Bioinformatics analysis reveals the landscape of immune cell infiltration and immune-related pathways participating in the progression of carotid atherosclerotic plaques

References

• Spence JD. Intensive risk factor control in stroke prevention. F1000Prime Rep. 2013;5:42.
   PubMedGoogle Scholar
• Narula J, Nakano M, Virmani R, et al. Histopathologic characteristics of atherosclerotic coronary disease and implications of the findings for the invasive and noninvasive detection of vulnerable plaques. J Am Coll Cardiol. 2013;61(10):1041–1051.
   PubMed Web of Science ®Google Scholar
• Mury P, Chirico EN, Mura M, et al. Oxidative stress and inflammation, key targets of atherosclerotic plaque progression and vulnerability: potential impact of physical activity. Sports Med. 2018;48(12):2725–2741.
   PubMed Web of Science ®Google Scholar
• Ammirati E, Moroni F, Norata GD, et al. Markers of inflammation associated with plaque progression and instability in patients with carotid atherosclerosis. Mediators Inflamm. 2015;2015:718329
   PubMed Web of Science ®Google Scholar
• van Puijvelde GH, van Wanrooij EJ, Hauer AD, et al. Effect of natural killer T cell activation on the initiation of atherosclerosis. Thromb Haemost. 2009;102(08):223–230.
   PubMed Web of Science ®Google Scholar
• Oliveira RT, Silva RM, Teo FH, et al. Detection of TCD4+ subsets in human carotid atheroma. Cytokine. 2013;62(1):131–140.
   PubMed Web of Science ®Google Scholar
• Olofsson PS, Soderstrom LA, Wagsater D, et al. CD137 is expressed in human atherosclerosis and promotes development of plaque inflammation in hypercholesterolemic mice. Circulation. 2008;117(10):1292–1301.
   PubMed Web of Science ®Google Scholar
• Herias V, Biessen EA, Beckers C, et al. Leukocyte cathepsin C deficiency attenuates atherosclerotic lesion progression by selective tuning of innate and adaptive immune responses. Arterioscler Thromb Vasc Biol. 2015;35(1):79–86.
   PubMed Web of Science ®Google Scholar
• Hung J, Scanlon JP, Mahmoud AD, et al. Novel Plaque Enriched Long Noncoding RNA in Atherosclerotic Macrophage Regulation (PELATON). Arterioscler Thromb Vasc Biol. 2020;40(3):697–713.
   PubMed Web of Science ®Google Scholar
• Golledge J, Greenhalgh RM, Davies AH. The symptomatic carotid plaque. Stroke. 2000;31(3):774–781.
   PubMed Web of Science ®Google Scholar
• Leek JT, Johnson WE, Parker HS, et al. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28(6):882–883.
   PubMed Web of Science ®Google Scholar
• Chen B, Khodadoust MS, Liu CL, et al. Profiling tumor infiltrating immune cells with CIBERSORT. Methods Mol Biol. 2018;1711:243–259.
   PubMedGoogle Scholar
• Ginestet C. ggplot2: elegant graphics for data analysis. J R Stat Soc A Stat. 2011;174(1):245–246.
   Web of Science ®Google Scholar
• Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550.
   PubMed Web of Science ®Google Scholar
• Liberzon A, Subramanian A, Pinchback R, et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011;27(12):1739–1740.
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47.
   PubMed Web of Science ®Google Scholar
• Kolde R. Pheatmap: Pretty Heatmaps. 2015. https://rdrr.io/cran/pheatmap/
   Google Scholar
• Yu G, Wang L-G, Han Y, et al. He Q: clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
   PubMed Web of Science ®Google Scholar
• Hild M, Beckmann B, Haas SA, et al. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome. Genome Biol. 2003;5(1):R3
   PubMed Web of Science ®Google Scholar
• Zhao W, Wang D, Zhao J, et al. Bioinformatic analysis of retinal gene function and expression in diabetic rats. Exp Ther Med. 2017;14(3):2485–2492.
   PubMed Web of Science ®Google Scholar
• Kamtchum-Tatuene J, Wilman A, Saqqur M, et al. Carotid plaque with high-risk features in embolic stroke of undetermined source: systematic review and meta-analysis. Stroke. 2020;51(1):311–314.
   PubMed Web of Science ®Google Scholar
• Wolf D, Ley K. Immunity and inflammation in atherosclerosis. Circ Res. 2019;124(2):315–327.
   PubMed Web of Science ®Google Scholar
• Stary HC, Chandler AB, Dinsmore RE, et al. A definition of advanced types of atherosclerotic lesions and a histological classification of atherosclerosis. A report from the Committee on Vascular Lesions of the Council on Arteriosclerosis, American Heart Association. Circulation. 1995;92(5):1355–1374.
   PubMed Web of Science ®Google Scholar
• Vorobyova DA, Lebedev AM, Vagida MS, et al. Immunological analysis of human atherosclerotic plaques in ex vivo culture system. Kardiologiia. 2016;11_2016(11):78–85.
   Web of Science ®Google Scholar
• Lebedeva A, Vorobyeva D, Vagida M, et al. Ex vivo culture of human atherosclerotic plaques: a model to study immune cells in atherogenesis. Atherosclerosis. 2017;267:90–98.
