ALUminating the Path of Atherosclerosis Progression: Chaos Theory Suggests a Role for Alu Repeats in the Development of Atherosclerotic Vascular Disease

Retrotransposon SINEs in age-related diseases: Mechanisms and therapeutic implications

Retrotransposons are self-replicating genomic elements that move from one genomic location to another using a "copy-and-paste" method involving RNA intermediaries. One family of retrotransposon that has garnered considerable attention for its association with age-related diseases and anti-aging interventions is the short interspersed nuclear elements (SINEs). This review summarizes current knowledge on the roles of SINEs in aging processes and therapies. To underscore the significant research on the involvement of SINEs in aging-related diseases, we commence by outlining compelling evidence on the classification and mechanism, highlighting implications in age-related phenomena. The intricate relationship between SINEs and diseases such as neurodegenerative disorders, heart failure, high blood pressure, atherosclerosis, type 2 diabetes mellitus, osteoporosis, visual system dysfunctions, and cancer is explored, emphasizing their roles in various age-related diseases. Recent investigations into the anti-aging potential of SINE-targeted treatments are examined, with particular attention to how SINE antisense RNA mitigate age-related alterations at the cellular and molecular levels, offering insights into potential therapeutic targets for age-related pathologies. This review aims to compile the most recent advances on the multifaceted roles of SINE retrotransposons in age-related diseases and anti-aging interventions, providing valuable insights into underlying mechanisms and therapeutic avenues for promoting healthy aging.

Developing Theoretical Models for Atherosclerotic Lesions: A Methodological Approach Using Interdisciplinary Insights

Atherosclerosis, a leading cause of cardiovascular disease, necessitates advanced and innovative modeling techniques to better understand and predict plaque dynamics. The present work presents two distinct hypothetical models inspired by different research fields: the logistic map from chaos theory and Markov models from stochastic processes. The logistic map effectively models the nonlinear progression and sudden changes in plaque stability, reflecting the chaotic nature of atherosclerotic events. In contrast, Markov models, including traditional Markov chains, spatial Markov models, and Markov random fields, provide a probabilistic framework to assess plaque stability and transitions. Spatial Markov models, visualized through heatmaps, highlight the spatial distribution of transition probabilities, emphasizing local interactions and dependencies. Markov random fields incorporate complex spatial interactions, inspired by advances in physics and computational biology, but present challenges in parameter estimation and computational complexity. While these hypothetical models offer promising insights, they require rigorous validation with real-world data to confirm their accuracy and applicability. This study underscores the importance of interdisciplinary approaches in developing theoretical models for atherosclerotic plaques.

Hsa_circRNA_0000284 acts as a ceRNA to participate in coronary heart disease progression by sponging miRNA-338-3p via regulating the expression of ETS1

Coronary heart disease (CHD) is a prevalent global cause of death. Research suggests that circular RNAs (circRNAs) play a role in the development of CHD. In this study, we investigated the expression of hsa_circRNA_0000284 in peripheral blood leukocytes (PBLs) obtained from a cohort of 94 CHD patients aged over 50 years, as well as 126 age-matched healthy controls (HC). An in vitro inflammatory and oxidative injury cell model that simulates CHD was used to evaluate changes in hsa_ circRNA _0000284 under stress. CRISPR/Cas9 technology was used to evaluate changes in hsa_circRNA_0000284 expression. An hsa_ circRNA_0000284 overexpression and silencing cell model was used to analyze the biological functions of hsa_circRNA_0000284. Bioinformatics, qRT-PCR, viral transfection technology, and luciferase assays were used to evaluate the potential hsa_circRNA_0000284/miRNA-338-3p/ETS1 axis. Western blotting analysis was performed to detect protein expression. Herein, PBLs from CHD patients exhibited downregulation of hsa_circRNA_0000284 expression. Exposure to oxidative stress and inflammation can induce damage to human umbilical endothelial cells, resulting in the downregulation of hsa_circRNA_0000284 expression. The expression of hsa_circRNA_0000284 in EA-hy926 cells was significantly reduced after the AluSq2 element of hsa_circRNA_0000284 had been knocked out. The expression of hsa_circRNA_0000284 affected proliferation, cycle distribution, aging, and apoptosis in EA-hy926 cells. Consistent with the results of cell transfection experiments and luciferase assays, Western blotting showed that hsa_circRNA_0000284 plays a role in the regulation of hsa-miRNA-338-3p expression. Subsequently, hsa-miRNA-338-3p was found to be involved in the regulation of ETS1 expression.Communicated by Ramaswamy H. Sarma.

