Systems biology surveillance decrypts pathological transcriptome remodeling

BMC Systems Biology

Carmen Perez-Terzic³  Andre Terzic²  Marek Michalak¹  Jody Groenendyk¹  Saranya P. Wyles²  Randolph S. Faustino² 

[1] Department of Biochemistry, University of Alberta, Edmonton, AB, Canada;Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester 55905, MN, USA;Rehabilitation Medicine Research Center, Rochester, MN, USA

关键词: Systems biology;    Bioinformatics;    Transcriptome;    Network;    Gene ontology;    Microarray;    Pluripotent;    Stem cells;   

Others  :  1230656
DOI  :  10.1186/s12918-015-0177-8

 received in 2014-08-28, accepted in 2015-06-05,  发布年份 2015

【 摘 要 】

Background

Pathological cardiac development is precipitated by dysregulation of calreticulin, an endoplasmic reticulum (ER)-resident calcium binding chaperone and critical contributor to cardiogenesis and embryonic viability. However, pleiotropic phenotype derangements induced by calreticulin deficiency challenge the identification of specific downstream transcriptome elements that direct proper cardiac formation. Here, differential transcriptome navigation was used to diagnose high priority calreticulin domain-specific gene expression changes and decrypt complex cardiac-specific molecular responses elicited by discrete functional regions of calreticulin.

Methods

Wild type (WT), calreticulin-deficient (CALR ^−/− ), and calreticulin truncation variant (CALR ^−/− -NP and CALR ^−/− -PC) pluripotent stem cells were used to investigate molecular remodeling underlying a model of cardiopathology. Bioinformatic deconvolution of isolated transcriptomes was performed to identify predominant expression trends, gene ontology prioritizations, and molecular network features characteristic of discrete cell types.

Results

Stem cell lines with wild type (WT), calreticulin-deficient (CALR ^−/− ) genomes, as well as calreticulin truncation variants exclusively expressing either the chaperoning (CALR ^−/− -NP) or the calcium binding (CALR ^−/− -PC) domain exhibited characteristic molecular signatures determined by unsupervised agglomerative clustering. Kohonen mapping of RNA expression changes identified transcriptome dynamics that segregated into 12 discrete gene expression meta-profiles which were enriched for regulation of Eukaryotic Initiation Factor 2 (EIF2) signaling. Focused examination of domain-specific gene ontology remodeling revealed a general enrichment of Cardiovascular Development in the truncation variants, with unique prioritization of “Cardiovascular Disease” exclusive to the cohort of down regulated genes of the PC truncation variant. Molecular cartography of genes that comprised this cardiopathological category revealed uncharacterized and novel gene relationships, with identification of Pitx2 as a critical hub within the topology of a CALR ^−/−compromised network.

Conclusions

Diagnostic surveillance, through an algorithm that integrates pluripotent stem cell transcriptomes with advanced high throughput assays and computational bioinformatics, revealed collective gene expression network changes that underlie differential phenotype development. Stem cell transcriptomes provide a deep collective molecular index that reflects ad hoc robustness of the pluripotent gene network. Remodeling events such as monogenic lesions provide a background by which high priority candidate disease effectors and regulators can be identified, demonstrated here by a molecular profiling algorithm that decrypts pluripotent wild type versus disrupted genomes.

【 授权许可】

   
2015 Faustino et al.

【 图 表 】

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

Fig. 5.

Fig. 6.

Fig. 1.

Fig. 2.

Fig. 3.

Fig. 4.

Fig. 5.

Fig. 6.

