Nuclear envelope disruption triggers hallmarks of aging in lung alveolar macrophages.

Animals Mice Macrophages, Alveolar Lamin Type A / genetics Nuclear Envelope Lung Aging / genetics Genomic Instability

Journal

Nature aging

ISSN: 2662-8465

Titre abrégé: Nat Aging

Pays: United States

ID NLM: 101773306

Informations de publication

Date de publication:
10 2023

Historique:

received: 15 04 2022

accepted: 16 08 2023

medline: 23 10 2023

pubmed: 19 9 2023

entrez: 18 9 2023

Statut: ppublish

Résumé

Aging is characterized by gradual immune dysfunction and increased disease risk. Genomic instability is considered central to the aging process, but the underlying mechanisms of DNA damage are insufficiently defined. Cells in confined environments experience forces applied to their nucleus, leading to transient nuclear envelope rupture (NER) and DNA damage. Here, we show that Lamin A/C protects lung alveolar macrophages (AMs) from NER and hallmarks of aging. AMs move within constricted spaces in the lung. Immune-specific ablation of lamin A/C results in selective depletion of AMs and heightened susceptibility to influenza virus-induced pathogenesis and lung cancer growth. Lamin A/C-deficient AMs that persist display constitutive NER marks, DNA damage and p53-dependent senescence. AMs from aged wild-type and from lamin A/C-deficient mice share a lysosomal signature comprising CD63. CD63 is required to limit damaged DNA in macrophages. We propose that NER-induced genomic instability represents a mechanism of aging in AMs.

Identifiants

DOI: 10.1038/s43587-023-00488-w PMID: 37723209

pubmed: 37723209

doi: 10.1038/s43587-023-00488-w

pii: 10.1038/s43587-023-00488-w

doi:

Substances chimiques

Lamin Type A 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

Pagination

1251-1268

Informations de copyright

Références

Schneider, J. L. et al. The aging lung: physiology, disease, and immunity. Cell 184, 1990–2019 (2021).

pubmed: 33811810 pmcid: 8052295 doi: 10.1016/j.cell.2021.03.005

Nikolich-Žugich, J. The twilight of immunity: emerging concepts in aging of the immune system. Nat. Immunol. 19, 10–19 (2018).

pubmed: 29242543 doi: 10.1038/s41590-017-0006-x

Yousefzadeh, M. J. et al. An aged immune system drives senescence and ageing of solid organs. Nature 594, 100–105 (2021).

pubmed: 33981041 pmcid: 8684299 doi: 10.1038/s41586-021-03547-7

Desdín-Micó, G. et al. T cells with dysfunctional mitochondria induce multimorbidity and premature senescence. Science 368, 1371–1376 (2020).

pubmed: 32439659 doi: 10.1126/science.aax0860

López-Otín, C., Blasco, M. A., Partridge, L., Serrano, M. & Kroemer, G. The hallmarks of aging. Cell 153, 1194–1217 (2013).

pubmed: 23746838 pmcid: 3836174 doi: 10.1016/j.cell.2013.05.039

Schumacher, B., Pothof, J., Vijg, J. & Hoeijmakers, J. H. J. The central role of DNA damage in the ageing process. Nature 592, 695–703 (2021).

pubmed: 33911272 pmcid: 9844150 doi: 10.1038/s41586-021-03307-7

Luster, A. D., Alon, R. & von Andrian, U. H. Immune cell migration in inflammation: present and future therapeutic targets. Nat. Immunol. 6, 1182–1190 (2005).

pubmed: 16369557 doi: 10.1038/ni1275

Raab, M. et al. ESCRT III repairs nuclear envelope ruptures during cell migration to limit DNA damage and cell death. Science 352, 359–362 (2016).

pubmed: 27013426 doi: 10.1126/science.aad7611

Pflicke, H. & Sixt, M. Preformed portals facilitate dendritic cell entry into afferent lymphatic vessels. J. Exp. Med. 206, 2925–2935 (2009).

pubmed: 19995949 pmcid: 2806476 doi: 10.1084/jem.20091739

Garcia-Arcos, J. M. et al. Reconstitution of cell migration at a glance. J. Cell Sci. 132, jcs225565 (2019).