   PubMed Web of Science ®Google Scholar
• Fernandez DM, Rahman AH, Fernandez NF, et al. Single-cell immune landscape of human atherosclerotic plaques. Nat Med. 2019;25(10):1576–1588.
   PubMed Web of Science ®Google Scholar
• Meeuwsen J, van Duijvenvoorde A, Gohar A, et al. High levels of (un)switched memory B cells are associated with better outcome in patients with advanced atherosclerotic disease. J Am Heart Assoc. 2017;6(9):e005747.
   PubMed Web of Science ®Google Scholar
• Tabas I, Lichtman AH. Monocyte-macrophages and T cells in atherosclerosis. Immunity. 2017;47(4):621–634.
   PubMed Web of Science ®Google Scholar
• Herrero-Fernandez B, Gomez-Bris R, Somovilla-Crespo B, et al. Immunobiology of atherosclerosis: a complex net of interactions. Int J Mol Sci. 2019;20(21):5293.
   Web of Science ®Google Scholar
• Libby P, Ridker PM, Maseri A. Inflammation and atherosclerosis. Circulation. 2002;105(9):1135–1143.
   PubMed Web of Science ®Google Scholar
• Hansson GK, Hermansson A. The immune system in atherosclerosis. Nat Immunol. 2011;12(3):204–212.
   PubMed Web of Science ®Google Scholar
• Hansson GK. Inflammation, atherosclerosis, and coronary artery disease. N Engl J Med. 2005;352(16):1685–1695.
   PubMed Web of Science ®Google Scholar
• Zernecke A, Weber C. Chemokines in the vascular inflammatory response of atherosclerosis. Cardiovasc Res. 2010;86(2):192–201.
   PubMed Web of Science ®Google Scholar
• Stemme S, Faber B, Holm J, et al. T lymphocytes from human atherosclerotic plaques recognize oxidized low density lipoprotein. Proc Natl Acad Sci U S A. 1995;92(9):3893–3897.
   PubMed Web of Science ®Google Scholar
• Sallusto F, Geginat J, Lanzavecchia A. Central memory and effector memory T cell subsets: function, generation, and maintenance. Annu Rev Immunol. 2004;22:745–763.
   PubMed Web of Science ®Google Scholar
• Ammirati E, Cianflone D, Vecchio V, et al. Effector memory T cells are associated with atherosclerosis in humans and animal models. J Am Heart Assoc. 2012;1(111):27–41.
   PubMed Web of Science ®Google Scholar
• Zernecke A. Dendritic cells in atherosclerosis: evidence in mice and humans. Arterioscler Thromb Vasc Biol. 2015;35(4):763–770.
   PubMed Web of Science ®Google Scholar
• Koltsova EK, Ley K. How dendritic cells shape atherosclerosis. Trends Immunol. 2011;32(11):540–547.
   PubMed Web of Science ®Google Scholar
• Alberts-Grill N, Denning TL, Rezvan A, et al. The role of the vascular dendritic cell network in atherosclerosis. Am J Physiol Cell Physiol. 2013;305(1):C1–C21.
   PubMed Web of Science ®Google Scholar
• van Dijk RA, Duinisveld AJ, Schaapherder AF, et al. A change in inflammatory footprint precedes plaque instability: a systematic evaluation of cellular aspects of the adaptive immune response in human atherosclerosis. J Am Heart Assoc. 2015;4(4):e001403.
   PubMed Web of Science ®Google Scholar
• Vivier E, Tomasello E, Baratin M, et al. Functions of natural killer cells. Nat Immunol. 2008;9(5):503–510.
   PubMed Web of Science ®Google Scholar
• Clerc G, Rouz PM. Lymphocyte subsets in severe atherosclerosis before revascularization. Ann Intern Med. 1997;126(12):1004–1005.
   PubMed Web of Science ®Google Scholar
• Martinez-Rodriguez JE, Munne-Collado J, Rasal R, et al. Expansion of the NKG2C + natural killer-cell subset is associated with high-risk carotid atherosclerotic plaques in seropositive patients for human cytomegalovirus. Arterioscler Thromb Vasc Biol. 2013;33(11):2653–2659.
   PubMed Web of Science ®Google Scholar
• Whitman SC, Rateri DL, Szilvassy SJ, et al. Depletion of natural killer cell function decreases atherosclerosis in low-density lipoprotein receptor null mice. Arterioscler Thromb Vasc Biol. 2004;24(6):1049–1054.
   PubMed Web of Science ®Google Scholar
• Selathurai A, Deswaerte V, Kanellakis P, et al. Natural killer (NK) cells augment atherosclerosis by cytotoxic-dependent mechanisms. Cardiovasc Res. 2014;102(1):128–137.
   PubMed Web of Science ®Google Scholar
• Hori S, Nomura T, Sakaguchi S. Control of regulatory T cell development by the transcription factor Foxp3. Science. 2003;299(5609):1057–1061.
   PubMed Web of Science ®Google Scholar
• Shevach EM. From vanilla to 28 flavors: multiple varieties of T regulatory cells. Immunity. 2006;25(2):195–201.
   PubMed Web of Science ®Google Scholar