Pharmaceutical Research

, Volume 34, Issue 8, pp 1648–1657 | Cite as

Regulatory Variants Modulate Protein Kinase C α (PRKCA) Gene Expression in Human Heart

  • Liang Li
  • Lizhi Zhang
  • Philip F. Binkley
  • Wolfgang Sadee
  • Danxin Wang
Research Paper



Protein kinase C α (PRKCA) is involved in multiple functions and has been implicated in heart failure risks and treatment outcomes. This study aims to identify regulatory variants affecting PRKCA expression in human heart, and evaluate attributable risk of heart disease.


mRNA expression quantitative trait loci (eQTLs) were extracted from the Genotype and Tissue Expression Project (GTEx). Allelic mRNA ratios were measured in 51 human heart tissues to identify cis-acting regulatory variants. Potential regulatory regions were tested with luciferase reporter gene assays and further evaluated in GTEx and genome-wide association studies.


Located in a region with robust enhancer activity in luciferase reporter assays, rs9909004 (T > C, minor allele frequency =0.47) resides in a haplotype displaying strong eQTLs for PRKCA in heart (p = 1.2 × 10−23). The minor C allele is associated with both decreased PRKCA mRNA expression and decreased risk of phenotypes characteristic of heart failure in GWAS analyses (QT interval p = 3.0 × 10−14). While rs9909004 is the likely regulatory variant, other variants in high linkage disequilibrium cannot be excluded. Distinct regulatory variants appear to affect expression in other tissues.


The haplotype carrying rs9909004 influences PRKCA expression in the heart and is associated with traits linked to heart failure, potentially affecting therapy of heart failure.


association gene expression genetic variant heart failure polymorphism protein kinase C α (PRKCA) 



beta-1 adrenergic receptor


Allelic expression imbalance


Expression quantitative trait loci


Genotype-Tissue Expression


Genome-wide association studies


Linkage disequilibrium


Minor allele frequency




Protein kinase C α subunit


Sarcoplasmic reticulum Ca2+ ATPase-2


Single nucleotide polymorphisms


Transcription factors


Acknowledgments and Disclosures

We thank Rosanna Asselta for giving us the primer sequences and PCR condition of rs35476409/rs61762387 and 15 × GCC microsatellite. This study was supported by National Institutes of Health Pharmacogenetics Research Network grant U01 GM092655 (WS), U01-GM074492 (JAJ), the National Institute of Health grant R01HL126969 (DW), and partially by a grant from the National Center for Research Resources (UL1RR025755). We also acknowledge support from the Ohio Supercomputer Center (grant #PAS0885). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health or the National Center for Research Resources. The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health. Additional funds were provided by the NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Donors were enrolled at Biospecimen Source Sites funded by NCI\SAIC-Frederick, Inc. (SAIC-F) subcontracts to the National Disease Research Interchange (10XS170), Roswell Park Cancer Institute (10XS171), and Science Care, Inc. (X10S172). The Laboratory, Data Analysis, and Coordinating Center (LDACC) was funded through a contract (HHSN268201000029C) to The Broad Institute, Inc. Biorepository operations were funded through an SAIC-F subcontract to Van Andel Institute (10ST1035). Additional data repository and project management were provided by SAIC-F (HHSN261200800001E). The Brain Bank was supported by a supplement to University of Miami grants DA006227 & DA033684 and to contract N01MH000028. Statistical Methods development grants were made to the University of Geneva (MH090941 & MH101814), the University of Chicago (MH090951, MH090937, MH101820, MH101825), the University of North Carolina - Chapel Hill (MH090936 & MH101819), Harvard University (MH090948), Stanford University (MH101782), Washington University St Louis (MH101810), and the University of Pennsylvania (MH101822). The data used for the analyses described in this manuscript were obtained from GTEx Analysis Release V6p, dbGaP Accession phs000424.v6.p1. Disclosures None.

Supplementary material

11095_2017_2102_MOESM1_ESM.docx (23 kb)
ESM 1 (DOCX 22 kb)