Molecular Mechanisms of Alu and LINE-1 Interspersed Repetitive Sequences Reveal Diseases of Visual System Dysfunction

BACKGROUND

Short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINE-1s) are the abundant and well-characterized repetitive elements in the human genome.

METHODS

For this review, all relevant original research studies were assessed by searching electronic databases, including PubMed, Google Scholar, and Web of Science, by using relevant keywords. Accumulating evidence indicates that the disorder of gene expression regulated by these repetitive sequences is one of the causes of the diseases of visual system dysfunction, including retinal degenerations, glaucoma, retinitis punctata albescens, retinitis pigmentosa, geographic atrophy, and age-related macular degeneration, suggesting that SINEs and LINE-1s may have great potential implications in ophthalmology.

RESULTS

Alu elements belonging to the SINEs are present in more than one million copies, comprising 10% of the human genome.

CONCLUSION

This study offers recent advances in Alu and LINE-1 mechanisms in the development of eye diseases. The current study could advance our knowledge of the roles of SINEs and LINE-1s in the developing process of eye diseases, suggesting new diagnostic biomarkers, therapeutic strategies, and significant points for future studies.

The role of long non-coding RNA ANRIL in the development of atherosclerosis

Atherosclerosis is an important pathological basis of coronary heart disease, and the antisense non-coding RNA in the INK4 locus (ANRIL) is located in the genetically susceptible segment with the strongest correlation with it - the short arm 2 region 1 of chromosome 9 (Chr9p21). ANRIL can produce linear, circular and other transcripts through different transcriptional splicing methods, which can regulate the proliferation and apoptosis of related cells and closely related to the development of atherosclerotic plaques. Linear ANRIL can regulate proliferation of vascular smooth muscle cells (VSMCs) in plaques by chromatin modification, as well as affecting on proliferation and the apoptosis of macrophages at the transcriptional level; circular ANRIL can affect on proliferation and apoptosis of VSMCs by chromatin modification as well as interfering with rRNA maturation. In this review we describe the evolutionary characteristics of ANRIL, the formation and structure of transcripts, and the mechanism by which each transcript regulates the proliferation and apoptosis of vascular cells and then participates in atherosclerosis.

Alu Deletions in LAMA2 and CDH4 Genes Are Key Components of Polygenic Predictors of Longevity

Longevity is a unique human phenomenon and a highly stable trait, characterized by polygenicity. The longevity phenotype occurs due to the ability to successfully withstand the age-related genomic instability triggered by Alu elements. The purpose of our cross-sectional study was to evaluate the combined contribution of ACE*Ya5ACE, CDH4*Yb8NBC516, COL13A1*Ya5ac1986, HECW1*Ya5NBC182, LAMA2*Ya5-MLS19, PLAT*TPA25, PKHD1L1*Yb8AC702, SEMA6A*Yb8NBC597, STK38L*Ya5ac2145 and TEAD1*Ya5ac2013 Alu elements to longevity. The study group included 2054 unrelated individuals aged from 18 to 113 years who are ethnic Tatars from Russia. We analyzed the dynamics of the allele and genotype frequencies of the studied Alu polymorphic loci in the age groups of young (18-44 years old), middle-aged (45-59 years old), elderly (60-74 years old), old seniors (75-89 years old) and long-livers (90-113 years old). Most significant changes in allele and genotype frequencies were observed between the long-livers and other groups. The search for polygenic predictors of longevity was performed using the APSampler program. Attaining longevity was associated with the combinations LAMA2*ID + CDH4*D (OR = 2.23, PBonf = 1.90 × 10-2) and CDH4*DD + LAMA2*ID + HECW1*D (OR = 4.58, PBonf = 9.00 × 10-3) among persons aged between 18 and 89 years, LAMA2*ID + CDH4*D + SEMA6A*I for individuals below 75 years of age (OR = 3.13, PBonf = 2.00 × 10-2), LAMA2*ID + HECW1*I for elderly people aged 60 and older (OR = 3.13, PBonf = 2.00 × 10-2) and CDH4*DD + LAMA2*D + HECW1*D (OR = 4.21, PBonf = 2.60 × 10-2) and CDH4*DD + LAMA2*D + ACE*I (OR = 3.68, PBonf = 1.90 × 10-2) among old seniors (75-89 years old). The key elements of combinations associated with longevity were the deletion alleles of CDH4 and LAMA2 genes. Our results point to the significance for human longevity of the Alu polymorphic loci in CDH4, LAMA2, HECW1, SEMA6A and ACE genes, involved in the integration systems.

