Identifying Immune Cell Infiltration and Hub Genes During the Myocardial Remodeling Process After Myocardial Infarction

References

• Curley D, Lavin Plaza B, Shah AM, Botnar RM. Molecular imaging of cardiac remodelling after myocardial infarction. Basic Res Cardiol. 2018;113(2):10. doi:10.1007/s00395-018-0668-z
   PubMed Web of Science ®Google Scholar
• Frangogiannis NG. The inflammatory response in myocardial injury, repair, and remodelling. Nat Rev Cardiol. 2014;11(5):255–265. doi:10.1038/nrcardio.2014.28
   PubMed Web of Science ®Google Scholar
• Swirski FK, Nahrendorf M. Cardioimmunology: the immune system in cardiac homeostasis and disease. Nat Rev Immunol. 2018;18(12):733–744. doi:10.1038/s41577-018-0065-8
   PubMed Web of Science ®Google Scholar
• Burke RM, Burgos Villar KN, Small EM. Fibroblast contributions to ischemic cardiac remodeling. Cell Signal. 2021;77:109824. doi:10.1016/j.cellsig.2020.109824
   PubMed Web of Science ®Google Scholar
• Sun K, Li YY, Jin J. A double-edged sword of immuno-microenvironment in cardiac homeostasis and injury repair. Signal Transduct Target Ther. 2021;6(1):79. doi:10.1038/s41392-020-00455-6
   PubMed Web of Science ®Google Scholar
• Frantz S, Hundertmark MJ, Schulz-Menger J, Bengel FM, Bauersachs J. Left ventricular remodelling post-myocardial infarction: pathophysiology, imaging, and novel therapies. Eur Heart J. 2022;43(27):2549–2561. doi:10.1093/eurheartj/ehac223
   PubMed Web of Science ®Google Scholar
• Gil-Cayuela C, Rivera M, Ortega A, et al. RNA sequencing analysis identifies new human collagen genes involved in cardiac remodeling. J Am Coll Cardiol. 2015;65(12):1265–1267. doi:10.1016/j.jacc.2015.01.029
   PubMed Web of Science ®Google Scholar
• Chan MY, Efthymios M, Tan SH, et al. Prioritizing Candidates of Post-Myocardial Infarction Heart Failure Using Plasma Proteomics and Single-Cell Transcriptomics. Circulation. 2020;142(15):1408–1421. doi:10.1161/CIRCULATIONAHA.119.045158
   PubMed Web of Science ®Google Scholar
• Deniset JF, Belke D, Lee WY, et al. Gata6(+) Pericardial Cavity Macrophages Relocate to the Injured Heart and Prevent Cardiac Fibrosis. Immunity. 2019;51(1):131–140 e5. doi:10.1016/j.immuni.2019.06.010
   PubMed Web of Science ®Google Scholar
• Zhao J, Lv T, Quan J, et al. Identification of target genes in cardiomyopathy with fibrosis and cardiac remodeling. J Biomed Sci. 2018;25(1):63. doi:10.1186/s12929-018-0459-8
   PubMedGoogle Scholar
• Rogers JD, Aguado BA, Watts KM, Anseth KS, Richardson WJ. Network modeling predicts personalized gene expression and drug responses in valve myofibroblasts cultured with patient sera. Proc Natl Acad Sci U S A. 2022;119(8). doi:10.1073/pnas.2117323119
   Web of Science ®Google Scholar
• Auwul MR, Rahman MR, Gov E, Shahjaman M, Moni MA. Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19. Brief Bioinform. 2021;22(5). doi:10.1093/bib/bbab120
   PubMed Web of Science ®Google Scholar
• Newman AM, Steen CB, Liu CL, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019;37(7):773–782. doi:10.1038/s41587-019-0114-2
   PubMed Web of Science ®Google Scholar
• Casarrubios M, Provencio M, Nadal E, et al. Tumor microenvironment gene expression profiles associated to complete pathological response and disease progression in resectable NSCLC patients treated with neoadjuvant chemoimmunotherapy. J Immunother Cancer. 2022;10(9). doi:10.1136/jitc-2022-005320
   PubMed Web of Science ®Google Scholar
• Nevalainen T, Autio A, Hurme M. Composition of the infiltrating immune cells in the brain of healthy individuals: effect of aging. Immun Ageing. 2022;19(1):45. doi:10.1186/s12979-022-00302-y
   PubMed Web of Science ®Google Scholar
