Recent Advances in the Genetics of Atherothrombotic Disease and Its Determinants

Six years' experience with LipidSeq: clinical and research learnings from a hybrid, targeted sequencing panel for dyslipidemias

BACKGROUND

In 2013, our laboratory designed a targeted sequencing panel, "LipidSeq", to study the genetic determinants of dyslipidemia and metabolic disorders. Over the last 6 years, we have analyzed 3262 patient samples obtained from our own Lipid Genetics Clinic and international colleagues. Here, we highlight our findings and discuss research benefits and clinical implications of our panel.

METHODS

LipidSeq targets 69 genes and 185 single-nucleotide polymorphisms (SNPs) either causally related or associated with dyslipidemia and metabolic disorders. This design allows us to simultaneously evaluate monogenic-caused by rare single-nucleotide variants (SNVs) or copy-number variants (CNVs)-and polygenic forms of dyslipidemia. Polygenic determinants were assessed using three polygenic scores, one each for low-density lipoprotein cholesterol, triglyceride, and high-density lipoprotein cholesterol.

RESULTS

Among 3262 patient samples evaluated, the majority had hypertriglyceridemia (40.1%) and familial hypercholesterolemia (28.3%). Across all samples, we identified 24,931 unique SNVs, including 2205 rare variants predicted disruptive to protein function, and 77 unique CNVs. Considering our own 1466 clinic patients, LipidSeq results have helped in diagnosis and improving treatment options.

CONCLUSIONS

Our LipidSeq design based on ontology of lipid disorders has enabled robust detection of variants underlying monogenic and polygenic dyslipidemias. In more than 50 publications related to LipidSeq, we have described novel variants, the polygenic nature of many dyslipidemias-some previously thought to be primarily monogenic-and have uncovered novel mechanisms of disease. We further demonstrate several tangible clinical benefits of its use.

Unveiling ncRNA regulatory axes in atherosclerosis progression

Completion of the human genome sequencing project highlighted the richness of the cellular RNA world, and opened the door to the discovery of a plethora of short and long non-coding RNAs (the dark transcriptome) with regulatory or structural potential, which shifted the balance of pathological gene alterations from coding to non-coding RNAs. Thus, disease risk assessment currently has to also evaluate the expression of new RNAs such as small micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), competing endogenous RNAs (ceRNAs), retrogressed elements, 3'UTRs of mRNAs, etc. We are interested in the pathogenic mechanisms of atherosclerosis (ATH) progression in patients suffering Chronic Kidney Disease, and in this review, we will focus in the role of the dark transcriptome (non-coding RNAs) in ATH progression. We will focus in miRNAs and in the formation of regulatory axes or networks with their mRNA targets and with the lncRNAs that function as miRNA sponges or competitive inhibitors of miRNA activity. In this sense, we will pay special attention to retrogressed genomic elements, such as processed pseudogenes and Alu repeated elements, that have been recently seen to also function as miRNA sponges, as well as to the use or miRNA derivatives in gene silencing, anti-ATH therapies. Along the review, we will discuss technical developments associated to research in lncRNAs, from sequencing technologies to databases, repositories and algorithms to predict miRNA targets, as well as new approaches to miRNA function, such as integrative or enrichment analysis and their potential to unveil RNA regulatory networks.

Hyperlipidemias and Obesity

The organs require oxygen and other types of nutrients (amino acids, sugars, and lipids) to function, the heart consuming large amounts of fatty acids for oxidation and adenosine triphosphate (ATP) generation.

MicroRNA-30c-5p inhibits NLRP3 inflammasome-mediated endothelial cell pyroptosis through FOXO3 down-regulation in atherosclerosis

Atherosclerosis is a chronic inflammatory disease involved in endothelial dysfunction. Pyroptosis is a pro-inflammatory form of cell death and plays pivotal roles in atherosclerosis. MicroRNAs (miRNAs) are implicated in atherosclerosis, however the mechanisms that underlie miR-30c-5p is required for endothelial cell pyroptosis remain elusive. In the present study, we probed the interaction of miR-30c-5p with forkhead box O3 (FOXO3) and investigated the effect of miR-30c-5p and FOXO3 on NLRP3 inflammasome and endothelial cell pyroptosis. Introduction of oxidized low density lipoprotein (ox-LDL) dose-dependently increased lactate dehydrogenase (LDH) release as well as pyroptosis in human aortic endothelial cells (HAECs). On the basis of ox-LDL treatment, we found the expression of miR-30c-5p was impaired and enrichment of miR-30c-5p protected HAECs from ox-LDL-induced pyroptosis. Moreover, addition of miR-30c-5p inhibited ox-LDL-activated NOD-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome, which was associated with HEACs pyroptosis. Nevertheless, miR-30c-5p failed to show efficacy of Toll-like receptor (TLR) signaling of NLRP3 inflammasome activation. Intriguingly, FOXO3 was suggested to be targeted by miR-30c-5p and addition of miR-30c-5p blocked FOXO3 expression, whereas miR-30c-5p depletion showed opposite effects. Furthermore, silencing of FOXO3 inhibited NLRP3-mediated pyroptosis and reversed anti-miR-30c-5p-induced activation of NLRP3 inflammasome and pyroptosis in HEACs with ox-LDL treatment. Our finding suggested that miR-30c-5p might play essential role in NLRP3 inflammasome-modulated cell pyroptosis by targeting FOXO3 in HAECs, providing a novel therapeutic avenue for atherosclerosis treatment.

Cardiovascular Risk Factors and Markers

Cardiovascular risk is assessed for the prediction and appropriate management of patients using collections of identified risk markers obtained from clinical questionnaire information, concentrations of certain blood molecules (e.g., N-terminal proB-type natriuretic peptide fragment and soluble receptors of tumor-necrosis factor-α and interleukin-2), imaging data using various modalities, and electrocardiographic variables, in addition to traditional risk factors.