Perspectives on Complexity, Chaos and Thermodynamics in Environmental Pathology

Though complexity science and chaos theory have become a common scientific divulgation theme, medical disciplines, and pathology in particular, still rely on a deterministic, reductionistic approach and still hesitate to fully appreciate the intrinsic complexity of living beings. Herein, complexity, chaos and thermodynamics are introduced with specific regard to biomedical sciences, then their interconnections and implications in environmental pathology are discussed, with particular regard to a morphopathological, image analysis-based approach to biological interfaces. Biomedical disciplines traditionally approach living organisms by dissecting them ideally down to the molecular level in order to gain information about possible molecule to molecule interactions, to derive their macroscopic behaviour. Given the complex and chaotic behaviour of living systems, this approach is extremely limited in terms of obtainable information and may lead to misinterpretation. Environmental pathology, as a multidisciplinary discipline, should grant privilege to an integrated, possibly systemic approach, prone to manage the complex and chaotic aspects characterizing living organisms. Ultimately, environmental pathology should be interested in improving the well-being of individuals and the population, and ideally the health of the entire ecosystem/biosphere and should not focus merely on single diseases, diseased organs/tissues, cells and/or molecules.

Emotional Dysregulation Mechanisms in Psychosomatic Chronic Diseases Revealed by the Instability Coefficient

In the present work, we analyzed some emotional mechanisms (emotion dysregulation—ED, negative affect—NA, and emotional vulnerability) involved in chronic diseases by means of an interdisciplinary approach. We started from the conceptualization of emotions as a complex dynamic system that can be investigated and understood within a framework inspired by Chaos Theory. An “instability coefficient” Δ was computed to analyze ED mechanisms, NA, and emotional vulnerability in different disease groups (blood cancer, breast cancer, hypertension) as well as in healthy persons. This coefficient, recently defined by our group, computes the Euclidian distance between the pairs of vectors whose components are similar or reverted items of a test measuring ED. The emotional and somatic systems were considered as two complex dynamical systems in interaction. Due to this interaction, and as a result of the laws of complexity, a small perturbation in an inner state of the emotional system could generate an important reaction in the somatic system in time. The emotional vulnerability reflected by high values of Δ was associated with the chronic disease condition. The differences between illness groups and healthy persons, as well as between the three disease groups in Δ values, were analyzed. The results showed that there were significant differences between the chronic disease groups in Δ values. The most highly significant differences in Δ values were reported between the breast cancer group and the healthy group on one hand and between the breast cancer group and the blood cancer group on the other hand. The less significant differences in Δ values were noticed between the hypertension group and the control group. Δ was significant in predicting ED and NA. Compared to the classical approaches, the original contribution of our research is that these results encourage us to propose this interdisciplinary method of assessment as a challenging, valid tool of investigation and understanding of complex phenomena that occur in the emotional and somatic system.

DICER1 in the Pathogenesis of Age-related Macular Degeneration (AMD) - Alu RNA Accumulation versus miRNA Dysregulation

DICER1 deficiency in the retinal pigment epithelium (RPE) was associated with the accumulation of Alu transcripts and implicated in geographic atrophy (GA), a form of age-related macular degeneration (AMD), an eye disease leading to blindness in millions of people. Although the exact mechanism of this association is not fully known, the activation of the NLRP3 inflammasome, maturation of caspase-1 and disruption in mitochondrial homeostasis in RPE cells were shown as critical for it. DICER1 deficiency results in dysregulation of miRNAs and changes in the expression of many genes important for RPE homeostasis, which may also contribute to AMD. DICER1 deficiency can change the functions of the miR-183/96/182 cluster that regulates photoreceptors and their synaptic transmission. Aging, the main AMD risk factor, is associated with decreased expression of DICER1 and changes in its diurnal pattern that are not synchronized with circadian regulation in the retina. The initial insult inducing DICER1 deficiency in AMD may be oxidative stress, another major risk factor of AMD, but further studies on the role of deficient DICER1 in AMD pathogenesis and its therapeutic potential are needed.

