Browsing by Author "Lipovich, Leonard"

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Activity-Dependent Non-Coding RNA MAPK Interactome of the Human Epileptic Brain
(2023) Lipovich, Leonard
Abstract: The human brain has evolved to have extraordinary capabilities, enabling complex behaviors. The uniqueness of the human brain is increasingly posited to be due in part to the functions of primate-specific, including human-specific, long non-coding RNA (lncRNA) genes, systemically less conserved than protein-coding genes in evolution. Patients who have surgery for drug-resistant epilepsy are subjected to extensive electrical recordings of the brain tissue that is subsequently removed in order to treat their epilepsy. Precise localization of brain tissues with distinct electrical properties offers a rare opportunity to explore the effects of brain activity on gene expression. Here, we identified 231 co-regulated, activity-dependent lncRNAs within the human MAPK signaling cascade. Six lncRNAs, four of which were antisense to known protein-coding genes, were further examined because of their high expression and potential impact on the disease phenotype. Using a model of repeated depolarizations in human neuronal-like cells (Sh-SY5Y), we show that five out of six lncRNAs were electrical activity-dependent, with three of four antisense lncRNAs having reciprocal expression patterns relative to their protein-coding gene partners. Some were directly regulated by MAPK signaling, while others effectively downregulated the expression of the protein-coding genes encoded on the opposite strands of their genomic loci. These lncRNAs, therefore, likely contribute to highly evolved and primate-specific human brain regulatory functions that could be therapeutically modulated to treat epilepsy.
Association of the ADIPOQ-AS LncRNA polymorphism rs2241766 with obesity: A Meta-analysis
(2022) Lipovich, Leonard
Abstract: Adipose tissue secretes different hormones to orchestrate lipid and glucose metabolism and insulin function. Adiponectin a key signaling peptide, is encoded by ADIPOQ gene and secreted by white adipose tissue. The ADIPOQ-AS gene encodes a long non-coding RNA and overlaps with the ADIPOQ on the anti-sense DNA strand. Adiponectin plasma levels are known to decrease in obesity. Moreover, several genetic variants have been reported to associate with diminishing Adiponectin levels and consequently with obesity, such as rs2241766 (+45 T > G). Allele frequencies of this SNP vary among populations and researchers have reported conflicting results about its association with the risk of developing obesity. Since 2016, many studies were conducted to evaluate role of polymorphism rs2241766 in predisposition to develop obesity among different populations, but not a single Meta-analysis was performed to pool all the results together. The present Meta-analysis is the first that aims to assess the involvement of rs2241766 in obesity development including clinical trials that have been conducted before and after 2016. We have systematically reviewed articles published from 2000 to 2022. A total of 1272 studies were obtained, of which only 15 case-control trials (including 4362 cases and 4338 controls) met the inclusion / exclusion criteria and were included in the statistical analysis. We could not detect significant association between the polymorphism rs2241766 and obesity (all P > 0.05). Further subgroup analysis revealed slight association and more prevalence of the minor allele G, and the homozygous genotype GG in obese compared to normal weight participants in Arab and African populations. Extensive work using larger sample sizes and additional ethnic groups is needed to better define the relationship between the rs2241766 polymorphism and predisposition to obesity. Depending on these future efforts and on evidence for its direct function in disease causality, this SNP can be developed as a diagnostic biomarker and/or as a therapeutic target for obesity and obesity-related metabolic diseases.