【 参考文献 】

• [1]Dixon JE, Dick E, Rajamohan D, Shakesheff KM, Denning C: Directed differentiation of human embryonic stem cells to interrogate the cardiac gene regulatory network. Mol Ther 2011, 19(9):1695-703.
• [2]Behfar A, Crespo-Diaz R, Terzic A, Gersh BJ: Cell therapy for cardiac repair–lessons from clinical trials. Nat Rev Cardiol 2014, 11(4):232-46.
• [3]Hoffman JI: Incidence of congenital heart disease: II. Prenatal incidence. Pediatr Cardiol 1995, 16(4):155-65.
• [4]Hoffman JI: Incidence of congenital heart disease: I. Postnatal incidence. Pediatr Cardiol 1995, 16(3):103-13.
• [5]Xin M, Olson EN, Bassel-Duby R: Mending broken hearts: cardiac development as a basis for adult heart regeneration and repair. Nat Rev Mol Cell Biol 2013, 14(8):529-41.
• [6]Zhang X, Chen S, Yoo S, Chakrabarti S, Zhang T, Ke T, Oberti C, Yong SL, Fang F, Li L, et al.: Mutation in nuclear pore component NUP155 leads to atrial fibrillation and early sudden cardiac death. Cell 2008, 135(6):1017-27.
• [7]Geva T, Martins JD, Wald RM. Atrial septal defects. Lancet. 2014
• [8]Andersen TA, Troelsen Kde L, Larsen LA: Of mice and men: molecular genetics of congenital heart disease. Cell Mol Life Sci 2014, 71(8):1327-52.
• [9]Faustino RS, Behfar A, Perez-Terzic C, Terzic A: Genomic chart guiding embryonic stem cell cardiopoiesis. Genome Biol 2008, 9(1):R6. BioMed Central Full Text
• [10]Arrell DK, Terzic A: Interpreting networks in systems biology. Clin Pharmacol Ther 2013, 93(5):389-92.
• [11]Arrell DK, Terzic A: Systems proteomics for translational network medicine. Circ Cardiovasc Genet 2012, 5(4):478.
• [12]Folmes CD, Dzeja PP, Nelson TJ, Terzic A: Metabolic plasticity in stem cell homeostasis and differentiation. Cell Stem Cell 2012, 11(5):596-606.
• [13]Folmes CD, Nelson TJ, Martinez-Fernandez A, Arrell DK, Lindor JZ, Dzeja PP, Ikeda Y, Perez-Terzic C, Terzic A: Somatic oxidative bioenergetics transitions into pluripotency-dependent glycolysis to facilitate nuclear reprogramming. Cell Metab 2011, 14(2):264-71.
• [14]Ma L, Sun B, Hood L, Tian Q: Molecular profiling of stem cells. Clin Chim Acta 2007, 378(1–2):24-32.
• [15]Beisel C, Paro R: Dissection of gene regulatory networks in embryonic stem cells by means of high-throughput sequencing. Biol Chem 2009, 390(11):1139-44.
• [16]Moignard V, Gottgens B: Transcriptional mechanisms of cell fate decisions revealed by single cell expression profiling. Bioessays 2014, 36(4):419-26.
• [17]Roy S, Kundu TK: Gene regulatory networks and epigenetic modifications in cell differentiation. IUBMB Life 2014, 66(2):100-9.
• [18]Faustino RS, Chiriac A, Niederlander NJ, Nelson TJ, Behfar A, Mishra PK, Macura S, Michalak M, Terzic A, Perez-Terzic C: Decoded calreticulin-deficient embryonic stem cell transcriptome resolves latent cardiophenotype. Stem Cells 2010, 28(7):1281-91.
• [19]Li J, Puceat M, Perez-Terzic C, Mery A, Nakamura K, Michalak M, Krause KH, Jaconi ME: Calreticulin reveals a critical Ca(2+) checkpoint in cardiac myofibrillogenesis. J Cell Biol 2002, 158(1):103-13.
• [20]Michalak M, Guo L, Robertson M, Lozak M, Opas M: Calreticulin in the heart. Mol Cell Biochem 2004, 263(1–2):137-42.
• [21]Arnaudeau S, Frieden M, Nakamura K, Castelbou C, Michalak M, Demaurex N: Calreticulin differentially modulates calcium uptake and release in the endoplasmic reticulum and mitochondria. J Biol Chem 2002, 277(48):46696-705.
• [22]Nakamura K, Zuppini A, Arnaudeau S, Lynch J, Ahsan I, Krause R, Papp S, De Smedt H, Parys JB, Muller-Esterl W, et al.: Functional specialization of calreticulin domains. J Cell Biol 2001, 154(5):961-72.
• [23]Albert R: Scale-free networks in cell biology. J Cell Sci 2005, 118(Pt 21):4947-57.
• [24]Winkler JM, Fox HS: Transcriptome meta-analysis reveals a central role for sex steroids in the degeneration of hippocampal neurons in Alzheimer’s disease. BMC Syst Biol 2013, 7:51. BioMed Central Full Text