pubmed: 30745333 doi: 10.1242/jcs.225565

Nader, G. P., de, F., Williart, A. & Piel, M. Nuclear deformations, from signaling to perturbation and damage. Curr. Opin. Cell Biol. 72, 137–145 (2021).

pubmed: 34461580 doi: 10.1016/j.ceb.2021.07.008

Denais, C. M. et al. Nuclear envelope rupture and repair during cancer cell migration. Science 352, 353–358 (2016).

pubmed: 27013428 pmcid: 4833568 doi: 10.1126/science.aad7297

Irianto, J. et al. DNA damage follows repair factor depletion and portends genome variation in cancer cells after pore migration. Curr. Biol. 27, 210–223 (2017).

pubmed: 27989676 doi: 10.1016/j.cub.2016.11.049

Cho, S. et al. Mechanosensing by the lamina protects against nuclear rupture, DNA damage, and cell-cycle arrest. Dev. Cell 49, 920–935 (2019).

pubmed: 31105008 pmcid: 6581604 doi: 10.1016/j.devcel.2019.04.020

Earle, A. J. et al. Mutant lamins cause nuclear envelope rupture and DNA damage in skeletal muscle cells. Nat. Mater. 19, 464–473 (2020).

pubmed: 31844279 doi: 10.1038/s41563-019-0563-5

Shah, P. et al. Nuclear deformation causes DNA damage by increasing replication stress. Curr. Biol. 31, 753–765 (2021).

pubmed: 33326770 doi: 10.1016/j.cub.2020.11.037

Xia, Y. et al. Nuclear rupture at sites of high curvature compromises retention of DNA repair factors. J. Cell Biol. 217, 3796–3808 (2018).

pubmed: 30171044 pmcid: 6219729 doi: 10.1083/jcb.201711161

Nader, G. P. et al. Compromised nuclear envelope integrity drives TREX1-dependent DNA damage and tumor cell invasion. Cell 184, 5230–5246 (2021).

pubmed: 34551315 doi: 10.1016/j.cell.2021.08.035

Gentili, M. et al. The N-terminal domain of cGAS determines preferential association with centromeric DNA and innate immune activation in the nucleus. Cell Rep. 26, 2377–2393 (2019).

pubmed: 30811988 pmcid: 6391843 doi: 10.1016/j.celrep.2019.01.105

Guey, B. et al. BAF restricts cGAS on nuclear DNA to prevent innate immune activation. Science 369, 823–828 (2020).

pubmed: 32792394 doi: 10.1126/science.aaw6421

Lan, Y. Y., Londono, D., Bouley, R., Rooney, M. S. & Hacohen, N. Dnase2a deficiency uncovers lysosomal clearance of damaged nuclear DNA via autophagy. Cell Rep. 9, 180–192 (2014).

pubmed: 25284779 pmcid: 4555847 doi: 10.1016/j.celrep.2014.08.074

Banerjee, D. et al. A non-canonical, interferon-independent signaling activity of cGAMP triggers DNA damage response signaling. Nat. Commun. 12, 6207 (2021).

pubmed: 34707113 pmcid: 8551335 doi: 10.1038/s41467-021-26240-9

Moiseeva, O., Mallette, F. A., Mukhopadhyay, U. K., Moores, A. & Ferbeyre, G. DNA damage signaling and p53-dependent senescence after prolonged β-interferon stimulation. Mol. Biol. Cell 17, 1583–1592 (2006).

pubmed: 16436515 pmcid: 1415317 doi: 10.1091/mbc.e05-09-0858

Morales, A. J. et al. A type I IFN-dependent DNA damage response regulates the genetic program and inflammasome activation in macrophages. Elife 6, e24655 (2017).

pubmed: 28362262 pmcid: 5409825 doi: 10.7554/eLife.24655

Li, Y. et al. Nuclear envelope rupture and NET formation is driven by PKCα‐mediated lamin B disassembly. EMBO Rep. 21, e48779 (2020).

pubmed: 32537912 pmcid: 7403722 doi: 10.15252/embr.201948779

Thiam, H. R. et al. NETosis proceeds by cytoskeleton and endomembrane disassembly and PAD4-mediated chromatin decondensation and nuclear envelope rupture. Proc. Natl Acad. Sci. USA 117, 7326–7337 (2020).

