Transcriptomics of Neonatal and Infant Human Thymus

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2022
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SPRINGER INTERNATIONAL PUBLISHING
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Moreira-Filho, C. A.; Bando, S. Y.; Bertonha, F. B.; Carneiro-Sampaio, M.. Transcriptomics of Neonatal and Infant Human Thymus. In: . Transcriptomics in Health and Disease, Second Edition: SPRINGER INTERNATIONAL PUBLISHING, 2022. p.109-125.
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Genomic studies on human thymic development, growth, and involution are crucially demanded for understanding the processes of immunosenescence and inflammaging. Age-related thymus decline is mainly associated with adaptative immune system malfunction, leading to autoimmunity and ineffective responses to infections. Thymic explants obtained at cardiac surgery constitute an asset for transcriptomic studies of human thymus at critical stages of organ growth and initial decline. This chapter deals with the interpretation of whole thymic tissue transcriptomic datasets using modular transcriptional analysis techniques and integrative mRNA–miRNA–transcription factor (TF) co-expression analysis. © The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG 2014, 2022.
Palavras-chave
Age-related, Age-related thymus decline, Aire, AIRE interactors, Co-expression analysis, Co-expression network analysis, Communities, Expression profiles, Gene co-expression, Gene expression, High-hierarchical genes, Highly connected genes (hubs), Immunosenescence, Microarray, Minipuberty, MiRNA-target analysis, Modular repertoire, Modular transcriptional repertoires, MRNA-miRNA, Neonate thymus, RT-qPCR, ScRNA-seq, Sex hormones, Sexual dimorphism, Thymic decline, Thymic epithelial cells, Thymus, Thymus development, Transcriptomics
Referências
  1. Abramson J., Goldfarb Y., AIRE: From promiscuous molecular partnerships to promiscuous gene expression, Eur J Immunol, 46, pp. 22-33, (2016)
  2. Abramson J., Giraud M., Benoist C., AIRE’s partners in the molecular control of immunological tolerance, Cell, 140, pp. 123-135, (2010)
  3. Azevedo H., Moreira-Filho C.A., Topological robustness analysis of protein interaction networks reveals key targets for overcoming chemotherapy resistance in glioma, Sci Rep, 5, (2015)
  4. Bando S.Y., Silva F.N., Costa L., Complex network analysis of CA3 transcriptome reveals pathogenic and compensatory pathways in refractory temporal lobe epilepsy, Plos One, e79913, (2013)
  5. Bando S.Y., Bertonha F.B., Pimentel-Silva L.R., Hippocampal CA3 transcriptional modules associated with granule cell alterations and cognitive impairment in refractory mesial temporal lobe epilepsy patients, Sci Rep, 11, 1, (2021)
  6. Barabasi A.L., Oltvai Z.N., Network biology: Understanding the cell’s functional organization, Nat Rev Genet, 5, pp. 101-113, (2004)
  7. Barabasi A.L., Gulbahce N., Loscalzo J., Network medicine: A network-based approach to human disease, Nat Rev Genet, 13, pp. 56-68, (2011)
  8. Becker M., Hesse V., Minipuberty: Why does it happen?, Horm Res Paediatr, 93, pp. 76-84, (2020)
  9. Berrih-Aknin S., Panse R.L., Dragin N., AIRE: A missing link to explain female susceptibility to autoimmune diseases, Ann N Y Acad Sci, 1412, pp. 21-32, (2018)
  10. Bertonha F.B., Bando S.Y., Ferreira L.R., Age-related transcriptional modules and TF- miRNA-mRNA interactions in neonatal and infant human thymus, Plos One, e0227547, (2020)
  11. Billi A.C., Kahlenberg J.M., Gudjonsson J.E., Sex bias in autoimmunity, Curr Opin Rheumatol, 31, pp. 53-61, (2019)
  12. Blondel V.D., Guillaume J.L., Lambiotte R., Fast unfolding of communities in large networks, J Stat Mech, (2008)
  13. Cao S., Carlesso G., Osipovich A.B., Subunit 1 of the prefoldin chaperone complex is required for lymphocyte development and function, J Immunol, 181, pp. 476-484, (2008)