A collective statement in support of saving pangolins
(2022) Lipovich, Leonard
Letter to the Editor: We are an international group of biological scientists, conservationists, and environmentalists who have been closely following the plight and conservation of pangolins over a number of years. Pangolins comprise the mammalian Order Pholidota, which contains eight living species found in diverse habitats in Africa (4 species) and Asia (4 species),which provide important ecosystem services, including providing “pest” control and improving soil quality (Chao et al., 2020). They remain the most threatened and trafficked mammal species in the world (Gaubert et al., 2018; Sarah Heinrich et al., 2016). For over a century, there have been numerous attempts to rescue and maintain these animals in captivity, but with very few examples of success, chiefly because they usually die of infection (Hua et al., 2015; Lihua et al., 2010). In 2016, the genomes of the Critically Endangered Chinese andMalayan pangolins (Fig. 1) were sequenced and revealed two important findings (Choo et al., 2016). First, to the best of our knowledge, pangolins are the onlymammals known to lack the IFNE (Interferon epsilon) gene (important for mucosal immunity), suggesting that their resistance to pathogens may be reduced. Moreover, we found that pangolins have a reduced number of the heat shock protein (HSP) gene family members, suggesting stress susceptibility inducing immunosuppression, more so than other mammalian lineages. These findings may help explain why captive pangolins frequently succumb to infection.
Dietary Patterns and Associated Microbiome Changes that Promote Oncogenesis
(2021) Ibragimova, Shakhzada; Ramachandran, Revathy; Ali, Fahad R; Lipovich, Leonard; Ho, Samuel B
Abstract: The recent increases in cancer incidences have been linked to lifestyle changes that result in obesity and metabolic syndrome. It is now evident that these trends are associated with the profound changes that occur in the intestinal microbiome, producing altered microbial population signatures that interact, directly or indirectly, with potentially pro-carcinogenic molecular pathways of transcription, proliferation, and inflammation. The effects of the entire gut microbial population on overall health are complex, but individual bacteria are known to play important and definable roles. Recent detailed examinations of a large number of subjects show a tight correlation between habitual diets, fecal microbiome signatures, and markers of metabolic health. Diets that score higher in healthfulness or diversity such as plant-based diets, have altered ratios of specific bacteria, including an increase in short-chain fatty acid producers, which in turn have been linked to improved metabolic markers and lowered cancer risk. Contrarily, numerous studies have implicated less healthy, lower-scoring diets such as the Western diet with reduced intestinal epithelial defenses and promotion of specific bacteria that affect carcinogenic pathways. In this review, we will describe how different dietary patterns affect microbial populations in the gut and illustrate the subsequent impact of bacterial products and metabolites on molecular pathways of cancer development, both locally in the gut and systemically in distant organs.
Estrogen distinctly regulates transcription and translation of lncRNAs and pseudogenes in breast cancer cells
(2022-07) Giordo, Roberta; Lipovich, Leonard
Abstract: Estrogen drives key transcriptional changes in breast cancer and stimulates breast cancer cells’ growth with multiple mechanisms to coordinate transcription and translation. In addition to protein-coding transcripts, estrogen can regulate long non-coding RNA (lncRNA) transcripts, plus diverse non-coding RNAs including antisense, enhancer, and intergenic. LncRNA genes comprise the majority of human genes. The accidental, or regulated, translation of their short open reading frames by ribosomes remains a controversial topic. Here we report for the first time an integrated analysis of RNA abundance and ribosome occupancy level, using Ribo-seq combined with RNA-Seq, in the estrogen-responsive, estrogen receptor α positive, human breast cancer cell model MCF7, before and after hormone treatment. Translational profiling can determine, in an unbiased manner, which fraction of the genome is actually translated into proteins, as well as resolving whether transcription and translation respond concurrently, or differentially, to estrogen treatment. Our data showed specific transcripts more robustly detected in RNA-Seq than in the ribosome-profiling data, and vice versa, suggesting distinct genespecific estrogen responses at the transcriptional and the translational level, respectively. Here, we showed that estrogen stimulation affects the expression levels of numerous lncRNAs, but not their association with ribosomes, and that most lncRNAs are not ribosome-bound. For the first time, we also demonstrated the transcriptional and translational response of expressed pseudogenes to estrogen, pointing to new perspectives for drug-target development in breast cancer in the future.