pubmed: 32170015 pmcid: 7132277 doi: 10.1073/pnas.1909546117

De Vos, W. H. et al. Repetitive disruptions of the nuclear envelope invoke temporary loss of cellular compartmentalization in laminopathies. Hum. Mol. Genet. 20, 4175–4186 (2011).

pubmed: 21831885 doi: 10.1093/hmg/ddr344

Vargas, J. D., Hatch, E. M., Anderson, D. J. & Hetzer, M. W. Transient nuclear envelope rupturing during interphase in human cancer cells. Nucleus 3, 88–100 (2012).

pubmed: 22567193 pmcid: 3342953 doi: 10.4161/nucl.18954

Saez, A. et al. Lamin A/C and the immune system: one intermediate filament, many faces. Int. J. Mol. Sci. 21, 6109 (2020).

pubmed: 32854281 pmcid: 7504305 doi: 10.3390/ijms21176109

Kim, Y. & Zheng, Y. Generation and characterization of a conditional deletion allele for Lmna in mice. Biochem. Biophys. Res. Commun. 440, 8–13 (2013).

pubmed: 23998933 doi: 10.1016/j.bbrc.2013.08.082

de Boer, J. et al. Transgenic mice with hematopoietic and lymphoid specific expression of Cre. Eur. J. Immunol. 33, 314–325 (2003).

pubmed: 12548562 doi: 10.1002/immu.200310005

Grigoryan, A. et al. Lamin A/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells. Genome Biol. 19, 189 (2018).

pubmed: 30404662 pmcid: 6223039 doi: 10.1186/s13059-018-1557-3

Hashimoto, D. et al. Tissue-resident macrophages self-maintain locally throughout adult life with minimal contribution from circulating monocytes. Immunity 38, 792–804 (2013).

pubmed: 23601688 doi: 10.1016/j.immuni.2013.04.004

Kopf, M., Schneider, C. & Nobs, S. P. The development and function of lung-resident macrophages and dendritic cells. Nat. Immunol. 16, 36–44 (2015).

pubmed: 25521683 doi: 10.1038/ni.3052

Sieweke, M. H. & Allen, J. E. Beyond stem cells: self-renewal of differentiated macrophages. Science 342, 1242974 (2013).

pubmed: 24264994 doi: 10.1126/science.1242974

Liu, Z. et al. Fate mapping via Ms4a3-expression history traces monocyte-derived cells. Cell 178, 1509–1525 (2019).

pubmed: 31491389 doi: 10.1016/j.cell.2019.08.009

Misharin, A. V. et al. Monocyte-derived alveolar macrophages drive lung fibrosis and persist in the lung over the lifespan. J. Exp. Med. 214, 2387–2404 (2017).

pubmed: 28694385 pmcid: 5551573 doi: 10.1084/jem.20162152

Chakarov, S. et al. Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches. Science 363, eaau0964 (2019).

pubmed: 30872492 doi: 10.1126/science.aau0964

Raredon, M. S. B. et al. Single-cell connectomic analysis of adult mammalian lungs. Sci. Adv. 5, eaaw3851 (2019).

pubmed: 31840053 pmcid: 6892628 doi: 10.1126/sciadv.aaw3851

Gorgoulis, V. et al. Cellular senescence: defining a path forward. Cell 179, 813–827 (2019).

pubmed: 31675495 doi: 10.1016/j.cell.2019.10.005

Yang, H., Wang, H., Ren, J., Chen, Q. & Chen, Z. J. cGAS is essential for cellular senescence. Proc. Natl Acad. Sci. USA 114, E4612–E4620 (2017).

pubmed: 28533362 pmcid: 5468617 doi: 10.1073/pnas.1705499114

Gluck, S. et al. Innate immune sensing of cytosolic chromatin fragments through cGAS promotes senescence. Nat. Cell Biol. 19, 1061–1070 (2017).

pubmed: 28759028 pmcid: 5826565 doi: 10.1038/ncb3586

Reinhardt, H. C. & Schumacher, B. The p53 network: cellular and systemic DNA damage responses in aging and cancer. Trends Genet. 28, 128–136 (2012).

pubmed: 22265392 pmcid: 4120491 doi: 10.1016/j.tig.2011.12.002

DeMicco, A., Yang-Iott, K. & Bassing, C. H. Somatic inactivation of Tp53 in hematopoietic stem cells or thymocytes predisposes mice to thymic lymphomas with clonal translocations. Cell Cycle 12, 3307–3316 (2013).

