ABSTRACT
INTRODUCTION: Mitochondrial DNA (mtDNA) is gaining increasing interest as a marker of cellular damage and could also act as an inflammatory mediator in cardiopulmonary bypass induced postoperative inflammatory response. Although minimally invasive heart valve surgery reportedly reduces inflammation, the mtDNA and cytokine profile in this context remains unclear. MATERIALS AND METHODS: Here, we report a prospective series of 40 elderly patients with aortic stenosis who underwent bioprosthetic aortic valve replacement (AVR) through upper ministernotomy with either a sutureless (n = 20) or a conventional (n = 20) valve. Primary end points included serial plasma levels of mtDNA (T1: at baseline; T2: 4 hours after surgery; and T3: 24s hour after surgery), cytokines (interleukin-6 [IL-6], tumor necrosis factor-α [TNF-α]), and myocardial necrosis biomarkers (MNBs), whereas secondary end points included clinical and echocardiographic data. RESULTS: Significant increases in the postoperative plasma levels (T2) of mtDNA, cytokines, and MNBs were observed in all patients. The postoperative plasma levels of mtDNA, TNF-α, and MNBs showed no significant differences between the treatment groups, although there was a trend toward lower levels in the sutureless group. The decreases in aortic cross-clamp and cardiopulmonary bypass times seen in the sutureless group were associated with significant lower postoperative levels (T2 and T3) of IL-6. CONCLUSION: AVR through upper ministernotomy was associated with a significant increase in postoperative plasma levels of mtDNA and cytokines. There was no difference in the mtDNA levels between the sutureless and conventional valve groups, suggesting a similar level of inflammation in both groups. However, the shorter operation time observed in the sutureless valve group was associated with significantly lower postoperative levels of IL-6, indicating potential clinical benefits.
Subject(s)
Aortic Valve Stenosis/surgery , Aortic Valve/surgery , Cell-Free Nucleic Acids/blood , Cytokines/blood , DNA, Mitochondrial/blood , Heart Valve Prosthesis Implantation , Inflammation Mediators/blood , Age Factors , Aged, 80 and over , Aortic Valve Stenosis/blood , Aortic Valve Stenosis/diagnosis , Biomarkers/blood , Bioprosthesis , Female , Heart Valve Prosthesis , Heart Valve Prosthesis Implantation/adverse effects , Heart Valve Prosthesis Implantation/instrumentation , Humans , Male , Operative Time , Prospective Studies , Severity of Illness Index , Sternotomy , Sutureless Surgical Procedures , Time Factors , Treatment OutcomeABSTRACT
In this study, 1,833 systemic sclerosis (SSc) cases and 3,466 controls were genotyped with the Immunochip array. Classical alleles, amino acid residues, and SNPs across the human leukocyte antigen (HLA) region were imputed and tested. These analyses resulted in a model composed of six polymorphic amino acid positions and seven SNPs that explained the observed significant associations in the region. In addition, a replication step comprising 4,017 SSc cases and 5,935 controls was carried out for several selected non-HLA variants, reaching a total of 5,850 cases and 9,401 controls of European ancestry. Following this strategy, we identified and validated three SSc risk loci, including DNASE1L3 at 3p14, the SCHIP1-IL12A locus at 3q25, and ATG5 at 6q21, as well as a suggested association of the TREH-DDX6 locus at 11q23. The associations of several previously reported SSc risk loci were validated and further refined, and the observed peak of association in PXK was related to DNASE1L3. Our study has increased the number of known genetic associations with SSc, provided further insight into the pleiotropic effects of shared autoimmune risk factors, and highlighted the power of dense mapping for detecting previously overlooked susceptibility loci.
Subject(s)
Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 3/genetics , Genetic Loci , Genetic Predisposition to Disease , Scleroderma, Systemic/genetics , Alleles , Autophagy-Related Protein 5 , Carrier Proteins/genetics , Case-Control Studies , DEAD-box RNA Helicases/genetics , Endodeoxyribonucleases/genetics , Female , Genome-Wide Association Study , Genotype , HLA Antigens/genetics , Humans , Interleukin-12 Subunit p35/genetics , Linkage Disequilibrium , Logistic Models , Male , Microchip Analytical Procedures , Microtubule-Associated Proteins/genetics , Polymorphism, Single Nucleotide , Proto-Oncogene Proteins/genetics , Risk Factors , White People/geneticsABSTRACT
Omics studies of systemic autoimmune diseases (SADs) in general, and SLE in particular, have delivered isolated information from transcriptome, epigenome, genome, cytokine and metabolome analyses. Such analyses have resulted in the identification of disease susceptibility genes and the description of IFN expression signatures, allowing extensive insight into the mechanisms of disease and the development of new therapies. Access to such technologies allows the recognition of patterns of disease at a pathway level, thereby, to reclassify SLE and other SADs and to develop new therapeutics from a personalized perspective. The use of omic information allows the discovery of correlative patterns involving drugs not currently suspected to be of value in SADs. In this review, we summarize the omics findings for SLE and propose ways of using the data for the identification of new biomarkers, finding new drugs and reclassifying patients not only with SLE, but also with other SADs.