• [25]Wang WA, Groenendyk J, Michalak M: Calreticulin signaling in health and disease. Int J Biochem Cell Biol 2012, 44(6):842-6.
• [26]Prell T, Lautenschlager J, Grosskreutz J: Calcium-dependent protein folding in amyotrophic lateral sclerosis. Cell Calcium 2013, 54(2):132-43.
• [27]Coe H, Michalak M: Calcium binding chaperones of the endoplasmic reticulum. Gen Physiol Biophys 2009, 28 Spec No Focus:F96-103.
• [28]Groenendyk J, Agellon LB, Michalak M: Coping with endoplasmic reticulum stress in the cardiovascular system. Annu Rev Physiol 2013, 75:49-67.
• [29]Groenendyk J, Sreenivasaiah PK, Kim do H, Agellon LB, Michalak M: Biology of endoplasmic reticulum stress in the heart. Circ Res 2010, 107(10):1185-97.
• [30]Sano R, Reed JC: ER stress-induced cell death mechanisms. Biochim Biophys Acta 2013, 1833(12):3460-70.
• [31]Hong M, Kim H, Kim I. Ribosomal protein L19 overexpression activates the unfolded protein response and sensitizes MCF7 breast cancer cells to endoplasmic reticulum stress-induced cell death. Biochem Biophys Res Commun. 2014;450(1):673–78.
• [32]Baird TD, Palam LR, Fusakio ME, Willy JA, Davis CM, McClintick JN, Anthony TG, Wek RC: Selective mRNA translation during eIF2 phosphorylation induces expression of IBTKalpha. Mol Biol Cell 2014, 25(10):1686-97.
• [33]Gold LI, Eggleton P, Sweetwyne MT, Van Duyn LB, Greives MR, Naylor SM, Michalak M, Murphy-Ullrich JE: Calreticulin: non-endoplasmic reticulum functions in physiology and disease. Faseb J 2010, 24(3):665-83.
• [34]Zamanian M, Veerakumarasivam A, Abdullah S, Rosli R: Calreticulin and cancer. Pathol Oncol Res 2013, 19(2):149-54.
• [35]Scardoni G, Petterlini M, Laudanna C: Analyzing biological network parameters with CentiScaPe. Bioinformatics 2009, 25(21):2857-9.
• [36]Chinchilla A, Daimi H, Lozano-Velasco E, Dominguez JN, Caballero R, Delpon E, Tamargo J, Cinca J, Hove-Madsen L, Aranega AE, et al.: PITX2 insufficiency leads to atrial electrical and structural remodeling linked to arrhythmogenesis. Circ Cardiovasc Genet 2011, 4(3):269-79.
• [37]Nakamura K, Robertson M, Liu G, Dickie P, Guo JQ, Duff HJ, Opas M, Kavanagh K, Michalak M: Complete heart block and sudden death in mice overexpressing calreticulin. J Clin Invest 2001, 107(10):1245-53.
• [38]Hattori K, Nakamura K, Hisatomi Y, Matsumoto S, Suzuki M, Harvey RP, Kurihara H, Hattori S, Yamamoto T, Michalak M, et al.: Arrhythmia induced by spatiotemporal overexpression of calreticulin in the heart. Mol Genet Metab 2007, 91(3):285-93.
• [39]Dagle JM, Sabel JL, Littig JL, Sutherland LB, Kolker SJ, Weeks DL: Pitx2c attenuation results in cardiac defects and abnormalities of intestinal orientation in developing Xenopus laevis. Dev Biol 2003, 262(2):268-81.
• [40]Tessari A, Pietrobon M, Notte A, Cifelli G, Gage PJ, Schneider MD, Lembo G, Campione M: Myocardial Pitx2 differentially regulates the left atrial identity and ventricular asymmetric remodeling programs. Circ Res 2008, 102(7):813-22.
• [41]Liu C, Liu W, Lu MF, Brown NA, Martin JF: Regulation of left-right asymmetry by thresholds of Pitx2c activity. Development 2001, 128(11):2039-48.
• [42]Franco D, Campione M: The role of Pitx2 during cardiac development. Linking left-right signaling and congenital heart diseases. Trends Cardiovasc Med 2003, 13(4):157-63.
• [43]Katz LA, Schultz RE, Semina EV, Torfs CP, Krahn KN, Murray JC: Mutations in PITX2 may contribute to cases of omphalocele and VATER-like syndromes. Am J Med Genet A 2004, 130A(3):277-83.
• [44]Rauch F, Prud’homme J, Arabian A, Dedhar S, St-Arnaud R: Heart, brain, and body wall defects in mice lacking calreticulin. Exp Cell Res 2000, 256(1):105-11.
• [45]Faustino RS, Chiriac A, Terzic A: Bioinformatic primer for clinical and translational science. Clin Transl Sci 2008, 1(2):174-80.