Bioinformatic-based Identification of Genes Associated with Aortic Valve Stenosis


  • Chao Song Medical School of Chinese PLA, Beijing, 100853, China
  • Shixiong Wei Medical School of Chinese PLA, Beijing, 100853, China
  • Yunlong Fan Medical School of Chinese PLA, Beijing, 100853, China
  • Shengli Jiang Department of Cardiovascular Surgery, the First Medical Centre of Chinese PLA General Hospital, Beijing 100853, China



Aortic valve stenosis, Integrated bioinformatics analyses, Differentially expressed genes, Functional enrichment analysis


Background: Aortic valve stenosis (AS) disease is the most common valvular disease in developed countries. The pathology of AS is complex, and its main processes include calcification of the valve stroma and involve genetic factors, lipoprotein deposition and oxidation, chronic inflammation, osteogenic transition of cardiac valve interstitial cells, and active valve calcification. The aim of this study was to identify potential genes associated with AS.

Methods: Three original gene expression profiles (GSE153555, GSE12644, and GSE51472) were downloaded from the Gene Expression Omnibus (GEO) database and analyzed by GEO2R tool or ‘limma’ in R to identify differentially expressed genes (DEGs). Functional enrichment was analyzed using the ClusterProfiler package in R Bioconductor. STRING was utilized for the Protein–Protein Interaction (PPI) Network construct, and tissue-specific gene expression were identified using BioGPS database. The hub genes were screened out using the Cytoscape software. Related miRNAs were predicted in Targetscan, miWalk, miRDB, Hoctar, and TarBase.

Results: A total of 58 upregulated genes and 20 downregulated genes were screened out, which were mostly enriched in matrix remodeling and the immune system process. A module was thus clustered into by PPI network analysis, which mainly involved in Fc gamma R-mediated phagocytosis, Osteoclast differentiation. Ten genes (IBSP, NCAM1, MMP9, FCGR3B, COL4A3, FCGR1A, THY1, RUNX2, ITGA4, and COL10A1) with the highest degree scores were subsequently identified as the hub genes for AS by applying the CytoHubba plugin. And hsa-miR-1276 was finally identified as potential miRNA and miRNA-gene regulatory network was constructed using NetworkAnalyst.

Conclusions: Our analysis suggested that IBSP, NCAM1, MMP9, FCGR3B, COL4A3, FCGR1A, THY1, RUNX2, ITGA4, and COL10A1 might be hub genes associated with AS, and hsa-miR-1276 was potential miRNA. This result could provide novel insight into pathology and therapy of AS in the future.


Ackermann MA, Petrosino JM, Manring HR, Wright P, Shettigar V, Kilic A, et al. 2017. TGF-β1 affects cell-cell adhesion in the heart in an NCAM1-dependent mechanism. J Mol Cell Cardiol. 112:49-57.

Aikawa E, Nahrendorf M, Sosnovik D, Lok VM, Jaffer FA, Aikawa M, et al. 2007. Multimodality molecular imaging identifies proteolytic and osteogenic activities in early aortic valve disease. Circulation. 115(3):377-386.

Altman R. 2016. Current Progress in Bioinformatics 2016. Brief Bioinform. 17(1):1.

Arnett DK, Meyers KJ, Devereux RB, Tiwari HK, Gu CC, Vaughan LK, et al. 2011. Genetic variation in NCAM1 contributes to left ventricular wall thickness in hypertensive families. Circ Res. 108(3):279-283.

Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, et al. 2013. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 41(Database issue):D991-995.

Bossé Y, Mathieu P, Pibarot P. 2008. Genomics: the next step to elucidate the etiology of calcific aortic valve stenosis. J Am Coll Cardiol. 51(14):1327-1336.

Bossé Y, Miqdad A, Fournier D, Pépin A, Pibarot P, Mathieu P. 2009. Refining molecular pathways leading to calcific aortic valve stenosis by studying gene expression profile of normal and calcified stenotic human aortic valves. Circ Cardiovasc Genet. 2(5):489-498.

Caira FC, Stock SR, Gleason TG, McGee EC, Huang J, Bonow RO, et al. 2006. Human degenerative valve disease is associated with up-regulation of low-density lipoprotein receptor-related protein 5 receptor-mediated bone formation. J Am Coll Cardiol. 47(8):1707-1712.

Carabello BA, Paulus WJ. 2009. Aortic stenosis. Lancet. 373(9667):956-966.