Gestational Age Dependence of the Maternal Circulating Long Non-Coding RNA Transcriptome During Normal Pregnancy Highlights Antisense and Pseudogene Transcripts
(2021) Lipovich, Leonard
Abstract: In the post-genomic era, our understanding of the molecular regulators of physiologic and pathologic processes in pregnancy is expanding at the whole-genome level. Longitudinal changes in the known protein-coding transcriptome during normal pregnancy, which we recently reported (Gomez-Lopez et al., 2019), have improved our definition of the major operant networks, yet pregnancy-related functions of the non-coding RNA transcriptome remain poorly understood. A key finding of the ENCODE (Encyclopedia of DNA Elements) Consortium, the successor of the Human Genome Project, was that the human genome contains approximately 60,000 genes, the majority of which do not encode proteins. The total transcriptional output of non-protein-coding RNA genes, collectively referred to as the noncoding transcriptome, is comprised mainly of long non-coding RNA (lncRNA) transcripts (Derrien et al., 2012). Although the ncRNA transcriptome eclipses its protein-coding counterpart in abundance, it has until recently lacked a comprehensive, unbiased, genome-scale characterization over the timecourse of normal human pregnancy. Here, we annotated, characterized, and selectively validated the longitudinal changes in the non-coding transcriptome of maternal whole blood during normal pregnancy to term. We identified nine long non-coding RNAs (lncRNAs), including long intergenic non-coding RNAs (lincRNAs) as well as lncRNAs antisense to or otherwise in the immediate vicinity of protein-coding genes, that were differentially expressed with advancing gestation in normal pregnancy: AL355711, BC039551 (expressed mainly in the placenta), JHDM1D-AS1, A2M-AS1, MANEA-AS1, NR_034004, LINC00649, LINC00861, and LINC01094. By cross-referencing our dataset Edited by: Naoyuki Kataoka, The University of Tokyo, Japan Reviewed by: James Dominic Mills, Academic Medical Center, Netherlands Andreas Werner, Newcastle University, United Kingdom *Correspondence: Roberto Romero prbchiefstaff@med.wayne.edu Leonard Lipovich leonard.lipovich@mbru.ac.ae Specialty section: This article was submitted to RNA, a section of the journal Frontiers in Genetics Received: 19 August 2021 Accepted: 29 October 2021 Published: 22 November 2021 Citation: Kleinbrink EL, Gomez-Lopez N, Ju D, Done B, Goustin A-S, Tarca AL, Romero R and Lipovich L (2021) Gestational Age Dependence of the Maternal Circulating Long Non-Coding RNA Transcriptome During Normal Pregnancy Highlights Antisense and Pseudogene Transcripts. Front. Genet. 12:760849. doi: 10.3389/fgene.2021.760849 Frontiers in Genetics | www.frontiersin.org 1 November 2021 | Volume 12 | Article 760849 ORIGINAL RESEARCH published: 22 November 2021 doi: 10.3389/fgene.2021.760849 against major public pseudogene catalogs, we also identified six transcribed pseudogenes that were differentially expressed over time during normal pregnancy in maternal blood: UBBP4, FOXO3B, two Makorin (MKRN) pseudogenes (MKRN9P and LOC441455), PSME2P2, and YBX3P1. We also identified three non-coding RNAs belonging to other classes that were modulated during gestation: the microRNA MIR4439, the small nucleolar RNA (snoRNA) SNORD41, and the small Cajal-body specific ncRNA SCARNA2. The expression profiles of most hits were broadly suggestive of functions in pregnancy. These time-dependent changes of the non-coding transcriptome during normal pregnancy, which may confer specific regulatory impacts on their protein-coding gene targets, will facilitate a deeper molecular understanding of pregnancy and lncRNA-mediated molecular pathways at the maternal-fetal interface and of how these pathways impact maternal and fetal health.