pubmed: 24036547 pmcid: 3885641 doi: 10.4161/cc.26299

Rodero, M. P. et al. Immune surveillance of the lung by migrating tissue monocytes. eLife 4, e07847 (2015).

pubmed: 26167653 pmcid: 4521583 doi: 10.7554/eLife.07847

Westphalen, K. et al. Sessile alveolar macrophages communicate with alveolar epithelium to modulate immunity. Nature 506, 503–506 (2014).

pubmed: 24463523 pmcid: 4117212 doi: 10.1038/nature12902

Neupane, A. S. et al. Patrolling alveolar macrophages conceal bacteria from the immune system to maintain homeostasis. Cell 183, 110–125 (2020).

pubmed: 32888431 doi: 10.1016/j.cell.2020.08.020

Amy, R. W., Bowes, D., Burri, P. H., Haines, J. & Thurlbeck, W. M. Postnatal growth of the mouse lung. J. Anat. 124, 131–151 (1977).

pubmed: 914698 pmcid: 1235518

Halfmann, C. T. et al. Repair of nuclear ruptures requires barrier-to-autointegration factor. J. Cell Biol. 218, 2136–2149 (2019).

pubmed: 31147383 pmcid: 6605789 doi: 10.1083/jcb.201901116

Haraguchi, T. et al. Live cell imaging and electron microscopy reveal dynamic processes of BAF-directed nuclear envelope assembly. J. Cell Sci. 121, 2540–2554 (2008).

pubmed: 18628300 doi: 10.1242/jcs.033597

Ding, P. et al. Intracellular complement C5a/C5aR1 stabilizes β-catenin to promote colorectal tumorigenesis. Cell Rep. 39, 110851 (2022).

pubmed: 35649359 doi: 10.1016/j.celrep.2022.110851

Pols, M. S. & Klumperman, J. Trafficking and function of the tetraspanin CD63. Exp. Cell. Res. 315, 1584–1592 (2009).

pubmed: 18930046 doi: 10.1016/j.yexcr.2008.09.020

Borghesan, M. et al. Small extracellular vesicles are key regulators of non-cell autonomous intercellular communication in senescence via the interferon protein IFITM3. Cell Rep. 27, 3956–3971 (2019).

pubmed: 31242426 pmcid: 6613042 doi: 10.1016/j.celrep.2019.05.095

Yokoi, A. et al. Mechanisms of nuclear content loading to exosomes. Sci. Adv. 5, eaax8849 (2019).

pubmed: 31799396 pmcid: 6867874 doi: 10.1126/sciadv.aax8849

Lanna, A. et al. An intercellular transfer of telomeres rescues T cells from senescence and promotes long-term immunological memory. Nat. Cell Biol. 24, 1461–1474 (2022).

pubmed: 36109671 pmcid: 7613731 doi: 10.1038/s41556-022-00991-z

Shen, Y. J. et al. Genome-derived cytosolic DNA mediates type I interferon-dependent rejection of B cell lymphoma cells. Cell Rep. 11, 460–473 (2015).

pubmed: 25865892 doi: 10.1016/j.celrep.2015.03.041

Xin, L., Jiang, T. T., Kinder, J. M., Ertelt, J. M. & Way, S. S. Infection susceptibility and immune senescence with advancing age replicated in accelerated aging Lmna

pubmed: 26248606 pmcid: 4693468 doi: 10.1111/acel.12385

Krishnarajah, S. et al. Single-cell profiling of immune system alterations in lymphoid, barrier and solid tissues in aged mice. Nat. Aging 2, 74–89 (2021).

pubmed: 37118354 doi: 10.1038/s43587-021-00148-x

Wong, C. K. et al. Aging impairs alveolar macrophage phagocytosis and increases influenza-induced mortality in mice. J. Immunol. 199, 1060–1068 (2017).

pubmed: 28646038 doi: 10.4049/jimmunol.1700397

The Tabula Muris Consortium. et al. A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Nature 583, 590–595 (2020).

pmcid: 8240505 doi: 10.1038/s41586-020-2496-1

Angelidis, I. et al. An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nat. Commun. 10, 963 (2019).

pubmed: 30814501 pmcid: 6393476 doi: 10.1038/s41467-019-08831-9

Heckenbach, I. et al. Nuclear morphology is a deep learning biomarker of cellular senescence. Nat. Aging 2, 742–755 (2022).