Carità P, Coppola G, Novo G, Caccamo G, Guglielmo M, Balasus F, et al. 2016. Aortic stenosis: insights on pathogenesis and clinical implications. J Geriatr Cardiol. 13(6):489-498.

Coffey S, Cox B, Williams MJ. 2014. The prevalence, incidence, progression, and risks of aortic valve sclerosis: a systematic review and meta-analysis. J Am Coll Cardiol. 63(25 Pt A):2852-2861.

Coté N, Mahmut A, Bosse Y, Couture C, Pagé S, Trahan S, et al. 2013. Inflammation is associated with the remodeling of calcific aortic valve disease. Inflammation. 36(3):573-581.

Cui L, Rashdan NA, Zhu D, Milne EM, Ajuh P, Milne G, et al. 2017. End stage renal disease-induced hypercalcemia may promote aortic valve calcification via Annexin VI enrichment of valve interstitial cell derived-matrix vesicles. J Cell Physiol. 232(11):2985-2995.

Cybularz M, Wydra S, Berndt K, Poitz DM, Barthel P, Alkouri A, et al. 2021. Frailty is associated with chronic inflammation and pro-inflammatory monocyte subpopulations. Exp Gerontol. 149:111317.

de Oliveira Sá M, Cavalcanti L, Perazzo ÁM, Gomes R, Clavel MA, Pibarot P, et al. 2020. Calcific Aortic Valve Stenosis and Atherosclerotic Calcification. Curr Atheroscler Rep. 22(2):2.

Fan X, Peng J, Lei L, He J, Huang J, Zheng D, et al. 2020. Integrated analysis of immunocyte infiltration and differential gene expression in tricuspid aortic valve-associated thoracic aortic aneurysms. Ann Transl Med. 8(6):285.

Fang M, Alfieri CM, Hulin A, Conway SJ, Yutzey KE. 2014. Loss of β-catenin promotes chondrogenic differentiation of aortic valve interstitial cells. Arterioscler Thromb Vasc Biol. 34(12):2601-2608.

Ferreira SA, Young G, Jones JR, Rankin S. 2021. Bioglass/carbonate apatite/collagen composite scaffold dissolution products promote human osteoblast differentiation. Mater Sci Eng C Mater Biol Appl. 118:111393.

Gambardella L, McManus SA, Moignard V, Sebukhan D, Delaune A, Andrews S, et al. 2019. BNC1 regulates cell heterogeneity in human pluripotent stem cell-derived epicardium. Development. 146(24).

Garg V, Muth AN, Ransom JF, Schluterman MK, Barnes R, King IN, et al. 2005. Mutations in NOTCH1 cause aortic valve disease. Nature. 437(7056):270-274.

George J, Afek A, Gilburd B, Blank M, Levy Y, Aron-Maor A, et al. 1998. Induction of early atherosclerosis in LDL-receptor-deficient mice immunized with beta2-glycoprotein I. Circulation. 98(11):1108-1115.

Ghaisas NK, Foley JB, Briain DS, Crean P, Kelleher D, et al. 2000. Adhesion molecules in nonrheumatic aortic valve disease: endothelial expression, serum levels and effects of valve replacement. J Am Coll Cardiol. 36(7):2257-2262.

Gharibeh L, Komati H, Bossé Y, Boodhwani M, Heydarpour M, Fortier M, et al. 2018. GATA6 Regulates Aortic Valve Remodeling, and Its Haploinsufficiency Leads to Right-Left Type Bicuspid Aortic Valve. Circulation. 138(10):1025-1038.

Ghosh S, Vivar J, Nelson CP, Willenborg C, Segrè AV, Mäkinen VP, et al. 2015. Systems Genetics Analysis of Genome-Wide Association Study Reveals Novel Associations Between Key Biological Processes and Coronary Artery Disease. Arterioscler Thromb Vasc Biol. 35(7):1712-1722.

Goody PR, Hosen MR, Christmann D, Niepmann ST, Zietzer A, Adam M, et al. 2020. Aortic Valve Stenosis: From Basic Mechanisms to Novel Therapeutic Targets. Arterioscler Thromb Vasc Biol. 40(4):885-900.

Gottschalk BH, Blankenstein J, Guo L. 2018. Ochronosis of Mitral Valve and Coronary Arteries. Ann Thorac Surg. 106(1):e19-19e20.

