Long Noncoding RNA in CVD
Definition
Long noncoding RNAs (lncRNAs) are RNA transcripts >200 nt that share many features of mRNAs (transcribed by RNA Pol II, 5'-capped, polyadenylated, spliced) but are not translated into protein. The human genome may contain >30,000 lncRNAs, with expression typically lower and less conserved than mRNAs. (sources/noncoding-rna-aha-2020 — high)
Key Concepts
Classification
- By genomic location: lincRNA (intergenic), intronic, eRNA (enhancer RNA), AS-lncRNA (antisense) (sources/noncoding-rna-aha-2020 — high)
- By function: guides (direct chromatin modifiers to DNA), scaffolds (tether protein complexes), decoys (bind proteins/miRNAs to block targets), ceRNAs (competing endogenous RNAs — sponge miRNAs)
- cis vs. trans: cis-acting lncRNAs regulate nearby genes; trans-acting lncRNAs function at distal loci; many lncRNAs are multifunctional and defy single classification
- HUGO nomenclature (2014): function-based names; antisense = suffix AS; intronic = IT; intergenic = LINC prefix
CVD Risk Loci lncRNAs
- ANRIL (antisense ncRNA in the INK4 locus at 9p21): scaffold regulating CDKN2a/B expression; certain variants circularise and take on atherogenic function; ANRIL variants correlate with stroke risk (9p21.3 locus). (sources/noncoding-rna-aha-2020 — high)
- MIAT (myocardial infarction–associated transcript): variant associated with MI risk; higher expression → poor prognosis in ischemic stroke (independent prognostic marker for functional outcome and death); ceRNA binding miR-150-5p to regulate endothelial function. (sources/noncoding-rna-aha-2020 — high)
- H19: variant increases IGF2 expression and CAD risk; stabilises SREBP-1c (hepatic lipogenesis); ceRNA binding let-7 to inhibit muscle differentiation; regulates aortic aneurysm and endothelial cell aging. (sources/noncoding-rna-aha-2020 — high)
Lipid and Cardiometabolic Roles
- MALAT1: stabilises SREBP-1c (lipogenesis); regulates angiogenesis; contributes to diabetic retinopathy and atherosclerosis; may protect against ischemic stroke by inhibiting proapoptotic proteins and proinflammatory cytokines. (sources/noncoding-rna-aha-2020 — high)
- LeXis (liver-expressed LXR-induced): LXR induces; reduces cholesterol synthesis by blocking RNA Pol II recruitment to Srebf2 and its targets. (sources/noncoding-rna-aha-2020 — high)
- MeXis (macrophage-expressed LXR-induced): LXR induces; acts in cis to promote ABCA1 cholesterol efflux by guiding helicase DDX17 to the Abca1 promoter. (sources/noncoding-rna-aha-2020 — high)
- APOA1-AS / APOA4-AS: antisense lncRNAs in the apolipoprotein gene cluster; APOA1-AS represses APOA1 via PRC2-mediated chromatin silencing; APOA4-AS stabilises APOA4 mRNA via HuR binding. (sources/noncoding-rna-aha-2020 — high)
- CHROME (macrophage): ceRNA binding miR-27b, -33a, -33b, -128 to regulate cholesterol efflux and HDL formation. (sources/noncoding-rna-aha-2020 — high)
Vascular Biology
- PUNISHER (AGAP2-AS1), MEG3, GATA6-AS: regulate vessel formation/angiogenesis. (sources/noncoding-rna-aha-2020 — high)
- LincRNA-p21: restricts smooth muscle cell proliferation; downregulated in mouse and human atherosclerosis
Cardiac Hypertrophy and Heart Failure
- Mhrt/MHRT: cardiac-specific; expressed in adult heart; regulates Myh6, Myh7, osteopontin via Brg1 chromatin remodeling factor; repressed during pressure overload–induced hypertrophy; restoring expression is cardioprotective in mice; MHRT levels proposed as HF biomarker. (sources/noncoding-rna-aha-2020 — high)
- Chast: upregulated in pressure overload hypertrophy in mice and humans; impedes cardiomyocyte autophagy by negatively regulating Plekhm1; silencing attenuates pathological remodeling. (sources/noncoding-rna-aha-2020 — high)
