Posts in Category: Genetics

Epigenomes in Cardiovascular Disease

Epigenomes in Cardiovascular Disease

Manuel Rosa-Garrido, Douglas J. Chapski, Thomas M. Vondriska

Occupancy of histone marks varies between cell types. Circos plot of mouse chr19 shows (A) repressive H3K27me3 and (B) active H3K4me3 peaks across different tissues. Color-coding of tissues (outside to inside): heart (red), cerebellum (blue), kidney (yellow), liver (green), thymus (orange), testis (dark red), and spleen (light blue). The black track represents mm10 gene density on chromosome 19. Data are from the ENCODE (Encyclopedia of DNA Elements) database. [Powerpoint File]

Epigenomes in Cardiovascular Disease

Epigenomes in Cardiovascular Disease

Manuel Rosa-Garrido, Douglas J. Chapski, Thomas M. Vondriska

Chromatin architectural features. A, The functional unit of chromatin is the nucleosome, which can be decorated by a variety of post-translational modifications that modulate accessibility to transcription factors or chromatin modifiers. B, At the gene level, transcription factors or repressors (green circles) confer context-specific regulation of transcription with varying levels of sequence specificity. DNA methylation (purple circles) typically repress promoter activity of genes although this phenomenon is associated with expression when found within gene bodies. C, Chromatin looping enables formation of gene expression or silencing neighborhoods, as well as facilitating structural units suitable for higher order packing. D, Topologically associating domains (TADs) are regions of preferential chromatin interactions. E, Hi-C data reveal chromatin compartmentalization into active and inactive, or A and B compartments of the genome, respectively (here shown in yellow and blue; note, this is a stylistic interpretation of how A and B compartments might interact because chromatin capture studies do not reveal actual localization coordinates within the nucleus). F, Chromosome paint experiments have revealed distinct territories that contain entire chromosomes within the nucleus, allowing formation of intra- and interchromosomal interactions that may regulate transcription or other tasks of the nucleus. [Powerpoint File]

PCSK9: From Basic Science Discoveries to Clinical Trials

PCSK9: From Basic Science Discoveries to Clinical Trials

Michael D. Shapiro, Hagai Tavori, Sergio Fazio

PCSK9 (proprotein convertase subtilisin/kexin type 9) compartmentalization and function in plasma. A, PCSK9 is found in plasma in primarily 2 monomeric forms: an active form representing the full-length plasma protein and an inactive/less-active, shorter fragment, which is a cleavage product of the full-length protein by the protease furin. The active PCSK9 is found predominantly on low-density lipoprotein (LDL) and lipoprotein(a; Lp[a]) particles but not on very LDL or chylomicron remnants. In contrast, the furin-cleaved PCSK9 is not found in association with these apoB lipoproteins. Although it is not clear whether PCSK9 (active or furin cleaved) is found in association with high-density lipoprotein (HDL), it was suggested the HDL can inhibit PCSK9 function. B, PCSK9 is secreted as an active form representing the full-length plasma protein. On secretion, PCSK9 can take on 1 of 2 fates, which ultimately determines its function. (1) PCSK9 can interact with an LDL particle, which protects PCSK9 from being cleaved by furin and leaves the protein bound to the particle in its active form, or alternatively, (2) PCSK9 can interact with furin, which leads to the formation of a shorter fragment of PCSK9 that exhibits at least 2-fold lower affinity to LDLR (low-density lipoprotein receptor) with limited ability/inability to degrade it. (Illustration credit: Ben Smith.) [Powerpoint File]

Omics of Blood Pressure and Hypertension

Omics of Blood Pressure and Hypertension

Donna K. Arnett, Steven A. Claas

Descriptions of the domains of omic disciplines. [Powerpoint File]

Emerging Role of Precision Medicine in Cardiovascular Disease

Emerging Role of Precision Medicine in Cardiovascular Disease

Jane A. Leopold, Joseph Loscalzo

Molecular interaction networks (interactome). The protein–protein interactome describes interactions between proteins in a scale-free (ie, interactions are not random but clustered) manner. Within the interactome, groups of proteins reside in disease neighborhoods (colored areas) that may overlap indicating common mediators (left, center). Within the neighborhood, there are several disease modules or groups of protein interactions that are related. Analysis of the interactome may uncover new or previously unrecognized relationships. Gray circles, nodes (ie, proteins in a protein–protein interaction network); black lines, edges (ie, interactions). [Powerpoint File]

Taking Systems Medicine to Heart

Taking Systems Medicine to Heart

Kalliopi Trachana, Rhishikesh Bargaje, Gustavo Glusman, Nathan D. Price, Sui Huang, Leroy E. Hood