• Innocenti F, Yazdani A, Rashid N, et al. Tumor Immunogenomic Features Determine Outcomes in Patients with Metastatic Colorectal Cancer Treated with Standard-of-Care Combinations of Bevacizumab and Cetuximab. Clin Cancer Res. 2022;28(8):1690–1700. doi:10.1158/1078-0432.CCR-21-3202
   PubMed Web of Science ®Google Scholar
• Stegle O, Teichmann SA, Marioni JC. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet. 2015;16(3):133–145. doi:10.1038/nrg3833
   PubMed Web of Science ®Google Scholar
• Artyomov MN, Van den Bossche J. Immunometabolism in the Single-Cell Era. Cell Metab. 2020;32(5):710–725. doi:10.1016/j.cmet.2020.09.013
   PubMed Web of Science ®Google Scholar
• Yokota T, McCourt J, Ma F, et al. Type V Collagen in Scar Tissue Regulates the Size of Scar after Heart Injury. Cell. 2020;182(3):545–562 e23. doi:10.1016/j.cell.2020.06.030
   PubMed Web of Science ®Google Scholar
• Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19(2):185–193. doi:10.1093/bioinformatics/19.2.185
   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. doi:10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Kirsch R, Koutrouli M, et al. The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 2023;51(D1):D638–D646. doi:10.1093/nar/gkac1000
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504. doi:10.1101/gr.1239303
   PubMed Web of Science ®Google Scholar
• Bader GD, Hogue CW. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinform. 2003;4:2. doi:10.1186/1471-2105-4-2
   PubMed Web of Science ®Google Scholar
• Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8 Suppl 4(Suppl 4):S11. doi:10.1186/1752-0509-8-S4-S11
   PubMed Web of Science ®Google Scholar
• Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. 2011;12:77. doi:10.1186/1471-2105-12-77
   PubMed Web of Science ®Google Scholar
• Forte E, Skelly DA, Chen M, et al. Dynamic Interstitial Cell Response during Myocardial Infarction Predicts Resilience to Rupture in Genetically Diverse Mice. Cell Rep. 2020;30(9):3149–3163 e6. doi:10.1016/j.celrep.2020.02.008
   PubMed Web of Science ®Google Scholar
• Wang Z, Qiu Z, Hua S, et al. Nuclear Tkt promotes ischemic heart failure via the cleaved Parp1/Aif axis. Basic Res Cardiol. 2022;117(1):18. doi:10.1007/s00395-022-00925-8
   PubMed Web of Science ®Google Scholar
• Dobaczewski M, Gonzalez-Quesada C, Frangogiannis NG. The extracellular matrix as a modulator of the inflammatory and reparative response following myocardial infarction. J Mol Cell Cardiol. 2010;48(3):504–511. doi:10.1016/j.yjmcc.2009.07.015
   PubMed Web of Science ®Google Scholar
• Frangogiannis NG. The extracellular matrix in myocardial injury, repair, and remodeling. J Clin Invest. 2017;127(5):1600–1612. doi:10.1172/JCI87491
   PubMed Web of Science ®Google Scholar
• Rasi K, Piuhola J, Czabanka M, et al. Collagen XV is necessary for modeling of the extracellular matrix and its deficiency predisposes to cardiomyopathy. Circ Res. 2010;107(10):1241–1252. doi:10.1161/CIRCRESAHA.110.222133
   PubMed Web of Science ®Google Scholar
• Rhee S, Paik DT, Yang JY, et al. Endocardial/endothelial angiocrines regulate cardiomyocyte development and maturation and induce features of ventricular non-compaction. Eur Heart J. 2021;42(41):4264–4276. doi:10.1093/eurheartj/ehab298
   PubMed Web of Science ®Google Scholar
• Jenkins E, Moss JB, Pace JM, Bridgewater LC. The new collagen gene COL27A1 contains SOX9-responsive enhancer elements. Matrix Biol. 2005;24(3):177–184. doi:10.1016/j.matbio.2005.02.004
   PubMed Web of Science ®Google Scholar
• Vranka JA, Sakai LY, Bachinger HP. Prolyl 3-hydroxylase 1, enzyme characterization and identification of a novel family of enzymes. J Biol Chem. 2004;279(22):23615–23621. doi:10.1074/jbc.M312807200
   PubMed Web of Science ®Google Scholar
• Ogle JD, Arlinghaus RB, Lgan MA. 3-Hydroxyproline, a new amino acid of collagen. J Biol Chem. 1962;237:3667–3673.