  1. 1.
    Coussens L, Parker PJ, Rhee L, Yang-Feng TL, Chen E, Waterfield MD, et al. Multiple, distinct forms of bovine and human protein kinase C suggest diversity in cellular signaling pathways. Science. 1986;233(4766):859–66.CrossRefPubMedGoogle Scholar
  2. 2.
    Dempsey EC, Newton AC, Mochly-Rosen D, Fields AP, Reyland ME, Insel PA, et al. Protein kinase C isozymes and the regulation of diverse cell responses. Am J Physiol Lung Cell Mol Physiol. 2000;279(3):L429–38.PubMedGoogle Scholar
  3. 3.
    Ma Y, Usuwanthim K, Munawara U, Quach A, Gorgani NN, Abbott CA, et al. Protein kinase cα regulates the expression of complement receptor Ig in human monocyte-derived macrophages. J Immunol. 2015;194(6):2855–61.CrossRefPubMedGoogle Scholar
  4. 4.
    Arking DE, Pulit SL, Crotti L, van der Harst P, Munroe PB, Koopmann TT, et al. Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization. Nat Genet. 2014;46(8):826–36.CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Turner ST, Boerwinkle E, O’Connell JR, Bailey KR, Gong Y, Chapman AB, et al. Genomic association analysis of common variants influencing antihypertensive response to hydrochlorothiazide. Hypertension. 2013;62(2):391–7.CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Carroll LS, Williams NM, Moskvina V, Russell E, Norton N, Williams HJ, et al. Evidence for rare and common genetic risk variants for schizophrenia at protein kinase C, alpha. Mol Psychiatry. 2010;15(11):1101–11.CrossRefPubMedGoogle Scholar
  7. 7.
    MacLeod CA, Donaldson DI. PRKCA polymorphism changes the neural basis of episodic remembering in healthy individuals. PLoS One. 2014;9(5), e98018.CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Murphy A, Tantisira KG, Soto-Quirós ME, Avila L, Klanderman BJ, Lake S, et al. PRKCA: a positional candidate gene for body mass index and asthma. Am J Hum Genet. 2009;85(1):87–96.CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Saarela J, Kallio SP, Chen D, Montpetit A, Jokiaho A, Choi E, et al. PRKCA and multiple sclerosis: association in two independent populations. PLoS Genet. 2006;2(3), e42.CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Galea GL, Meakin LB, Williams CM, Hulin-Curtis SL, Lanyon LE, Poole AW, et al. Protein kinase Cα (PKCα) regulates bone architecture and osteoblast activity. J Biol Chem. 2014;289(37):25509–22.CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Quack I, Woznowski M, Potthoff SA, Palmer R, Königshausen E, Sivritas S, et al. PKC alpha mediates beta-arrestin2-dependent nephrin endocytosis in hyperglycemia. J Biol Chem. 2011;286(15):12959–70.CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Kopach O, Viatchenko-Karpinski V, Atianjoh FE, Belan P, Tao YX, Voitenko N. PKCα is required for inflammation-induced trafficking of extrasynaptic AMPA receptors in tonically firing lamina II dorsal horn neurons during the maintenance of persistent inflammatory pain. J Pain. 2013;14(2):182–92.CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    He J, Kelly TN, Zhao Q, Li H, Huang J, Wang L, et al. Genome-wide association study identifies 8 novel loci associated with blood pressure responses to interventions in Han Chinese. Circ Cardiovasc Genet. 2013;6(6):598–607.CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Paraboschi EM, Rimoldi V, Soldà G, Tabaglio T, Dall’Osso C, Saba E, et al. Functional variations modulating PRKCA expression and alternative splicing predispose to multiple sclerosis. Hum Mol Genet. 2014;23(25):6746–61.CrossRefPubMedGoogle Scholar
  15. 15.
    GTEx Consortium. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015;348(6235):648–60.CrossRefGoogle Scholar
  16. 16.
    Braz JC, Gregory K, Pathak A, Zhao W, Sahin B, Klevitsky R, et al. PKC-alpha regulates cardiac contractility and propensity toward heart failure. Nat Med. 2004;10(3):248–54.CrossRefPubMedGoogle Scholar
  17. 17.
    Wang D, Johnson AD, Papp AC, Kroetz DL, Sadée W. Multidrug resistance polypeptide 1 (MDR1, ABCB1) variant 3435C > T affects mRNA stability. Pharmacogenet Genomics. 2005;15(10):693–704.CrossRefPubMedGoogle Scholar
  18. 18.
    Johnson AD, Gong Y, Wang D, Langaee TY, Shin J, Cooper-Dehoff RM, et al. Promoter polymorphisms in ACE (angiotensin I-converting enzyme) associated with clinical outcomes in hypertension. Clin Pharmacol Ther. 2009;85(1):36–44.CrossRefPubMedGoogle Scholar
  19. 19.
    Smith RM, Alachkar H, Papp AC, Wang D, Mash DC, Wang JC, et al. Nicotinic α5 receptor subunit mRNA expression is associated with distant 5′ upstream polymorphisms. Eur J Hum Genet. 2011;19(1):76–8.CrossRefPubMedGoogle Scholar
  20. 20.
    Wang D, Chen H, Momary KM, Cavallari LH, Johnson JA, Sadée W. Regulatory polymorphism in vitamin K epoxide reductase complex subunit 1 (VKORC1) affects gene expression and warfarin dose requirement. Blood. 2008;112(4):1013–21.CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Wang D, Guo Y, Wrighton SA, Cooke GE, Sadee W. Intronic polymorphism in CYP3A4 affects hepatic expression and response to statin drugs. Pharmacogenomics J. 2011;11(4):274–86.CrossRefPubMedGoogle Scholar