A new strategy to stratify health prevention and identify early disease signs. Recovery time after exposure to a specific risk factor (stress test) can be a new biomarker to stratify patients. A and C, The individuals exhibit a similar profile before stress test—although their resilience (width and steepness of the potential well) is different. B and D, After the stress test, omics profiling can identify the most variable proteins/metabolites for each individual (red boxes) enabling personalized recommendations. Although the recovery time (t1 vs t2) can identify the high-risk individuals (longer time, higher risk), who can be further profiled for early disease biomarkers (black boxes). U: landscape potential (Table 2). [Powerpoint File]

Advances in Transcriptomics: Investigating Cardiovascular Disease at Unprecedented Resolution

Advances in Transcriptomics: Investigating Cardiovascular Disease at Unprecedented Resolution

Robert C. Wirka, Milos Pjanic, Thomas Quertermous

RNA sequencing (RNAseq) in complex diseases—coronary artery disease. A, Schematic overview of coronary artery smooth muscle cells and progression to disease state in vivo, as well as modeling disease progression in vitro and RNAseq profiling. B, Fine-mapping disease-associated risk single-nucleotide polymorphisms from the GWAS catalog using various RNAseq applications. C, CAD GWAS candidate gene TCF21 overexpression in HCASMC leads to the perturbation of the transcriptome profile that recapitulates disease phenotype in vitro, as shown using gene ontologies. Right, Detection of immediate response genes after the treatment with PDGF that recapitulates similar disease cellular phenotype in vitro. D, Construction of the gene network using WGCNA modules or edge weighted force layout clustering that clustered genes from ≈4000 public RNAseq data sets into smooth muscle- (TCF21, PDGFD, SMAD3, etc) and lipid- (APOA1, APOB, etc) related clusters. E, An excerpt of the network constructed using cis- and trans-expression quantitative trait loci (eQTL) connections defined with causal inference test in the STARNET data set. Multi-tissue eQTL analysis enables the construction of the network of genes as shown with the example of TCF21 and PDGFD genes that are interconnected with the LIPA gene in the disease core network only when incorporating eQTLs from the liver with those from the diseased atherosclerotic aorta. APO indicates apolipoprotein; CAD, coronary artery disease; DE, differential expression; GWAS, Genome-Wide Association Studies; HCASMC, human coronary artery smooth muscle cells; PDGF, platelet-derived growth factor; PDGFD, platelet-derived growth factor D; SMAD3, mothers against decapentaplegic homolog 3; TCF21, transcription factor 21; TF, transcription factor; and WGCNA, weighted gene correlation network analysis. [Powerpoint File]

Epigenomics: Technologies and Applications

Epigenomics: Technologies and Applications

Kevin C. Wang, Howard Y. Chang

New molecular tools available to interrogate chromatin accessibility and chromosomal organization. A, Measurement of long-range contact of DNA elements highlighted by single-cell ATAC-seq (scATACT-seq). Structured cis-variability across single epigenomes highlighted by scATACT-seq. Pearson correlation coefficient representing chromosome compartment signal of interaction frequency from a population chromatin conformation capture assay (left) or scATAC-seq (middle) from chromosome 1. Data in white represent masked regions because of highly repetitive regions. Right, upper box, Permuted cis-correlation map for chromosome 1. Right, lower box, Representative region depicting long-range covariability. Reprinted from Buenrostro et al40 with permission. Copyright ©2017, Macmillan Publishers Limited, part of Springer Nature. B, Schematic of chromatin loop reorganization using clustered regularly interspaced short palindromic repeats–deactivated Cas9 (CLOuD9) as a reversible method for manipulating chromosomal loops. Addition of abscisic acid (ABA, green) brings 2 complementary CLOuD9 constructs (CLOuD9 Streptococcus pyogenes [CSP], CLOuD9 Streptococcus aureus [CSA], red and blue, respectively) into proximity, remodeling chromatin structure. Removal of ABA restores the endogenous chromatin conformation. Reprinted from Morgan et al38 with permission. Copyright ©2015, Macmillan Publishers Limited, part of Springer Nature. [Powerpoint File]

Long Noncoding RNA Discovery in Cardiovascular Disease: Decoding Form to Function

Long Noncoding RNA Discovery in Cardiovascular Disease: Decoding Form to Function

Tamer Sallam, Jaspreet Sandhu, Peter Tontonoz

Pipeline of long noncoding RNA (lncRNA) discovery and characterization. ASO indicates antisense oligonucleotide; ChiRP, chromatin isolation by RNA purification; qPCR, quantitative polymerase chain reaction; RAP, RNA antisense purification; and RIP, RNA immunoprecipitation. [Powerpoint File]