Greene CL, Jaatinen KJ, Wang H, Koyano TK, Bilbao MS, Woo YJ. 2020. Transcriptional Profiling of Normal, Stenotic, and Regurgitant Human Aortic Valves. Genes (Basel). 11(7).

Guauque-Olarte S, Droit A, Tremblay-Marchand J, Gaudreault N, Kalavrouziotis D, Dagenais F, et al. 2016. RNA expression profile of calcified bicuspid, tricuspid, and normal human aortic valves by RNA sequencing. Physiol Genomics. 48(10):749-761.

Hadji F, Boulanger MC, Guay SP, Gaudreault N, Amellah S, Mkannez G, et al. 2016. Altered DNA Methylation of Long Noncoding RNA H19 in Calcific Aortic Valve Disease Promotes Mineralization by Silencing NOTCH1. Circulation. 134(23):1848-1862.

Hewing B, Au SC, Ludwig A, Ellerbroek R, van Dijck P, Hartmann L, et al. 2017. Severe Aortic Valve Stenosis in Adults is Associated with Increased Levels of Circulating Intermediate Monocytes. J Cardiovasc Transl Res. 10(1):27-34.

Hewing B, Ellerbroek R, Au SC, Stangl V, Dreger H, Laule M, et al. 2017. Levels of Circulating Intermediate Monocytes Decrease after Aortic Valve Replacement in Patients with Severe Aortic Stenosis. Thromb Haemost. 117(12):2346-2355.

Ibarrola J, Sadaba R, Martinez-Martinez E, Garcia-Peña A, Arrieta V, Alvarez V, et al. 2018. Aldosterone Impairs Mitochondrial Function in Human Cardiac Fibroblasts via A-Kinase Anchor Protein 12. Sci Rep. 8(1):6801.

Iung B, Baron G, Butchart EG, Delahaye F, Gohlke-Bärwolf C, Levang OW, et al. 2003. A prospective survey of patients with valvular heart disease in Europe: The Euro Heart Survey on Valvular Heart Disease. Eur Heart J. 24(13):1231-1243.

Kamperidis V, Delgado V, van Mieghem NM, Kappetein AP, Leon MB, Bax JJ. 2016. Diagnosis and management of aortic valve stenosis in patients with heart failure. Eur J Heart Fail. 18(5):469-481.

Kerr JM, Fisher LW, Termine JD, Wang MG, McBride OW, Young MF. 1993. The human bone sialoprotein gene (IBSP): genomic localization and characterization. Genomics. 17(2):408-415.

Kostyunin A, Mukhamadiyarov R, Glushkova T, Bogdanov L, Shishkova D, Osyaev N, et al. 2020. Ultrastructural Pathology of Atherosclerosis, Calcific Aortic Valve Disease, and Bioprosthetic Heart Valve Degeneration: Commonalities and Differences. Int J Mol Sci. 21(20).

Kostyunin AE, Yuzhalin AE, Ovcharenko EA, Kutikhin AG. 2019. Development of calcific aortic valve disease: Do we know enough for new clinical trials. J Mol Cell Cardiol. 132:189-209.

Lindman BR, Clavel MA, Mathieu P, Iung B, Lancellotti P, Otto CM, et al. 2016. Calcific aortic stenosis. Nat Rev Dis Primers. 2:16006.

Lok ZS, Goldstein J, Smith JA. 2013. Alkaptonuria-associated aortic stenosis. J Card Surg. 28(4):417-420.

Ma F, Li T, Zhang H, Wu G. 2016. MiR-30s Family Inhibit the Proliferation and Apoptosis in Human Coronary Artery Endothelial Cells Through Targeting the 3'UTR Region of ITGA4 and PLCG1. J Cardiovasc Pharmacol. 68(5):327-333.

Mazur P, Mielimonka A, Natorska J, Wypasek E, Gawęda B, Sobczyk D, et al. 2018. Lymphocyte and monocyte subpopulations in severe aortic stenosis at the time of surgical intervention. Cardiovasc Pathol. 35:1-7.

Michaud M, Balardy L, Moulis G, Gaudin C, Peyrot C, Vellas B, et al. 2013. Proinflammatory cytokines, aging, and age-related diseases. J Am Med Dir Assoc. 14(12):877-882.

Miller JD, Weiss RM, Heistad DD. 2011. Calcific aortic valve stenosis: methods, models, and mechanisms. Circ Res. 108(11):1392-1412.

