scholarly journals El epigenoma circulante

2020 ◽  
Author(s):  
José Darío Martínez-Ezquerro
Keyword(s):  
Nucleic Acids ◽  
Target Genes ◽  
Metabolic Diseases ◽  
Expression Patterns ◽  
Body Fluids ◽  
Dna And Rna ◽  
Expresión Génica ◽  
A Cell ◽  
Clinical Conditions ◽  
First Time

ResumenDesde el descubrimiento de los ácidos nucleicos en circulación sanguínea humana por Mandel y Métais en 1948, se ha demostrado la presencia del ADN y ARN circulantes (ANcir) en los distintos fluidos corporales tanto de plantas como animales. En humanos, esta presencia extracelular de ácidos nucleicos ocurre en personas sanas o con distintas condiciones clínicas.Por otro lado, la epigenética hace referencia tanto a los cambios heredables en la actividad y expresión génica (en la progenie de células o individuos), así como a las alteraciones estables de largo plazo en el potencial transcripcional de una célula que no necesariamente son heredables. Mientras tanto, el estudio del epigenoma implica la descripción completa de las modificaciones químicas tanto del DNA como de las histonas a lo largo del genoma, así como a los transcritos no codificantes (ncRNA), los cuales conforman una red de regulación que modula la estructura de la cromatina y la función del genoma, generando patrones de expresión particulares a cada tipo celular, mecanismo mediante el cual los genes establecen sus efectos fenotípicos involucrando interacciones adaptativas con el ambiente. El epigenoma circulante se observa mediante el análisis en los fluidos corporales de las modificaciones al DNA e histonas, así como de los ncRNA, que de manera individual o conjunta participan en la regulación de la expresión de transcritos, tanto codificantes como no codificantes.En este capítulo se sintetiza el conocimiento de los ANcir en distintas condiciones clínicas y del epigenoma circulante, incluyendo diversos abordajes de su investigación en condiciones complejas: cáncer, embarazo, trasplante de órganos, trastornos neurodegenerativos, enfermedades cardiovasculares, enfermedades metabólicas, entre otras. Además, se presenta por primera vez el concepto del exoepigenoma: el estudio del efecto regulatorio de los ácidos nucleicos y proteínas exógenas sobre la expresión de genes blancos ajenos, como un mecanismo de comunicación celular sistémico e inter-organísmico. La función y biología de este mecanismo de regulación exoepigenómico requieren de mayor estudio, en particular, para el abordaje de condiciones normales y patológicas desde una perspectiva ecológico-evolutiva compleja.AbstractSince the discovery of nucleic acids in human blood circulation by Mandel and Métais in 1948, the presence of circulating DNA and RNA (CNAs) in body fluids of both plants and animals has been demonstrated. In humans, this extracellular presence of nucleic acids occurs in healthy people and in those with clinical conditions.On the other hand, epigenetics refers to both heritable changes in gene activity and expression (in the progeny of cells or individuals), as well as long-term stable alterations in the transcriptional potential of a cell that are not necessarily heritable. Meanwhile, the study of the epigenome involves the complete description of the chemical modifications of both DNA and histones throughout the genome, as well as non-coding transcripts (ncRNA), which form a regulatory network that modulates chromatin structure and genome function, generating expression patterns particular to each cell type, a mechanism by which genes establish their phenotypic effects involving adaptive interactions with the environment. The circulating epigenome is observed through the analysis in body fluids of modifications to DNA and histones, as well as ncRNA, which individually or jointly participate in the regulation of transcriptional expression, both coding and non-coding.This chapter synthesizes the knowledge of CNAs in different clinical conditions and of the circulating epigenome, including various research approaches in complex conditions: cancer, pregnancy, organ transplantation, neurodegenerative disorders, cardiovascular diseases, and metabolic diseases, among others. In addition, the concept of the exoepigenome is presented for the first time, which refers to the study of the regulatory role of exogenous nucleic acids and proteins on the expression of foreign target genes, as a systemic and inter-organismic cellular communication mechanism. The function and biology of this exoepigenomic regulatory mechanism require further study, particularly, to address normal and pathological conditions from a complex ecological-evolutionary perspective.