pubmed: 37118134 pmcid: 10154217 doi: 10.1038/s43587-022-00263-3

Hall, B. M. et al. p16(Ink4a) and senescence-associated β-galactosidase can be induced in macrophages as part of a reversible response to physiological stimuli. Aging 9, 1867–1884 (2017).

pubmed: 28768895 pmcid: 5611982 doi: 10.18632/aging.101268

Purnama, C. et al. Transient ablation of alveolar macrophages leads to massive pathology of influenza infection without affecting cellular adaptive immunity: Immunity to infection. Eur. J. Immunol. 44, 2003–2012 (2014).

pubmed: 24687623 doi: 10.1002/eji.201344359

Schneider, C. et al. Alveolar macrophages are essential for protection from respiratory failure and associated morbidity following influenza virus infection. PLoS Pathog. 10, e1004053 (2014).

pubmed: 24699679 pmcid: 3974877 doi: 10.1371/journal.ppat.1004053

Alonso, R. et al. Induction of anergic or regulatory tumor-specific CD4

pubmed: 29844317 pmcid: 5974295 doi: 10.1038/s41467-018-04524-x

Swift, J. et al. Nuclear lamin-A scales with tissue stiffness and enhances matrix-directed differentiation. Science 341, 1240104 (2013).

pubmed: 23990565 pmcid: 3976548 doi: 10.1126/science.1240104

Maciejowski, J., Li, Y., Bosco, N., Campbell, P. J. & de Lange, T. Chromothripsis and kataegis induced by telomere crisis. Cell 163, 1641–1654 (2015).

pubmed: 26687355 pmcid: 4687025 doi: 10.1016/j.cell.2015.11.054

Gruenbaum, Y. & Foisner, R. Lamins: nuclear intermediate filament proteins with fundamental functions in nuclear mechanics and genome regulation. Annu. Rev. Biochem. 84, 131–164 (2015).

pubmed: 25747401 doi: 10.1146/annurev-biochem-060614-034115

Ivanov, A. et al. Lysosome-mediated processing of chromatin in senescence. J. Cell Biol. 202, 129–143 (2013).

pubmed: 23816621 pmcid: 3704985 doi: 10.1083/jcb.201212110

Braidy, N. et al. Age related changes in NAD

pubmed: 21541336 pmcid: 3082551 doi: 10.1371/journal.pone.0019194

Lee, S. et al. Molecular programs of fibrotic change in aging human lung. Nat. Commun. 12, 6309 (2021).

pubmed: 34728633 pmcid: 8563941 doi: 10.1038/s41467-021-26603-2

Jaitin, D. A. et al. Lipid-associated macrophages control metabolic homeostasis in a Trem2-dependent manner. Cell 178, 686–698 (2019).

pubmed: 31257031 pmcid: 7068689 doi: 10.1016/j.cell.2019.05.054

Fabre, T. et al. Identification of a broadly fibrogenic macrophage subset induced by type 3 inflammation. Sci. Immunol. 8, eadd8945 (2023).

pubmed: 37027478 doi: 10.1126/sciimmunol.add8945

Keren-Shaul, H. et al. A unique microglia type associated with restricting development of Alzheimer’s disease. Cell 169, 1276–1290 (2017).

pubmed: 28602351 doi: 10.1016/j.cell.2017.05.018

McQuattie-Pimentel, A. C. et al. The lung microenvironment shapes a dysfunctional response of alveolar macrophages in aging. J. Clin. Invest. 131, 140299 (2021).

pubmed: 33586677 doi: 10.1172/JCI140299

Sicard, D. et al. Aging and anatomical variations in lung tissue stiffness. Am. J. Physiol. Lung Cell. Mol. Physiol. 314, L946–L955 (2018).

pubmed: 29469613 pmcid: 6032071 doi: 10.1152/ajplung.00415.2017

Szymczak, K. et al. Expression levels of lamin A or C are critical to nuclear maturation, functional responses, and gene expression profiles in differentiating mouse neutrophils. Immunohorizons 6, 16–35 (2022).

pubmed: 35039433 doi: 10.4049/immunohorizons.2100072

Blagosklonny, M. V., Campisi, J. & Sinclair, D. A. Aging: past, present and future. Aging 1, 1–5 (2009).