  22. 22.
    Pinsonneault JK, Han DD, Burdick KE, Kataki M, Bertolino A, Malhotra AK, et al. Dopamine transporter gene variant affecting expression in human brain is associated with bipolar disorder. Neuropsychopharmacology. 2011;36(8):1644–55.CrossRefPubMedPubMedCentralGoogle Scholar
  23. 23.
    Barrie ES, Weinshenker D, Verma A, Pendergrass SA, Lange LA, Ritchie MD, et al. Regulatory polymorphisms in human DBH affect peripheral gene expression and sympathetic activity. Circ Res. 2014;115(12):1017–25.CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 1988;16(3):1215.CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Wang D, Papp AC, Binkley PF, Johnson JA, Sadée W. Highly variable mRNA expression and splicing of L-type voltage-dependent calcium channel alpha subunit 1C in human heart tissues. Pharmacogenet Genomics. 2006;16(10):735–45.CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Li L, Li CJ, Zhang YJ, Zheng L, Jiang HX, Si-Tu B. Simultaneous detection of CYP3A5 and MDR1 polymorphisms based on the SNaPshot assay. Clin Biochem. 2011;44(5-6):418–22.CrossRefPubMedGoogle Scholar
  27. 27.
    Sotoodehnia N, Isaacs A, de Bakker PI, Dörr M, Newton-Cheh C, Nolte IM, et al. Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet. 2010;42(12):1068–76.CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Meyer WK, Arbeithuber B, Ober C, Ebner T, Tiemann-Boege I, Hudson RR, et al. Evaluating the evidence for transmission distortion in human pedigrees. Genetics. 2012;191(1):215–32.CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Carty CL, Johnson NA, Hutter CM, Reiner AP, Peters U, Tang H, et al. Genome-wide association study of body height in African Americans: the Women’s Health Initiative SNP Health Association Resource (SHARe). Hum Mol Genet. 2012;21(3):711–20.CrossRefPubMedGoogle Scholar
  30. 30.
    Athanasiadis G, Sabater-Lleal M, Buil A, Souto JC, Borrell M, Lathrop M, et al. Genetic determinants of plasma β2 -glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain. J Thromb Haemost. 2013;11(3):521–8.CrossRefPubMedGoogle Scholar
  31. 31.
    Malovini A, Illario M, Iaccarino G, Villa F, Ferrario A, Roncarati R, et al. Association study on long-living individuals from Southern Italy identifies rs10491334 in the CAMKIV gene that regulates survival proteins. Rejuvenation Res. 2011;14(3):283–91.CrossRefPubMedGoogle Scholar
  32. 32.
    Cai DC, Fonteijn H, Guadalupe T, Zwiers M, Wittfeld K, Teumer A, et al. A genome-wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl’s gyrus. Genes Brain Behav. 2014;13(7):675–85.CrossRefPubMedGoogle Scholar
  33. 33.
    Wojczynski MK, Li M, Bielak LF, Kerr KF, Reiner AP, Wong ND, et al. Genetics of coronary artery calcification among African Americans, a meta-analysis. BMC Med Genet. 2013;14:75.CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Vasan RS, Glazer NL, Felix JF, Lieb W, Wild PS, Felix SB, et al. Genetic variants associated with cardiac structure and function: a meta-analysis and replication of genome-wide association data. JAMA. 2009;302(2):168–78.CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Xie P, Kranzler HR, Yang C, Zhao H, Farrer LA, Gelernter J. Genome-wide association study identifies new susceptibility loci for posttraumatic stress disorder. Biol Psychiatry. 2013;74(9):656–63.CrossRefPubMedGoogle Scholar
  36. 36.
    Bowling N, Walsh RA, Song G, Estridge T, Sandusky GE, Fouts RL, et al. Increased protein kinase C activity and expression of Ca2 + -sensitive isoformsin the failing human heart. Circulation. 1999;99(3):384–91.CrossRefPubMedGoogle Scholar
  37. 37.
    Liu Q, Chen X, Macdonnell SM, Kranias EG, Lorenz JN, Leitges M, et al. Protein kinase Cα, but not PKCβ or PKCγ, regulates contractility and heart failure susceptibility: implications for ruboxistaurin as a novel therapeutic approach. Circ Res. 2009;105(2):194–200.CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, et al. Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. Nat Genet. 2015;47(12):1393–401.CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Rau T, Düngen HD, Edelmann F, Waagstein F, Lainščak M, Dimković S, et al. Impact of the β1-adrenoceptor Arg389Gly polymorphism on heart-rate responses to bisoprolol and carvedilol in heart-failure patients. Clin Pharmacol Ther. 2012;92(1):21–8.CrossRefPubMedGoogle Scholar
  40. 40.
    Baudhuin LM, Miller WL, Train L, Bryant S, Hartman KA, Phelps M, et al. Relation of ADRB1, CYP2D6, and UGT1A1 polymorphisms with dose of, and response to, carvedilol or metoprolol therapy in patients with chronic heart failure. Am J Cardiol. 2010;106(3):402–8.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of MedicineThe Ohio State UniversityColumbusUSA
  2. 2.Department of Internal Medicine, College of MedicineThe Ohio State UniversityColumbusUSA
  3. 3.Center for Pharmacogenomics and Department of Cancer Biology and Genetics, College of MedicineThe Ohio State UniversityColumbusUSA

Personalised recommendations