scholarly journals Characterization of nucleic acids from extracellular vesicle-enriched human sweat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Geneviève Bart ◽  
Daniel Fischer ◽  
Anatoliy Samoylenko ◽  
Artem Zhyvolozhnyi ◽  
Pavlo Stehantsev ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Body Fluids ◽  
Lower Percentage ◽  
Rna Seq ◽  
Protein Coding ◽  
Human Sweat ◽  
Dna And Rna ◽  
Ribonucleoprotein Complexes ◽  
Eccrine Glands

Abstract Background The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids have been shown to contain nucleic acids, both as ribonucleoprotein complexes and associated with extracellular vesicles (EVs), these have not been investigated in sweat. In this study we aimed to explore and characterize the nucleic acids associated with sweat particles. Results We used next generation sequencing (NGS) to characterize DNA and RNA in pooled and individual samples of EV-enriched sweat collected from volunteers performing rigorous exercise. In all sequenced samples, we identified DNA originating from all human chromosomes, but only the mitochondrial chromosome was highly represented with 100% coverage. Most of the DNA mapped to unannotated regions of the human genome with some regions highly represented in all samples. Approximately 5 % of the reads were found to map to other genomes: including bacteria (83%), archaea (3%), and virus (13%), identified bacteria species were consistent with those commonly colonizing the human upper body and arm skin. Small RNA-seq from EV-enriched pooled sweat RNA resulted in 74% of the trimmed reads mapped to the human genome, with 29% corresponding to unannotated regions. Over 70% of the RNA reads mapping to an annotated region were tRNA, while misc. RNA (18,5%), protein coding RNA (5%) and miRNA (1,85%) were much less represented. RNA-seq from individually processed EV-enriched sweat collection generally resulted in fewer percentage of reads mapping to the human genome (7–45%), with 50–60% of those reads mapping to unannotated region of the genome and 30–55% being tRNAs, and lower percentage of reads being rRNA, LincRNA, misc. RNA, and protein coding RNA. Conclusions Our data demonstrates that sweat, as all other body fluids, contains a wealth of nucleic acids, including DNA and RNA of human and microbial origin, opening a possibility to investigate sweat as a source for biomarkers for specific health parameters.

Identification and Analysis of lncRNAs by Whole-Transcriptome Sequencing in Porcine Preadipocytes Induced by BMP2

2019 ◽  
Vol 158 (3) ◽  
pp. 133-144
Author(s):  
Sheng Li ◽  
Chengzhen Chen ◽  
Menglong Chai ◽  
Jiawei Wang ◽  
Bao Yuan ◽  
...  
Keyword(s):  
Target Genes ◽  
Metabolic Diseases ◽  
Enrichment Analysis ◽  
Fat Deposition ◽  
Bone Morphogenetic Protein 2 ◽  
Morphogenetic Protein ◽  
Whole Transcriptome Sequencing ◽  
Mirna Sponges ◽  
Whole Transcriptome ◽  
First Time

Bone morphogenetic protein 2 (BMP2) can mediate the signaling of R-Smads and regulate different biological functions, including adipocyte differentiation. Long noncoding RNAs (lncRNAs) can be involved in many important biological processes, including fat metabolism, as miRNA sponges. This study aimed to investigate the molecular mechanism of fat deposition and to provide useful information for the prevention and treatment of lipid-related diseases. lncRNA sequencing was performed to compare and analyze, for the first time, the expression of lncRNAs in BMP2-induced and non-BMP2-induced preadipocytes from Junmu1 pigs. In addition, functional annotation and enrichment analysis of differentially expressed lncRNA target genes were carried out. lncRNAs and mRNAs were compared and analyzed. lncRNAs were identified that may regulate adipogenesis and lipid metabolism. The results give a theoretical basis for further studies on fat deposition mechanisms and provide potential therapeutic targets for metabolic diseases.