pubmed: 20157590 pmcid: 2815757 doi: 10.18632/aging.100009

Casanova-Acebes, M. et al. Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells. Nature 595, 578–584 (2021).

pubmed: 34135508 pmcid: 8923521 doi: 10.1038/s41586-021-03651-8

Haston, S. et al. Clearance of senescent macrophages ameliorates tumorigenesis in KRAS-driven lung cancer. Cancer Cell 41, 1242–1260 (2023).

pubmed: 37267953 doi: 10.1016/j.ccell.2023.05.004

Prieto, L. I. et al. Senescent alveolar macrophages promote early-stage lung tumorigenesis. Cancer Cell 41, 1261–1275 (2023).

pubmed: 37267954 doi: 10.1016/j.ccell.2023.05.006

Worman, H. J. & Bonne, G. ‘Laminopathies’: a wide spectrum of human diseases. Exp. Cell. Res. 313, 2121–2133 (2007).

pubmed: 17467691 pmcid: 2964355 doi: 10.1016/j.yexcr.2007.03.028

Clausen, B. E., Burkhardt, C., Reith, W., Renkawitz, R. & Förster, I. Conditional gene targeting in macrophages and granulocytes using LysMcre mice. Transgenic Res. 8, 265–277 (1999).

pubmed: 10621974 doi: 10.1023/A:1008942828960

Jonkers, J. et al. Synergistic tumor suppressor activity of BRCA2 and p53 in a conditional mouse model for breast cancer. Nat. Genet. 29, 418–425 (2001).

pubmed: 11694875 doi: 10.1038/ng747

Schröder, J. et al. Deficiency of the tetraspanin CD63 associated with kidney pathology but normal lysosomal function. Mol. Cell. Biol. 29, 1083–1094 (2009).

pubmed: 19075008 doi: 10.1128/MCB.01163-08

Cleary, S. J. et al. Complement activation on endothelium initiates antibody-mediated acute lung injury. J. Clin. Invest. 130, 5909–5923 (2020).

pubmed: 32730229 pmcid: 7598054 doi: 10.1172/JCI138136

Gilhodes, J. -C. et al. Quantification of pulmonary fibrosis in a bleomycin mouse model using automated histological image analysis. PLoS ONE 12, e0170561 (2017).

pubmed: 28107543 pmcid: 5249201 doi: 10.1371/journal.pone.0170561

Michaudel, C., Fauconnier, L., Julé, Y. & Ryffel, B. Functional and morphological differences of the lung upon acute and chronic ozone exposure in mice. Sci. Rep. 8, 10611 (2018).

pubmed: 30006538 pmcid: 6045627 doi: 10.1038/s41598-018-28261-9

Watson, J. K. et al. Distal lung epithelial progenitor cell function declines with age. Sci. Rep. 10, 10490 (2020).

pubmed: 32591591 pmcid: 7319976 doi: 10.1038/s41598-020-66966-y

Zheng, G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).

pubmed: 28091601 pmcid: 5241818 doi: 10.1038/ncomms14049

Satija, R., Farrell, J. A., Gennert, D., Schier, A. F. & Regev, A. Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495–502 (2015).

pubmed: 25867923 pmcid: 4430369 doi: 10.1038/nbt.3192

Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015).

pubmed: 26653891 pmcid: 4676162 doi: 10.1186/s13059-015-0844-5

Clarke, D. J. B. et al. eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. Nucleic Acids Res. 46, W171–W179 (2018).

pubmed: 29800326 pmcid: 6030863 doi: 10.1093/nar/gky458

Kwon, A. T., Arenillas, D. J., Hunt, R. W. & Wasserman, W. W. oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-seq datasets. G3 2, 987–1002 (2012).

pubmed: 22973536 pmcid: 3429929 doi: 10.1534/g3.112.003202

Smyth, G. Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor (eds. R. Gentleman et al.) 397–420 (Springer, 2005).

Yu, G., Wang, L. -G., Han, Y. & He, Q. -Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16, 284–287 (2012).

pubmed: 22455463 pmcid: 3339379 doi: 10.1089/omi.2011.0118

Subramanian, A. et al. Gene-set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545–15550 (2005).

pubmed: 16199517 pmcid: 1239896 doi: 10.1073/pnas.0506580102