   PubMed Web of Science ®Google Scholar
• Hudson DM, Eyre DR. Collagen prolyl 3-hydroxylation: a major role for a minor post-translational modification? Connect Tissue Res. 2013;54(4–5):245–251. doi:10.3109/03008207.2013.800867
   PubMed Web of Science ®Google Scholar
• Heard ME, Besio R, Weis M, et al. Sc65-Null Mice Provide Evidence for a Novel Endoplasmic Reticulum Complex Regulating Collagen Lysyl Hydroxylation. PLoS Genet. 2016;12(4):e1006002. doi:10.1371/journal.pgen.1006002
   PubMed Web of Science ®Google Scholar
• Hudson DM, Weis M, Rai J, et al. P3h3-null and Sc65-null Mice Phenocopy the Collagen Lysine Under-hydroxylation and Cross-linking Abnormality of Ehlers-Danlos Syndrome Type VIA. J Biol Chem. 2017;292(9):3877–3887. doi:10.1074/jbc.M116.762245
   PubMed Web of Science ®Google Scholar
• Kumar V, Prabhu SD, Bansal SS. CD4(+) T-lymphocytes exhibit biphasic kinetics post-myocardial infarction. Front Cardiovasc Med. 2022;9:992653. doi:10.3389/fcvm.2022.992653
   PubMedGoogle Scholar
• van der Laan AM, Ter Horst EN, Delewi R, et al. Monocyte subset accumulation in the human heart following acute myocardial infarction and the role of the spleen as monocyte reservoir. Eur Heart J. 2014;35(6):376–385. doi:10.1093/eurheartj/eht331
   PubMed Web of Science ®Google Scholar
• Tang TT, Yuan J, Zhu ZF, et al. Regulatory T cells ameliorate cardiac remodeling after myocardial infarction. Basic Res Cardiol. 2012;107(1):232. doi:10.1007/s00395-011-0232-6
   PubMed Web of Science ®Google Scholar
• Xia N, Lu Y, Gu M, et al. A Unique Population of Regulatory T Cells in Heart Potentiates Cardiac Protection From Myocardial Infarction. Circulation. 2020;142(20):1956–1973. doi:10.1161/CIRCULATIONAHA.120.046789
   PubMed Web of Science ®Google Scholar
• Hofmann U, Beyersdorf N, Weirather J, et al. Activation of CD4+ T lymphocytes improves wound healing and survival after experimental myocardial infarction in mice. Circulation. 2012;125(13):1652–1663. doi:10.1161/CIRCULATIONAHA.111.044164
   PubMed Web of Science ®Google Scholar
• Kumar V, Rosenzweig R, Asalla S, Nehra S, Prabhu SD, Bansal SS. TNFR1 Contributes to Activation-Induced Cell Death of Pathological CD4(+) T Lymphocytes During Ischemic Heart Failure. JACC Basic Transl Sci. 2022;7(10):1038–1049. doi:10.1016/j.jacbts.2022.05.005
   PubMedGoogle Scholar
• Horckmans M, Ring L, Duchene J, et al. Neutrophils orchestrate post-myocardial infarction healing by polarizing macrophages towards a reparative phenotype. Eur Heart J. 2017;38(3):187–197. doi:10.1093/eurheartj/ehw002
   PubMed Web of Science ®Google Scholar
• ter Horst EN, Hakimzadeh N, van der Laan AM, Krijnen PA, Niessen HW, Piek JJ. Modulators of Macrophage Polarization Influence Healing of the Infarcted Myocardium. Int J Mol Sci. 2015;16(12):29583–29591. doi:10.3390/ijms161226187
   PubMed Web of Science ®Google Scholar
• Kivirikko S, Saarela J, Myers JC, Autio-Harmainen H, Pihlajaniemi T. Distribution of type XV collagen transcripts in human tissue and their production by muscle cells and fibroblasts. Am J Pathol. 1995;147(5):1500–1509.
   PubMed Web of Science ®Google Scholar
• Lozano J, Rai A, Lees JG, et al. Scalable Generation of Nanovesicles from Human-Induced Pluripotent Stem Cells for Cardiac Repair. Int J Mol Sci. 2022;23(22). doi:10.3390/ijms232214334
   Web of Science ®Google Scholar