Periodontal Pathogens and Neuropsychiatric Health

2020 ◽  
Vol 20 (15) ◽  
pp. 1353-1397 ◽  
Author(s):  
Abhishek Wadhawan ◽  
Mark A. Reynolds ◽  
Hina Makkar ◽  
Alison J. Scott ◽  
Eileen Potocki ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Metabolic Diseases ◽  
Low Grade ◽  
Periodontal Pathogens ◽  
Synergistic Interactions ◽  
Brain Vasculature ◽  
Micro Rnas ◽  
Clinical Conditions ◽  
Low Grade Inflammation ◽  
Neuropsychiatric Illness

Increasing evidence incriminates low-grade inflammation in cardiovascular, metabolic diseases, and neuropsychiatric clinical conditions, all important causes of morbidity and mortality. One of the upstream and modifiable precipitants and perpetrators of inflammation is chronic periodontitis, a polymicrobial infection with Porphyromonas gingivalis (P. gingivalis) playing a central role in the disease pathogenesis. We review the association between P. gingivalis and cardiovascular, metabolic, and neuropsychiatric illness, and the molecular mechanisms potentially implicated in immune upregulation as well as downregulation induced by the pathogen. In addition to inflammation, translocation of the pathogens to the coronary and peripheral arteries, including brain vasculature, and gut and liver vasculature has important pathophysiological consequences. Distant effects via translocation rely on virulence factors of P. gingivalis such as gingipains, on its synergistic interactions with other pathogens, and on its capability to manipulate the immune system via several mechanisms, including its capacity to induce production of immune-downregulating micro-RNAs. Possible targets for intervention and drug development to manage distal consequences of infection with P. gingivalis are also reviewed.

Detection and Quantification of 7-Hydroxydehydroepiandrosterone Epimers in Three Body Fluids

2002 ◽  
Vol 67 (1) ◽  
pp. 10-18 ◽  
Author(s):  
Richard Hampl ◽  
Martin Hill ◽  
Luboslav Stárka
Keyword(s):  
Healthy Subjects ◽  
Serum Levels ◽  
Body Fluids ◽  
Gas Chromatography Mass Spectrometry ◽  
Specific Radioimmunoassay ◽  
Order Of Magnitude ◽  
Three Body ◽  
First Time ◽  
Nanomolar Range ◽  
Detection And Quantification

3β,7α-Dihydroxyandrost-5-en-17-one (1) (7α-OH-DHEA) and its 7β-hydroxy epimer 2 (7β-OH-DHEA) - 7α- and 7β-hydroxydehydroepiandrosterone - were detected and quantified in three human body fluids: in blood serum, saliva and ejaculate. Specific radioimmunoassay and gas chromatography-mass spectrometry have been used. For the first time the data on changes of these dehydroepiandrosterone metabolites are reported for a representative group of healthy subjects of both sexes (172 females and 217 males) during the life span. The serum levels of both 7-hydroxydehydroepiandrosterone epimers in serum and also in semen were in the low nanomolar range, while concentrations by one order of magnitude lower were found in saliva, but still within the detection limit. The results will serve as a basis for comparative studies of 7-hydroxydehydroepiandrosterone levels under various pathophysiological conditions, with a particular respect to autoimmune disorders.

scholarly journals Graphene Oxide: A Smart (Starting) Material for Natural Methylxanthines Adsorption and Detection

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4247 ◽  
Author(s):  
Rita Petrucci ◽  
Isabella Chiarotto ◽  
Leonardo Mattiello ◽  
Daniele Passeri ◽  
Marco Rossi ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Graphene Oxide ◽  
Nucleic Acids ◽  
Reduced Graphene Oxide ◽  
Electrochemical Sensors ◽  
Enzymatic Digestion ◽  
Biologically Active ◽  
Polar Solvents ◽  
Dna And Rna ◽  
Reduced Graphene