LncRNA-Associated Genetic Etiologies Are Shared between Type 2 Diabetes and Cancers in the UAE Population
(2022) Giordo, Roberta; Gulsha, Rida; Kalla, Sarah; Lipovich, Leonard
Abstract: Numerous epidemiological studies place patients with T2D at a higher risk for cancer. Many risk factors, such as obesity, ageing, poor diet and low physical activity, are shared between T2D and cancer; however, the biological mechanisms linking the two diseases remain largely unknown. The advent of genome wide association studies (GWAS) revealed large numbers of genetic variants associated with both T2D and cancer. Most significant disease-associated variants reside in noncoding regions of the genome. Several studies show that single nucleotide polymorphisms (SNPs) at or near long non-coding RNA (lncRNA) genes may impact the susceptibility to T2D and cancer. Therefore, the identification of genetic variants predisposing individuals to both T2D and cancer may help explain the increased risk of cancer in T2D patients. We aim to investigate whether lncRNA genetic variants with significant diabetes and cancer associations overlap in the UAE population. We first performed an annotation-based analysis of UAE T2D GWAS, confirming the high prevalence of variants at or near non-coding RNA genes. We then explored whether these T2D SNPs in lncRNAs were relevant to cancer. We highlighted six non-coding genetic variants, jointly reaching statistical significance in T2D and cancer, implicating a shared genetic architecture between the two diseases in the UAE population.
miRCOVID-19: Potential Targets of Human miRNAs in SARS-CoV-2 for RNA-Based Drug Discovery
(2021) Lipovich, Leonard
Abstract: Sense-antisense interactions of long and short RNAs in human cells are integral to posttranscriptional gene regulation, in particular that of mRNAs by microRNAs. Many viruses, including severe acute respiratory syndrome coronavirus 2 SARS-CoV-2 (the causative agent of coronavirus disease 2019, COVID-19), have RNA genomes, and interactions between host and viral RNAs, while known to be functional in other viral diseases, have not yet been investigated in COVID-19. To remedy this gap in knowledge, we present miRCOVID-19, a computational meta-analysis framework identifying the predicted binding sites of human microRNAs along the SARS-CoV-2 RNA genome. To highlight the potential relevance of SARS-CoV-2-genome-complementary miRNAs to COVID-19 pathogenesis, we assessed their expression in COVID-19-relevant tissues using public transcriptome data. miRCOVID-19 identified 14 high-confidence mature miRNAs that are highly likely to interact with the SARS-CoV-2 genome and are expressed in diverse respiratory epithelial and immune cell types that are relevant to COVID-19 pathogenesis. As a proof of principle, we have shown that human miR-122, a previously known co-factor of another RNA virus, the hepatitis C virus (HCV) whose genome it binds as a prerequisite for pathogenesis, was predicted to also bind the SARS-CoV-2 RNA genome with high affinity, suggesting the perspective of repurposing anti-HCV RNA-based drugs, such as Miravirsen, to treat COVID-19. Our study is the first to identify all high-confidence binding sites of human miRNAs in the SARS-CoV-2 genome using multiple tools. Our work directly facilitates experimental validation of the reported targets, which would accelerate RNA-based drug discovery for COVID-19 and has the potential to provide new avenues for treating symptomatic COVID-19, and block SARS-CoV-2 replication, in humans.
