology, Division of Endocrinology, Diabetes and Nutrition, Mayo Clinic, Rochester, MN, United States
| | - Jorge L. Ruas
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Biomedicum. Karolinska Institute, Stockholm, Sweden
- *Correspondence: Jorge L. Ruas,
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1796
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Silva-Pereira TT, Ikuta CY, Zimpel CK, Camargo NCS, de Souza Filho AF, Ferreira Neto JS, Heinemann MB, Guimarães AMS. Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens). BMC Genomics 2019; 20:1030. [PMID: 31888476 PMCID: PMC6937676 DOI: 10.1186/s12864-019-6407-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/17/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization. RESULTS We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC. CONCLUSION The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.
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Affiliation(s)
- Taiana T Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cristina K Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila C S Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Antônio F de Souza Filho
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José S Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcos B Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana M S Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil. .,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
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1797
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Lee IPA, Andam CP. Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle. BMC Microbiol 2019; 19:306. [PMID: 31881843 PMCID: PMC6935241 DOI: 10.1186/s12866-019-1664-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/26/2019] [Indexed: 01/14/2023] Open
Abstract
Background Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources. Results The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production. Conclusions Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.
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Affiliation(s)
- Isaiah Paolo A Lee
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA
| | - Cheryl P Andam
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
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1798
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A systems biology approach reveals neuronal and muscle developmental defects after chronic exposure to ionising radiation in zebrafish. Sci Rep 2019; 9:20241. [PMID: 31882844 PMCID: PMC6934629 DOI: 10.1038/s41598-019-56590-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/13/2019] [Indexed: 11/11/2022] Open
Abstract
Contamination of the environment after the Chernobyl and Fukushima Daiichi nuclear power plant (NPP) disasters led to the exposure of a large number of humans and wild animals to radioactive substances. However, the sub-lethal consequences induced by these absorbed radiological doses remain understudied and the long-term biological impacts largely unknown. We assessed the biological effects of chronic exposure to ionizing radiation (IR) on embryonic development by exposing zebrafish embryo from fertilization and up to 120 hours post-fertilization (hpf) at dose rates of 0.5 mGy/h, 5 mGy/h and 50 mGy/h, thereby encompassing the field of low dose rates defined at 6 mGy/h. Chronic exposure to IR altered larval behaviour in a light-dark locomotor test and affected cardiac activity at a dose rate as low as 0.5 mGy/h. The multi-omics analysis of transcriptome, proteome and transcription factor binding sites in the promoters of the deregulated genes, collectively points towards perturbations of neurogenesis, muscle development, and retinoic acid (RA) signaling after chronic exposure to IR. Whole-mount RNA in situ hybridization confirmed the impaired expression of the transcription factors her4.4 in the central nervous system and myogenin in the developing muscles of exposed embryos. At the organ level, the assessment of muscle histology by transmission electron microscopy (TEM) demonstrated myofibers disruption and altered neuromuscular junctions in exposed larvae at 5 mGy/h and 50 mGy/h. The integration of these multi-level data demonstrates that chronic exposure to low dose rates of IR has an impact on neuronal and muscle progenitor cells, that could lead to motility defects in free swimming larvae at 120 hpf. The mechanistic understanding of these effects allows us to propose a model where deregulation of RA signaling by chronic exposure to IR has pleiotropic effects on neurogenesis and muscle development.
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1799
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Single Nucleotide Polymorphism rs6942067 Is a Risk Factor in Young and in Non-Smoking Patients with HPV Negative Head and Neck Squamous Cell Carcinoma. Cancers (Basel) 2019; 12:cancers12010055. [PMID: 31878157 PMCID: PMC7017251 DOI: 10.3390/cancers12010055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 12/04/2019] [Accepted: 12/20/2019] [Indexed: 12/24/2022] Open
Abstract
Genetic factors behind the increasing incidence of human papillomavirus (HPV) negative head and neck squamous cell carcinoma (HNSCC) in young non-smokers are suspected, but have not been identified. Recently, rs6942067, a single nucleotide polymorphism (SNP) located upstream of the DCBLD1 gene, was found associated with non-smoking lung adenocarcinoma. To validate if this SNP is also implicated in HNSCC, participants of The Cancer Genome Atlas HNSCC cohort were investigated for rs6942067 status, associated DCBLD1 expression, and clinical characteristics. Occurrence of the rs6942067 GG genotype is significantly higher in young and in HPV negative non-smoking HNSCC than in other HNSCC. Additionally, rs6942067 GG is associated with higher DCBLD1 expression in HNSCC and patients with high DCBLD1 expression have a worse overall survival at three years, both in univariate and multivariate analysis. Furthermore, high DCBLD1 expression is associated with activation of the integrin signaling pathway and its phosphorylation with EGFR and MET. Collectively, these findings suggest that DCBLD1 plays a critical role in HNSCC and demonstrate an association between rs6942067 and clinical characteristics of young age and HPV negative non-smoking status in HNSCC patients.
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1800
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Kaalia R, Rajapakse JC. Refining modules to determine functionally significant clusters in molecular networks. BMC Genomics 2019; 20:901. [PMID: 31874644 PMCID: PMC6929267 DOI: 10.1186/s12864-019-6294-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/15/2019] [Indexed: 12/12/2022] Open
Abstract
Background Module detection algorithms relying on modularity maximization suffer from an inherent resolution limit that hinders detection of small topological modules, especially in molecular networks where most biological processes are believed to form small and compact communities. We propose a novel modular refinement approach that helps finding functionally significant modules of molecular networks. Results The module refinement algorithm improves the quality of topological modules in protein-protein interaction networks by finding biologically functionally significant modules. The algorithm is based on the fact that functional modules in biology do not necessarily represent those corresponding to maximum modularity. Larger modules corresponding to maximal modularity are incrementally re-modularized again under specific constraints so that smaller yet topologically and biologically valid modules are recovered. We show improvement in quality and functional coverage of modules using experiments on synthetic and real protein-protein interaction networks. We also compare our results with six existing methods available for clustering biological networks. Conclusion The proposed algorithm finds smaller but functionally relevant modules that are undetected by classical quality maximization approaches for modular detection. The refinement procedure helps to detect more functionally enriched modules in protein-protein interaction networks, which are also more coherent with functionally characterised gene sets.
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Affiliation(s)
- Rama Kaalia
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Jagath C Rajapakse
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
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