  14. Chaussabel D., Baldwin N., Democratizing systems immunology with modular transcriptional repertoire analyses, Nat Rev Immunol, 14, pp. 271-280, (2014)
  15. Chen E.Y., Tan C.M., Kou Y., Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool, BMC Bioinf, 14, (2013)
  16. Cheng M., Anderson M.S., Thymic tolerance as a key brake on autoimmunity, Nat Immunol, 19, pp. 659-664, (2018)
  17. Chinn I.K., Blackburn C.C., Manley N.R., Changes in primary lymphoid organs with aging, Semin Immunol, 24, pp. 309-320, (2012)
  18. Clauset A., Newman M.E.J., Moore C., Finding community structure in very large networks, Phys Rev, 66111, (2004)
  19. Cowan J.E., Takahama Y., Bhandoola A., Postnatal involution and counter-involution of the thymus, Front Immunol, 11, (2020)
  20. Dragin N., Bismuth J., Cizeron-Clairac G., Estrogen-mediated downregulation of AIRE influences sexual dimorphism in autoimmune diseases, J Clin Invest, 126, pp. 1525-1537, (2016)
  21. Dumont-Lagace M., St-Pierre C., Perreault C., Sex hormones have pervasive effects on thymic epithelial cells, Sci Rep, 5, (2015)
  22. Farooqui A., Tazyeen S., Ahmed M.M., Assessment of the key regulatory genes and their Interologs for Turner Syndrome employing network approach, Sci Rep, 8, (2018)
  23. Fu G., Rybakin V., Brzostek J., Fine-tuning T cell receptor signaling to control T cell development, Trends Immunol, 35, pp. 311-318, (2014)
  24. Gaiteri C., Ding Y., French B., Beyond modules and hubs: The potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders, Genes Brain Behav, 13, pp. 13-24, (2014)
  25. Ghisi M., Corradin A., Basso K., Modulation of microRNA expression in human T-cell development: Targeting of NOTCH3 by miR-150, Blood, 117, pp. 7053-7062, (2011)
  26. Gui J., Mustachio L.M., Su D.M., Thymus size and age-related thymic involution: Early programming, sexual dimorphism, progenitors and stroma, Aging Dis, 3, pp. 280-290, (2012)
  27. Guo D., Ye Y., Qi J., MicroRNA-181a-5p enhances cell proliferation in medullary thymic epithelial cells via regulating TGF-β signaling, Acta Biochim Biophys Sin Shanghai, 48, pp. 840-849, (2016)
  28. Haljasorg U., Bichele R., Saare M., A highly conserved NF-κB-responsive enhancer is critical for thymic expression of Aire in mice, Eur J Immunol, 45, pp. 3246-3256, (2015)
  29. Hao Y., Hao S., Andersen-Nissen E., Integrated analysis of multimodal single-cell data, Cell, 583-583, pp. S0092-S8674, (2021)
  30. Kernfeld E.M., Genga R.M.J., Neherin K., A single-cell transcriptomic atlas of thymus organogenesis resolves cell types and developmental maturation, Immunity 48, e6, pp. 1258-1270, (2018)
  31. Klein S.L., Flanagan K.L., Sex differences in immune responses, Nat Rev Immunol, 16, pp. 626-638, (2016)
  32. Kondo K., Ohigashi I., Takahama Y., Thymus machinery for T-cell selection, Int Immunol, 31, pp. 119-125, (2019)
  33. Kuiri-Hanninen T., Sankilampi U., Dunkel L., Activation of the hypothalamic-pituitary-gonadal axis in infancy: Minipuberty, Horm Res Paediatr, 82, pp. 73-80, (2014)
  34. Kuleshov M.V., Jones M.R., Rouillard A.D., Enrichr: A comprehensive gene set enrichment analysis web server 2016 update, Nucleic Acids Res, 44, W1, pp. W90-W97, (2016)
  35. Laios K., The thymus gland in ancient Greek medicine, Hormones (Athens), 17, pp. 285-286, (2018)
  36. Langfelder P., Horvath S., WGCNA: An R package for weighted correlation network analysis, BMC Bioinf, 9, (2008)
  37. Merrheim J., Villegas J., van Wassenhove J., Estrogen, estrogen-like molecules and autoimmune diseases, Autoimmun Rev, (2020)
  38. Miller J.F.A.P., The function of the thymus and its impact on modern medicine, Science, 369, 6503, (2020)