Nagy E, Andersson DC, Caidahl K, Eriksson MJ, Eriksson P, Franco-Cereceda A, et al. 2011. Upregulation of the 5-lipoxygenase pathway in human aortic valves correlates with severity of stenosis and leads to leukotriene-induced effects on valvular myofibroblasts. Circulation. 123(12):1316-1325.

Nishimura RA, Otto CM, Bonow RO, Carabello BA, Erwin JP 3rd, Fleisher LA, et al. 2017. 2017 AHA/ACC Focused Update of the 2014 AHA/ACC Guideline for the Management of Patients With Valvular Heart Disease: A Report of the American College of Cardiology/American Heart Association Task Force on Clinical Practice Guidelines. Circulation. 135(25):e1159-1159e1195.

Nkomo VT, Gardin JM, Skelton TN, Gottdiener JS, Scott CG, Enriquez-Sarano M. 2006. Burden of valvular heart diseases: a population-based study. Lancet. 368(9540):1005-1011.

O', Brien KD. 2006. Pathogenesis of calcific aortic valve disease: a disease process comes of age (and a good deal more). Arterioscler Thromb Vasc Biol. 26(8):1721-1728.

Olesen P, Nguyen K, Wogensen L, Ledet T, Rasmussen LM. 2007. Calcification of human vascular smooth muscle cells: associations with osteoprotegerin expression and acceleration by high-dose insulin. Am J Physiol Heart Circ Physiol. 292(2):H1058-1064.

Otto CM, Kuusisto J, Reichenbach DD, Gown AM, Brien KD. 1994. Characterization of the early lesion of 'degenerative' valvular aortic stenosis. Histological and immunohistochemical studies. Circulation. 90(2):844-853.

Padang R, Bagnall RD, Tsoutsman T, Bannon PG, Semsarian C. 2015. Comparative transcriptome profiling in human bicuspid aortic valve disease using RNA sequencing. Physiol Genomics. 47(3):75-87.

Pasipoularides A. 2016. Calcific Aortic Valve Disease: Part 1--Molecular Pathogenetic Aspects, Hemodynamics, and Adaptive Feedbacks. J Cardiovasc Transl Res. 9(2):102-118.

Pfluecke C, Berndt K, Wydra S, Tarnowski D, Barthel P, Quick S, et al. 2016. Atrial fibrillation is associated with high levels of monocyte-platelet-aggregates and increased CD11b expression in patients with aortic stenosis. Thromb Haemost. 115(5):993-1000.

Pfluecke C, Wydra S, Berndt K, Tarnowski D, Cybularz M, Jellinghaus S, et al. 2020. Mon2-monocytes and increased CD-11b expression before transcatheter aortic valve implantation are associated with earlier death. Int J Cardiol. 318:115-120.

Pohjolainen V, Taskinen P, Soini Y, Rysä J, Ilves M, Juvonen T, et al. 2008. Noncollagenous bone matrix proteins as a part of calcific aortic valve disease regulation. Hum Pathol. 39(11):1695-1701.

Schlotter F, Halu A, Goto S, Blaser MC, Body SC, Lee LH, et al. 2018. Spatiotemporal Multi-Omics Mapping Generates a Molecular Atlas of the Aortic Valve and Reveals Networks Driving Disease. Circulation. 138(4):377-393.

Sen J, Chung E, Neil C, Marwick T. 2020. Antihypertensive therapies in moderate or severe aortic stenosis: a systematic review and meta-analysis. BMJ Open. 10(10):e036960.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13(11):2498-2504.

Shao JS, Cai J, Towler DA. 2006. Molecular mechanisms of vascular calcification: lessons learned from the aorta. Arterioscler Thromb Vasc Biol. 26(7):1423-1430.

Soini Y, Satta J, Määttä M, Autio-Harmainen H. 2001. Expression of MMP2, MMP9, MT1-MMP, TIMP1, and TIMP2 mRNA in valvular lesions of the heart. J Pathol. 194(2):225-231.

Stritzke J, Linsel-Nitschke P, Markus MR, Mayer B, Lieb W, Luchner A, et al. 2009. Association between degenerative aortic valve disease and long-term exposure to cardiovascular risk factors: results of the longitudinal population-based KORA/MONICA survey. Eur Heart J. 30(16):2044-2053.