Non-coding regions of nuclear-DNA-encoded mitochondrial genes and intergenic sequences are targeted by autoantibodies in breast cancer
(2023) Giordo, Roberta; Lipovich, Leonard
Introduction: Autoantibodies against mitochondrial-derived antigens play a key role in chronic tissue inflammation in autoimmune disorders and cancers. Here, we identify autoreactive nuclear genomic DNA (nDNA)-encoded mitochondrial gene products (GAPDH, PKM2, GSTP1, SPATA5, MFF, TSPOAP1, PHB2, COA4, and HAGH) recognized by breast cancer (BC) patients’ sera as nonself, supporting a direct relationship of mitochondrial autoimmunity to breast carcinogenesis. Autoreactivity of multiple nDNA-encoded mitochondrial gene products was mapped to protein-coding regions, 3’ untranslated regions (UTRs), as well as introns. In addition, autoantibodies in BC sera targeted intergenic sequences that may be parts of long non-coding RNA (lncRNA) genes, including LINC02381 and other putative lncRNA neighbors of the protein-coding genes ERCC4, CXCL13, SOX3, PCDH1, EDDM3B, and GRB2. Increasing evidence indicates that lncRNAs play a key role in carcinogenesis. Consistent with this, our findings suggest that lncRNAs, as well as mRNAs of nDNA-encoded mitochondrial genes, mechanistically contribute to BC progression. This work supports a new paradigm of breast carcinogenesis based on a globally dysfunctional genome with altered function of multiple mitochondrial and non-mitochondrial oncogenic pathways caused by the effects of autoreactivity-induced dysregulation of multiple genes and their products. This autoimmunity-based model of carcinogenesis will open novel avenues for BC treatment.
The Role of Genetic Variants in the Long Non-Coding RNA Genes MALAT1 and H19 in the Pathogenesis of Childhood Obesity
(2023) Lipovich, Leonard
Abstract: Long non-coding RNAs (lncRNAs) play important roles in the maintenance of metabolic homeostasis. Recently, many studies have suggested that lncRNAs, such as Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) and Imprinted Maternally Expressed Transcript (H19), might participate in the pathogenesis of metabolic disorders such as obesity. We conducted a case-control study with 150 Russian children and adolescents aged between 5 and 17 years old in order to assess the statistical association between the single nucleotide polymorphisms (SNPs) rs3200401 in MALAT1 and rs217727 in H19, and the risk of developing obesity in this population. We further explored the possible association of rs3200401 and rs217727 with BMI Z-score and insulin resistance. The MALAT1 rs3200401 and H19 rs217727 SNPs were genotyped using Taqman SNP genotyping assay. The MALAT1 rs3200401 SNP was identified as a risk factor for childhood obesity (p < 0.05) under the dominant and allelic models, and the CT heterozygous genotype was associated with the risk of increased BMI and with insulin resistance. The H19 rs217727 SNP had no significant association with obesity risk (all p > 0.05). Our findings thus suggest that MALAT1 SNP rs3200401 is a potential indicator of obesity susceptibility and pathogenesis in children and adolescents.
YY1 directly interacts with myocardin to repress the triad myocardin/SRF/CArG box‑mediated smooth muscle gene transcription during smooth muscle phenotypic modulation
(2020) Lipovich, Leonard
Summary : Yang 1 (YY1) regulates gene transcription in a variety of biological processes. In this study, we aim to determine the role of YY1 in vascular smooth muscle cell (VSMC) phenotypic modulation both in vivo and in vitro. Here we show that vascular injury in rodent carotid arteries induces YY1 expression along with reduced expression of smooth muscle differentiation markers in the carotids. Consistent with this finding, YY1 expression is induced in differentiated VSMCs in response to serum stimulation. To determine the underlying molecular mechanisms, we found that YY1 suppresses the transcription of CArG box dependent SMC-specific genes including SM22α, SMα-actin and SMMHC. Interestingly, YY1 suppresses the transcriptional activity of the SM22α promoter by hindering the binding of serum response factor (SRF) to the proximal CArG box. YY1 also suppresses the transcription and the transactivation of myocardin (MYOCD), a master regulator for SMC-specific gene transcription by binding to SRF to form the MYOCD/SRF/CArG box triad (known as the ternary complex). Mechanistically, YY1 directly interacts with MYOCD to competitively displace MYOCD from SRF. This is the first evidence showing that YY1 inhibits SMC differentiation by directly targeting MYOCD. These findings provide new mechanistic insights into the regulatory mechanisms that govern SMC phenotypic modulation in the pathogenesis of vascular diseases.