Natural methylxanthines, caffeine, theophylline and theobromine, are widespread biologically active alkaloids in human nutrition, found mainly in beverages (coffee, tea, cocoa, energy drinks, etc.). Their detection is thus of extreme importance, and many studies are devoted to this topic. During the last decade, graphene oxide (GO) and reduced graphene oxide (RGO) gained popularity as constituents of sensors (chemical, electrochemical and biosensors) for methylxanthines. The main advantages of GO and RGO with respect to graphene are the easiness and cheapness of synthesis, the notable higher solubility in polar solvents (water, among others), and the higher reactivity towards these targets (mainly due to – interactions); one of the main disadvantages is the lower electrical conductivity, especially when using them in electrochemical sensors. Nonetheless, their use in sensors is becoming more and more common, with the obtainment of very good results in terms of selectivity and sensitivity (up to 5.4 × 10−10 mol L−1 and 1.8 × 10−9 mol L−1 for caffeine and theophylline, respectively). Moreover, the ability of GO to protect DNA and RNA from enzymatic digestion renders it one of the best candidates for biosensors based on these nucleic acids. This is an up-to-date review of the use of GO and RGO in sensors.

scholarly journals Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 628
Author(s):  
Dagmara Baraniak ◽  
Jerzy Boryski
Keyword(s):  
Nucleic Acids ◽  
State Of The Art ◽  
Modified Oligonucleotides ◽  
Synthetic Genes ◽  
Chemically Modified ◽  
Amide Linkage ◽  
Dna And Rna ◽  
Modified Dna ◽  
Modified Nucleic Acids ◽  
Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

scholarly journals Histone deacetylase (HDAC) 9: versatile biological functions and emerging roles in human cancer

2021 ◽  
Author(s):  
Chun Yang ◽  
Stéphane Croteau ◽  
Pierre Hardy
Keyword(s):  
Histone Deacetylase ◽  
Posttranslational Modifications ◽  
Histone Deacetylases ◽  
Muscle Development ◽  
Target Genes ◽  
Human Cancer ◽  
Expression Patterns ◽  
Aberrant Expression ◽  
Physiological Processes ◽  
Cancer Pathogenesis

Abstract Background HDAC9 (histone deacetylase 9) belongs to the class IIa family of histone deacetylases. This enzyme can shuttle freely between the nucleus and cytoplasm and promotes tissue-specific transcriptional regulation by interacting with histone and non-histone substrates. HDAC9 plays an essential role in diverse physiological processes including cardiac muscle development, bone formation, adipocyte differentiation and innate immunity. HDAC9 inhibition or activation is therefore a promising avenue for therapeutic intervention in several diseases. HDAC9 overexpression is also common in cancer cells, where HDAC9 alters the expression and activity of numerous relevant proteins involved in carcinogenesis. Conclusions This review summarizes the most recent discoveries regarding HDAC9 as a crucial regulator of specific physiological systems and, more importantly, highlights the diverse spectrum of HDAC9-mediated posttranslational modifications and their contributions to cancer pathogenesis. HDAC9 is a potential novel therapeutic target, and the restoration of aberrant expression patterns observed among HDAC9 target genes and their related signaling pathways may provide opportunities to the design of novel anticancer therapeutic strategies.

scholarly journals Extract of Wax Gourd Peel Prevents High-Fat Diet-Induced Hyperlipidemia in C57BL/6 Mice via the Inhibition of the PPARγPathway

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Ming Gu ◽  
Shengjie Fan ◽  
Gaigai Liu ◽  
Lu Guo ◽  
Xiaobo Ding ◽  
...  
Keyword(s):  
Blood Glucose ◽  
High Fat Diet ◽  
Target Genes ◽  
Metabolic Diseases ◽  
Body Weight Gain ◽  
Fasting Blood Glucose ◽  
Peroxisome Proliferator ◽  
Mrna Levels ◽  
High Fat ◽  
Wax Gourd