Heart Failure in Pediatric Patients With Congenital Heart Disease

Heart Failure in Pediatric Patients With Congenital Heart Disease

Robert B. Hinton, Stephanie M. Ware

Genes causing congenital heart disease (CHD) and cardiomyopathy form a complex network. The network diagrams were generated using ToppCluster (www.toppcluster.cchmc.org) software. Gene lists were derived from clinically available next-generation sequencing panels for cardiomyopathy genes (n=50) and CHD genes (n=44). A, Abstracted cluster network showing a selected subset of features from the following categories: Gene ontology (GO): molecular function; GO: biological processes; GO: cellular component; human phenotype; mouse phenotype; pathway; disease (cardiomyopathy and CHD). The features are color coded by category and connected to cardiomyopathy (white circle) and CHD gene nodes. B, Gene level network with nodes (blue) selected from features in GO: biological processes category. The network illustrates that regulation of cellular component of movement, actin filament-based processes, and cardiac chamber morphogenesis are shared in common between cardiomyopathy and CHD genes, whereas regulation of force of heart contraction and tube development are unshared. [Powerpoint File]

Genetics and Genomics of Congenital Heart Disease

Genetics and Genomics of Congenital Heart Disease

Samir Zaidi, Martina Brueckner

NOTCH signaling in congenital heart disease (CHD) (A) the outline of NOTCH signaling pathway showing signal-sending cell in yellow and signal receiving cell in green. B, Syndromes and CHD associated with NOTCH pathway gene mutations. BAV indicates bicuspid aortic valve; CoA, coarctation of the aorta; HLHS, hypoplastic left heart syndrome; HTX, heterotaxy-associated defects; NA, not applicable; NICD, Notch intracellular domain; VSD, ventricular septal defect; TA, truncus arteriosus; and TOF, tetralogy of Fallot. [Powerpoint File]

Genetics and Genomics of Congenital Heart Disease

Genetics and Genomics of Congenital Heart Disease

Samir Zaidi, Martina Brueckner

A, Outline of human heart development. The x axis displays days of human and mouse gestation. B, The spectrum of congenital heart disease from mild to severe. The lesions indicated as “severe” are expected to require intervention in the first year of life. Classes of CHD based on proposed developmental-genetic mechanisms are indicated in parentheses. C, Genetic causes of CHD identified to date. ASD indicates atrial septal defect; CHD, congenital heart disease; CoA, coarctation of the aorta; CTD, conotruncal defect; HLHS, hypoplastic left heart syndrome; HTX, heterotaxy; LVO, left ventricular outflow obstruction; TGA, transposition of the great arteries; TOF, tetralogy of Fallot; and VSD, ventricular septal defect. [Powerpoint File]

Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease

Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease

Thomas Doetschman, Teodora Georgieva

Cas9 RNA-guided nuclease system. Schematic representation of the Streptococcus pyogenes Cas9 nuclease (green) targeted to genomic DNA by a single-guide RNA (sgRNA) consisting of an ≈20-nt guide sequence (blue) and a scaffold (red). The guide sequence is directly upstream of the protospacer adjacent motif (PAM), NGG (orange circles). Cas9 mediates a double-strand DNA break (DSB) ≈3 bp upstream of the PAM (red triangles). The break is repaired by 1 of 2 mechanisms: nonhomologous end joining (NHEJ) that creates random insertions or deletions at the target site or homology-directed repair (HDR). Two types of template can be used for HDR: small single-stranded DNA (ssDNA) oligonucleotide donor with short 60- 70-bp homology arms and a linear or circular dsDNA plasmid with long homology arms of 1 to 3 kb. [Powerpoint File]

Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease

Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease

Thomas Doetschman, Teodora Georgieva

Large deletions, marker insertions, and single-nucleotide polymorphism (SNP) insertions. A, Multiple exons can be deleted by nonhomologous end joining (NHEJ) by designing single-guide RNAs (sgRNAs) that flank the region to be deleted. In the presence of Cas9 double-strand DNA breaks (DSBs) will occur resulting in small indels at the site of end joining. The double bar at the sgRNA:gene hybridization site represents the DSB caused by Cas9. Cas9 can be introduced as either mRNA or recombinant protein. B, Marker gene insertion can be achieved through homology-directed repair (HDR) in which the homologous regions are introduced in a plasmid as would be done by gene targeting. C, A chromosomal region deletion has been done using HDR in which 2 sgRNAs were designed at each end of the region to be deleted. The homology template was an single-strand DNA (ssDNA) oligo with homology at each end of the region to be deleted. D, SNP insertion using HDR with ssDNA oligo as homology template. [Powerpoint File]