Sun JY, Hua Y, Shen H, Qu Q, Kan JY, Kong XQ, et al. 2021. Identification of key genes in calcific aortic valve disease via weighted gene co-expression network analysis. BMC Med Genomics. 14(1):135.

Swaminathan G, Krishnamurthy VK, Sridhar S, Robson DC, Ning Y, Grande-Allen KJ. 2019. Hypoxia Stimulates Synthesis of Neutrophil Gelatinase-Associated Lipocalin in Aortic Valve Disease. Front Cardiovasc Med. 6:156.

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. 2019. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47(D1):D607-607D613.

Teng P, Xu X, Ni C, Yan H, Sun Q, Zhang E, et al. 2020. Identification of key genes in calcific aortic valve disease by integrated bioinformatics analysis. Medicine (Baltimore). 99(29):e21286.

Thakur S, Markman P, Cullen H. 2013. Choice of valve prosthesis in a rare clinical condition: aortic stenosis due to alkaptonuria. Heart Lung Circ. 22(10):870-872.

Thériault S, Gaudreault N, Lamontagne M, Rosa M, Boulanger MC, Messika-Zeitoun D, et al. 2018. A transcriptome-wide association study identifies PALMD as a susceptibility gene for calcific aortic valve stenosis. Nat Commun. 9(1):988.

Touchberry CD, Green TM, Tchikrizov V, Mannix JE, Mao TF, Carney BW, et al. 2013. FGF23 is a novel regulator of intracellular calcium and cardiac contractility in addition to cardiac hypertrophy. Am J Physiol Endocrinol Metab. 304(8):E863-873.

Tur MK, Etschmann B, Benz A, Leich E, Waller C, Schuh K, et al. 2013. The 140-kD isoform of CD56 (NCAM1) directs the molecular pathogenesis of ischemic cardiomyopathy. Am J Pathol. 182(4):1205-1218.

Urban P, Rabajdová M, Špaková I, Sabol F, Mičková H, Lakatosová K, et al. 2019. Molecular recognition of aortic valve stenosis and regurgitation. Eur Rev Med Pharmacol Sci. 23(24):10996-11003.

VeDepo M, Buse E, Quinn R, Hopkins R, Converse G. 2018. Extended bioreactor conditioning of mononuclear cell-seeded heart valve scaffolds. J Tissue Eng. 9:2041731418767216.

Wasywich CA, Webster MW, Richards AM, Stewart RA. 2006. Coronary sinus and ascending aortic levels of aldosterone, angiotensin II, and B-type natriuretic peptide in patients with aortic stenosis and in patients with coronary heart disease. Am J Cardiol. 97(7):1068-1072.

Wu HD, Maurer MS, Friedman RA, Marboe CC, Ruiz-Vazquez EM, Ramakrishnan R, et al. 2007. The lymphocytic infiltration in calcific aortic stenosis predominantly consists of clonally expanded T cells. J Immunol. 178(8):5329-5339.

Yadgir S, Johnson CO, Aboyans V, Adebayo OM, Adedoyin RA, Afarideh M, et al. 2020. Global, Regional, and National Burden of Calcific Aortic Valve and Degenerative Mitral Valve Diseases, 1990-2017. Circulation. 141(21):1670-1680.

Yousefi K, Irion CI, Takeuchi LM, Ding W, Lambert G, Eisenberg T, et al. 2019. Osteopontin Promotes Left Ventricular Diastolic Dysfunction Through a Mitochondrial Pathway. J Am Coll Cardiol. 73(21):2705-2718.

Yu G, Wang LG, Han Y, He QY. 2012. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 16(5):284-287.

Zhao Q, Wang X, Liu Y, He A, Jia R. 2010. NFATc1: functions in osteoclasts. Int J Biochem Cell Biol. 42(5):576-579.

Zhao X, Hou C, Xiao T, Xie L, Li Y, Jia J, et al. 2020. An interesting Mybpc3 heterozygous mutation associated with bicuspid aortic valve. Transl Pediatr. 9(5):610-618.

Zhou G, Soufan O, Ewald J, Hancock R, Basu N, Xia J. 2019. NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis. Nucleic Acids Res. 47(W1):W234-234W241.



How to Cite

Song, C., Wei, S., Fan, Y., & Jiang, S. (2022). Bioinformatic-based Identification of Genes Associated with Aortic Valve Stenosis. The Heart Surgery Forum, 25(1), E069-E078.