Wax gourd is a popular vegetable in East Asia. In traditional Chinese medicine, wax gourd peel is used to prevent and treat metabolic diseases such as hyperlipidemia, hyperglycemia, obesity, and cardiovascular disease. However, there is no experimental evidence to support these applications. Here, we examined the effect of the extract of wax gourd peel (EWGP) on metabolic disorders in diet-induced C57BL/6 obese mice. In the preventive experiment, EWGP blocked body weight gain and lowered serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-c), liver TG and TC contents, and fasting blood glucose in mice fed with a high-fat diet. In the therapeutic study, we induced obesity in the mice and treated with EWGP for two weeks. We found that EWGP treatment reduced serum and liver triglyceride (TG) contents and fasting blood glucose and improved glucose tolerance in the mice. Reporter assay and gene expression analysis showed that EWGP could inhibit peroxisome proliferator-activated receptorγ(PPARγ) transactivities and could decrease mRNA levels of PPARγand its target genes. We also found that HMG-CoA reductase (HMGCR) was downregulated in the mouse liver by EWGP. Our data suggest that EWGP lowers hyperlipidemia of C57BL/6 mice induced by high-fat diet via the inhibition of PPARγand HMGCR signaling.

scholarly journals Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Peirong Li ◽  
Tongbing Su ◽  
Deshuang Zhang ◽  
Weihong Wang ◽  
Xiaoyun Xin ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Leaf Development ◽  
Target Genes ◽  
Expression Patterns ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Leaf Morphogenesis ◽  
Expression Levels ◽  
Parental Lines

AbstractHeterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.

scholarly journals Circular RNA circSDHC serves as a sponge for miR-127-3p to promote the proliferation and metastasis of renal cell carcinoma via the CDKN3/E2F1 axis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Junjie Cen ◽  
Yanping Liang ◽  
Yong Huang ◽  
Yihui Pan ◽  
Guannan Shu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Target Genes ◽  
Expression Patterns ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Proliferation And Metastasis

Abstract Background There is increasing evidence that circular RNAs (circRNAs) have significant regulatory roles in cancer development and progression; however, the expression patterns and biological functions of circRNAs in renal cell carcinoma (RCC) remain largely elusive. Method Bioinformatics methods were applied to screen for circRNAs differentially expressed in RCC. Analysis of online circRNAs microarray datasets and our own patient cohort indicated that circSDHC (hsa_circ_0015004) had a potential oncogenic role in RCC. Subsequently, circSDHC expression was measured in RCC tissues and cell lines by qPCR assay, and the prognostic value of circSDHC evaluated. Further, a series of functional in vitro and in vivo experiments were conducted to assess the effects of circSDHC on RCC proliferation and metastasis. RNA pull-down assay, luciferase reporter and fluorescent in situ hybridization assays were used to confirm the interactions between circSDHC, miR-127-3p and its target genes. Results Clinically, high circSDHC expression was correlated with advanced TNM stage and poor survival in patients with RCC. Further, circSDHC promoted tumor cell proliferation and invasion, both in vivo and in vitro. Analysis of the mechanism underlying the effects of circSDHC in RCC demonstrated that it binds competitively to miR-127-3p and prevents its suppression of a downstream gene, CDKN3, and the E2F1 pathway, thereby leading to RCC malignant progression. Furthermore, knockdown of circSDHC caused decreased CDKN3 expression and E2F1 pathway inhibition, which could be rescued by treatment with an miR-127-3p inhibitor. Conclusion Our data indicates, for the first time, an essential role for the circSDHC/miR-127-3p/CDKN3/E2F1 axis in RCC progression. Thus, circSDHC has potential to be a new therapeutic target in patients with RCC.

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