title: Systems biology surveillance decrypts pathological transcriptome remodeling.
abstract: 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.
authors.affiliation: Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA. Faustino.Randolph@mayo.edu.
authors.forename: Randolph S
authors.initials: RS
authors.lastname: Faustino
authors.affiliation: Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA. Wyles.Saranya@mayo.edu.
authors.forename: Saranya P
authors.initials: SP
authors.lastname: Wyles
authors.affiliation: Department of Biochemistry, University of Alberta, Edmonton, AB, Canada. jlg2@ualberta.ca.
authors.forename: Jody
authors.initials: J
authors.lastname: Groenendyk
authors.affiliation: Department of Biochemistry, University of Alberta, Edmonton, AB, Canada. mmichala@ualberta.ca.
authors.forename: Marek
authors.initials: M
authors.lastname: Michalak
authors.affiliation: Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA. Terzic.Andre@mayo.edu.
authors.forename: Andre
authors.initials: A
authors.lastname: Terzic
authors.affiliation: Division of Cardiovascular Diseases, Departments of Medicine, Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA. Terzic.Carmen@mayo.edu.|Department of Physical Medicine and Rehabilitation, Mayo Clinic College of Medicine, Rochester, MN, USA. Terzic.Carmen@mayo.edu.|Rehabilitation Medicine Research Center, Rochester, MN, USA. Terzic.Carmen@mayo.edu.
authors.forename: Carmen
authors.initials: C
authors.lastname: Perez-Terzic
mesh_terms: D000465:Algorithms; D000818:Animals; D037282:Calreticulin / Q000737:chemistry / Q000235:genetics; D002460:Cell Line; D004194:Disease / Q000235:genetics*; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D051379:Mice; D039904:Pluripotent Stem Cells / Q000378:metabolism; D017434:Protein Structure, Tertiary; D017384:Sequence Deletion; D049490:Systems Biology / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D037282:Calreticulin