- Chaer: interacts with catalytic subunit of PRC2 to alter epigenetic reprogramming at hypertrophy gene promoters; silencing attenuates pathological remodeling and dysfunction. (sources/noncoding-rna-aha-2020 — high)
- Both Chast and Chaer act via different mechanisms but silencing either is sufficient for cardioprotection — suggests multiple independent lncRNA pathways regulate hypertrophic remodeling
Stroke
- Broadly dysregulated lncRNA expression in ischemic stroke whole blood (vs. control); some differentially expressed lncRNAs in proximity to stroke-risk genes. (sources/noncoding-rna-aha-2020 — high)
- Most highly upregulated after oxygen-glucose deprivation in brain microvascular endothelium: Snhg12, Malat1, lnc-OGD 1006
- Malat1 may protect against ischemic injury by inhibiting proapoptotic proteins and proinflammatory cytokines
- Proposed lncRNA mechanisms in ischemic brain injury: epigenetic transcriptional regulation, miRNA modulation, translational repression
Investigational Tools
- Expression profiling: RNA-seq (require sufficient depth for low-abundance lncRNAs); cap-assisted gene expression sequencing; global run-on sequencing for nascent transcription. (sources/noncoding-rna-aha-2020 — high)
- Loss-of-function: ASOs/Gapmers (no genomic engineering; limited by secondary structure); CRISPRi (catalytically inactive Cas9); CRISPR/Cas9 deletion (requires large genomic deletion — often >1 kb); early poly(A) insertion to halt transcription
- Gain-of-function: ectopic expression (not amenable for cis-acting lncRNAs); CRISPRa
- Interactome: ChIRP (chromatin isolation by RNA purification) + mass spec/RNA-seq/DNA-seq; RNA antisense purification; CLIP (cross-linking immunoprecipitation)
- Localisation: single-molecule RNA-FISH; digital droplet PCR for copy number
- Nuclear lncRNAs may be resistant to siRNA/shRNA approaches; cis-acting lncRNAs cannot be studied by ectopic overexpression — complementary approaches essential
ceRNA Validation Requirements
For a valid lncRNA ceRNA claim, evidence required: (1) coprecipitation of lncRNA-miRNA; (2) miRNA target derepression upon lncRNA deletion/depletion; (3) loss of sponging activity upon mutation of miRNA binding sites. (sources/noncoding-rna-aha-2020 — high)
Contradictions / Open Questions
- ceRNA stoichiometry controversy: A functional ceRNA requires the lncRNA to be present at sufficient copy numbers to compete with miRNA targets. Most reports do not formally validate stoichiometry — many putative ceRNA claims are likely not physiologically relevant. (sources/noncoding-rna-aha-2020 — high)
- Micropeptide boundary: Up to 20% of lncRNAs in the human heart encode micropeptides — several established lncRNAs (DANCR, TUG1, JPX, myheart, UPPERHAND) have now been shown to also code for microproteins, blurring the functional definition. (sources/noncoding-rna-aha-2020 — high)
- lncRNA delivery challenge: Large RNA size makes lncRNA delivery via AAV or lipid nanoparticles extremely difficult; no clinical-stage lncRNA therapeutic exists. This stands in contrast to siRNA/ASO therapeutics that are now FDA-approved. (sources/noncoding-rna-aha-2020 — high)
Connections
- Related to concepts/Noncoding-RNA-in-CVD
- Related to concepts/Gene-Silencing-Therapy
- Related to concepts/AAV-Gene-Delivery
- Related to entities/HCM — Mhrt/MHRT in pressure overload hypertrophy
- Related to entities/Heart-Failure — Mhrt, Chast, Chaer in cardiac remodeling
- Related to entities/Atrial-Fibrillation — ANRIL 9p21 locus
- Related to concepts/Lipoprotein-a — CHROME, LeXis, MeXis in cholesterol regulation