[Research advance of ANRIL on atherosclerosis by regulating cell proliferation and apoptosis]

Atherosclerosis is an important pathological basis for coronary artery disease. ANRIL is an antisense non-coding RNA located in Chr9p21 locus, which was identified as the most significant risk locus associated with atherosclerosis. ANRIL can produce multiple transcripts including linear and circular transcripts after various transcript splicing. It has been illustrated that ANRIL plays important roles in the pathology of atherosclerosis by regulating the proliferation and apoptosis of vascular cells. Linear ANRIL can regulate the proliferation of vascular smooth muscle cells (VSMCs) in plaques by chromatin modification, as well as influence the proliferation and the apoptosis of macrophages in post transcription; circular ANRIL can affect the proliferation and apoptosis of VSMCs by chromatin modification as well as interfering with rRNA maturation. In this review, we describe the ANRIL evolution, different transcripts characteristics, and their roles in the proliferation and apoptosis of vascular cells to participate in the process of atherosclerosis, for further understanding the pathogenesis of atherosclerosis and finding potential targets for diagnosis and treatment of atherosclerosis.

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alus are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alus and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses significant problems for phasing these insertions with other variants that comprise the haplotype. To ameliorate this issue, we introduce a new pipeline - TypeTE - which genotypes Alu insertions from whole-genome sequencing data. Starting from a list of polymorphic Alus, TypeTE identifies the hallmarks (poly-A tail and target site duplication) and orientation of Alu insertions using local re-assembly to reconstruct presence and absence alleles. Genotype likelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles. Using a high-quality set of PCR-based genotyping of >200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics.

A novel plasma lncRNA ENST00000416361 is upregulated in coronary artery disease and is related to inflammation and lipid metabolism

Coronary artery disease (CAD) is a serious threat to human health and a major cause of mortality worldwide. Long noncoding RNAs (lncRNAs) affect the occurrence and development of CAD via the regulation of cell proliferation and apoptosis, inflammatory responses and lipid metabolism. Screening methods and therapeutic strategies for CAD have been extensively studied. The present study analyzed clinical indexes of 187 patients with CAD and 150 healthy subjects. The data showed significant differences in diabetes mellitus, hypertension, high-density lipoprotein level and smoking history between the CAD group and the control group. A series of differentially expressed lncRNAs were detected in the plasma samples of three patients with CAD by high-throughput sequencing. Reverse transcription-quantitative (RT-q)PCR data revealed that the expression level of the novel lncRNA ENST00000416361 was ~2.3-fold higher in the plasma of 50 patients with CAD compared with the 50 control subjects. Receiver operating characteristic (ROC) curves were generated, and the area under the ROC curve was 0.7902. Knockdown of ENST00000416361 in human umbilical vein endothelial cells markedly downregulated interleukin-6 and tumor necrosis factor-α levels. In addition, sterol regulatory element binding transcription factor (SREBP)1 and SREBP2 were upregulated in patients with CAD, and they were positively correlated with the expression of ENST00000416361. RT-qPCR further demonstrated that knockdown of ENST00000416361 led to the downregulation of SREBP1 and SREBP2. Overall, the novel lncRNA ENST00000416361 may be associated with CAD-induced inflammation and lipid metabolism, and it may serve as a potential biomarker for CAD.

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.

ANRIL and atherosclerosis

WHAT IS KNOWN AND OBJECTIVE

The 3.8-kb-long antisense non-coding RNA at the INK4 locus (ANRIL) is transcribed from the short arm of human chromosome 9 on P21 and is associated with malfunction of the vascular endothelium, vascular smooth muscle cell (VSMC) proliferation/migration/senescence/apoptosis, mononuclear cell adhesion and proliferation, glycolipid metabolism disorder and DNA damage. Hence, ANRIL plays an important role in atherogenesis. Moreover, genome-wide association studies (GWAS) have identified ANRIL as a biomarker that is closely related to coronary heart disease (CHD). The objective of this review was to discuss the pathological mechanism of ANRIL in atherosclerotic development and its significance as a predictor of cardiovascular disease.

METHODS

Review of the PubMed, EMBASE and Cochrane databases for articles demonstrating the roles of ANRIL in the development of atherosclerotic diseases.

RESULTS AND DISCUSSION

The abnormal expression of ANRIL is linked to vascular endothelium injury; the proliferation, migration, senescence and apoptosis of VSMCs; mononuclear cell adhesion and proliferation; glycolipid metabolism disorder; DNA damage; and competing endogenous RNAs. Moreover, ANRIL accelerates the progression of CHD by regulating its single nucleotide polymorphisms (SNPs).

WHAT IS NEW AND CONCLUSION

Considering that ANRIL accelerates atherosclerosis (AS) development and is a risk factor for CHD, it is reasonable for us to explore an efficacious ANRIL-based therapy for AS in CHD.