  39. Moreira-Filho C.A., Bando S.Y., Bertonha F.B., Community structure analysis of transcriptional networks reveals distinct molecular pathways for early- and late-onset temporal lobe epilepsy with childhood febrile seizures, Plos One 10(5), e0128174, (2015)
  40. Moreira-Filho C.A., Bando S.Y., Bertonha F.B., Modular transcriptional repertoire and MicroRNA target analyses characterize genomic dysregulation in the thymus of Down syndrome infants, Oncotarget, 7, pp. 7497-74533, (2016)
  41. Moreira-Filho C.A., Bando S.Y., Bertonha F.B., Minipuberty and sexual dimorphism in the infant human thymus, Sci Rep, 8, (2018)
  42. Nakaya H.I., Wrammert J., Lee E.K., Systems biology of vaccination for seasonal influenza in humans, Nat Immunol, 12, pp. 786-795, (2011)
  43. Narayanan T., Subramaniam S., Community structure analysis of gene interaction networks in Duchenne muscular dystrophy, Plos One, e67237, (2013)
  44. Newman M.E.J., Networks: An Introduction. Oxford University Press, (2010)
  45. Newman M.E.J., Girvan M., Finding and evaluating community structure in networks, Phys Rev E, 26113, (2004)
  46. Obermoser G., Presnell S., Domico K., Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines, Immunity, 38, pp. 831-844, (2013)
  47. Ohigashi I., Tanaka Y., Kondo K., Trans-omics impact of thymoproteasome in cortical thymic epithelial cells, Cell Rep 29, e6, pp. 2901-2916, (2019)
  48. Park J.E., Botting R.A., Dominguez Conde C., A cell atlas of human thymic development defines T cell repertoire formation, Science, 367, 6480, (2020)
  49. Passos G.A., Speck-Hernandez C.A., Assis A.F., Update on Aire and thymic negative selection, Immunology, 153, pp. 10-20, (2018)
  50. Perniola R., Twenty years of AIRE, Front Immunol, 9, (2018)
  51. Pobezinsky L.A., Etzensperger R., Jeurling S., Let-7 microRNAs target the lineage-specific transcription factor PLZF to regulate terminal NKT cell differentiation and effector function, Nat Immunol, 16, pp. 517-524, (2015)
  52. Rezzani R., Nardo L., Favero G., Thymus and aging: Morphological, radiological, and functional overview, Age (Dordr), 36, pp. 313-351, (2014)
  53. Shannon P., Markiel A., Ozier O., Cytoscape: A software environment for integrated models of biomolecular interaction networks, Genome Res, 13, pp. 2498-2504, (2003)
  54. Singh Y., Garden O.A., Lang F., MicroRNA-15b/16 enhances the induction of regulatory T cells by regulating the expression of rictor and mTOR, J Immunol, 195, pp. 5667-5677, (2015)
  55. Steinmann G.G., Changes in the human thymus during aging, Curr Top Pathol, 75, pp. 43-88, (1986)
  56. Steinmann G.G., Klaus B., Muller-Hermelink H.K., The involution of the ageing human thymic epithelium is independent of puberty. A morphometric study, Scand J Immunol, 22, pp. 563-575, (1985)
  57. Thapa P., Farber D.L., The role of the thymus in the immune response, Thorac Surg Clin, 29, pp. 123-131, (2019)
  58. Tusher V.G., Tibshirani R., Chu G., Significance analysis of microarrays applied to the ionizing radiation response, Proc Natl Acad Sci U S A, 98, pp. 5116-5121, (2001)
  59. van Dam S., Vosa U., van der Graaf A., Gene co-expression analysis for functional classification and gene-disease predictions, Brief Bioinform, 19, pp. 575-592, (2018)
  60. Varas A., Jimenez E., Sacedon R., Analysis of the human neonatal thymus: Evidence for a transient thymic involution, J Immunol, 164, pp. 6260-6267, (2000)
  61. Zhao L., Zhang Y (2015) miR-342-3p affects hepatocellular carcinoma cell proliferation via regulating NF-κB pathway, Biochem Biophys Res Commun, 457, pp. 370-377
  62. Zhu M., Chin R.K., Christiansen P.A., NF-kappaB2 is required for the establishment of central tolerance through an Aire-dependent pathway, J Clin Invest, 116, pp. 2964-2971, (2006)
  63. Zhu X., Gerstein M., Snyder M., Getting connected: Analysis and principles of biological networks, Genes Dev, 21, pp. 1010-1024, (2007)