Application of Chaotic Laws to Improve Haplotype Assembly Using Chaos Game Representation

Sequence data are deposited in the form of unphased genotypes and it is not possible to directly identify the location of a particular allele on a specific parental chromosome or haplotype. This study employed nonlinear time series modeling approaches to analyze the haplotype sequences obtained from the NGS sequencing method. To evaluate the chaotic behavior of haplotypes, we analyzed their whole sequences, as well as several subsequences from distinct haplotypes, in terms of the SNP distribution on their chromosomes. This analysis utilized chaos game representation (CGR) followed by the application of two different scaling methods. It was found that chaotic behavior clearly exists in most haplotype subsequences. For testing the applicability of the proposed model, the present research determined the alleles in gap positions and positions with low coverage by using chromosome subsequences in which 10% of each subsequence's alleles are replaced by gaps. After conversion of the subsequences' CGR into the coordinate series, a Local Projection (LP) method predicted the measure of ambiguous positions in the coordinate series. It was discovered that the average reconstruction rate for all input data is more than 97%, demonstrating that applying this knowledge can effectively improve the reconstruction rate of given haplotypes.

Promising member of the short interspersed nuclear elements (Alu elements): mechanisms and clinical applications in human cancers

Alu elements are one of most ubiquitous repetitive sequences in human genome, which were considered as the junk DNA in the past. Alu elements have been found to be associated with human diseases including cancers via events such as amplification, insertion, recombination or RNA editing, which provide a new perspective of oncogenesis at both DNA and RNA levels. Due to the prevalent distribution, Alu elements are widely used as target molecule of liquid biopsy. Alu-based cell-free DNA shows feasible application value in tumour diagnosis, postoperative monitoring and adjuvant therapy. In this review, the special tumourigenesis mechanism of Alu elements in human cancers is discussed, and the application of Alu elements in various tumour liquid biopsy is summarised.

An Exonic Switch Regulates Differential Accession of microRNAs to the Cd34 Transcript in Atherosclerosis Progression

BACKGROUND

CD34⁺ Endothelial Progenitor Cells (EPCs) play an important role in the recovery of injured endothelium and contribute to atherosclerosis (ATH) pathogenesis. Previously we described a potential atherogenic role for miR-125 that we aimed to confirm in this work.

METHODS

Microarray hybridization, TaqMan Low Density Array (TLDA) cards, qPCR, and immunohistochemistry (IHC) were used to analyze expression of the miRNAs, proteins and transcripts here studied.

RESULTS

Here we have demonstrated an increase of resident CD34-positive cells in the aortic tissue of human and mice during ATH progression, as well as the presence of clusters of CD34-positive cells in the intima and adventitia of human ATH aortas. We introduce miR-351, which share the seed sequence with miR-125, as a potential effector of CD34. We show a splicing event at an internal/cryptic splice site at exon 8 of the murine Cd34 gene (exonic-switch) that would regulate the differential accession of miRNAs (including miR-125) to the coding region or to the 3'UTR of Cd34.

CONCLUSIONS

We introduce new potential mediators of ATH progression (CD34 cell-clusters, miR-351), and propose a new mechanism of miRNA action, linked to a cryptic splicing site in the target-host gene, that would regulate the differential accession of miRNAs to their cognate binding sites.

Analytical Value of Cell-Free DNA Based on Alu in Psychiatric Disorders

Psychiatric disorders impose a huge burden on individuals, families, and society. The Alu repeat sequence is a member of the short interspersed nuclear element (SINE) family of mammalian genomes, however, its expression pattern and role in psychiatric disorders is unclear. The current paper aimed at determining the concentrations of Alu in patients with schizophrenia (SZ), major depressive disorder (MDD), and alcohol-induced psychotic disorder (AIPD), and to further define the role and value of Alu as a potential biomarker in psychiatric disorders. In this work, we found that the concentration of Alu was considerably incremented in patients with SZ, and a significant difference existed between patients diagnosed with SZ and MDD or AIPD. ROC analysis also indicated that Alu was effective in the complementary diagnosis of SZ, and differentially diagnosed between SZ patients and patients with MDD or AIPD. In addition, we found a positive relationship between the Alu concentrations and interleukin-1β (IL-1β) in patients with SZ, MDD, and AIPD, and between the concentrations of Alu and interleukin-18 (IL-18) in patients with SZ. Overall, the present work indicates that Alu might be an innovative biomarker for diagnosing psychiatric disorders, and provides the basis for hypotheses about the pathophysiology of psychiatric disorders.