Subject(s)
Autoimmune Diseases/genetics , Gene Expression Profiling , Genomics , Lupus Erythematosus, Systemic/genetics , Metabolomics , Autoimmune Diseases/classification , Autoimmune Diseases/diagnosis , Autoimmune Diseases/immunology , Cytokines/immunology , Drug Discovery , Epigenomics , Genetic Predisposition to Disease , Humans , Lupus Erythematosus, Systemic/diagnosis , Lupus Erythematosus, Systemic/drug therapy , Lupus Erythematosus, Systemic/immunology , MicroRNAs/geneticsABSTRACT
PURPOSE OF REVIEW: DNA methylation has emerged as an important contributing factor in the pathogenesis of systemic lupus erythematosus (SLE). Here, we describe the DNA methylation patterns identified in SLE and how these epigenetic changes can influence disease susceptibility, clinical heterogeneity, and disease flares. RECENT FINDINGS: Several genome-wide DNA methylation studies have been recently completed in SLE. Important observations include robust demethylation of interferon-regulated genes, which is consistent across all cell types studied to date, and is independent of disease activity. This interferon epigenetic signature was shown to precede interferon transcription signature in SLE, suggesting it might be an early event in the disease process. Recent studies also revealed DNA methylation changes specific for renal and skin involvement in SLE, providing a proof of principle for a value of DNA methylation studies in exploring mechanisms of specific disease manifestations, and potentially as prognostic biomarkers. Inherited ethnicity-specific DNA methylation patterns have also been shown to possibly contribute to differences in SLE susceptibility between populations. Finally, a recent study revealed that DNA methylation levels at IFI44L can accurately distinguish SLE patients from healthy controls, and from patients with other autoimmune diseases, promising to be the first epigenetic diagnostic marker for SLE. Genome-wide DNA methylation studies in SLE have provided novel insights into disease pathogenesis, clinical heterogeneity, and disease flares. Further studies promise to reveal novel diagnostic, prognostic, and therapeutic targets for SLE.
Subject(s)
DNA Methylation , Epigenesis, Genetic , Lupus Erythematosus, Systemic/genetics , Genome-Wide Association Study , HumansABSTRACT
PURPOSE OF REVIEW: To describe the recent studies on the genetics of systemic lupus erythematosus (SLE) and Sjögren's syndrome. RECENT FINDINGS: We overview the most recent findings on the genetic susceptibility of the diseases and provide information on their genetic similarities and differences. SUMMARY: SLE and Sjögren's syndrome are two closely related systemic autoimmune diseases that share multiple clinical and molecular aspects, including a significant number of susceptibility genes. Several genome-wide association studies were recently published in different populations that provide a better picture of their molecular mechanisms. It is becoming clear that their genetic architecture is quite well established, but more information is required on expression quantitative trait loci, epigenetic genome-wide analyses, gene × gene interactions and the role of rare variants.
Subject(s)
Histocompatibility Antigens Class II/genetics , Lupus Erythematosus, Systemic/genetics , Sjogren's Syndrome/genetics , CD11b Antigen/genetics , DNA-Binding Proteins/genetics , Genetic Predisposition to Disease , Genome-Wide Association Study , HLA-DQ beta-Chains/genetics , HLA-DRB1 Chains/genetics , Humans , Interferon Regulatory Factors/genetics , Lupus Erythematosus, Systemic/immunology , OX40 Ligand/genetics , STAT4 Transcription Factor/genetics , Sjogren's Syndrome/immunology , beta Karyopherins/geneticsABSTRACT
The genome-wide association study is a free-hypothesis approach based on screening of thousands or even millions of genetic variants distributed throughout the whole human genome in relation to a phenotype. The relevant role of the genome-wide association studies in the last decade is undisputed because it has permitted to elucidate multiple risk genetic factors associated with the susceptibility to several human complex diseases. Regarding systemic lupus erythematosus (SLE) this approach has allowed to identify more than 60 risk loci for SLE susceptibility across populations to date, increasing our understanding on the pathogenesis of this disease. We present the latest findings in the genetic of SLE across populations using genome-wide approaches. These studies revealed that most of the genetic risk is shared across borders and ethnicities. Finally, we focus on describing the most important risk loci for SLE attempting to cover the genetic findings in relation to functional polymorphisms, such as missense single nucleotide polymorphisms (SNPs) or regulatory variants involved in the development of the disease. The functional studies try to identify the causality of some GWAS-associated variants, many of which fall in non-coding regions of the genome, suggesting a regulatory role. Many loci show an environmental interaction, another aspect revealed by the studies of epigenetic modifications and those associated with genetic variants. Finally, new-generation sequencing technologies can open other paths in the research on SLE genetics, the role of rare variants and the detailed identification of causal regulatory variation. The clinical relevance of the genetic factors will be shown when we are able to use them or in combination with other molecular measurements to re-classify a heterogeneous disease such as SLE.
Subject(s)
Genetic Predisposition to Disease , Lupus Erythematosus, Systemic/genetics , Animals , Chromosome Mapping , Epigenesis, Genetic , Gene Expression Regulation , Gene-Environment Interaction , Genetic Association Studies , Genetic Variation , Genome-Wide Association Study , Genomics/methods , Humans , Lupus Erythematosus, Systemic/immunology , Quantitative Trait Loci , Risk FactorsABSTRACT
OBJECTIVE: Certain HLA-DRB1 alleles and single-nucleotide polymorphisms (SNPs) are associated with rheumatoid arthritis (RA). Our objective was to examine the combined effect of these associated variants, calculated as a cumulative genetic risk score (GRS) on RA predisposition, as well as the number of autoantibodies (none, one or two present). METHOD: We calculated four GRSs in 4956 patients and 4983 controls from four European countries. All four scores contained data on 22 non-HLA-risk SNPs, and three scores also contained HLA-DRB1 genotypes but had different HLA typing resolution. Most patients had data on both rheumatoid factor (RF) and anti-citrullinated proteins antibodies (ACPA). The GRSs were standardised (std.GRS) to account for population heterogeneity. Discrimination between patients and controls was examined by receiveroperating characteristics curves, and the four std.GRSs were compared across subgroups according to autoantibody status. RESULTS: The std.GRS improved its discriminatory ability between patients and controls when HLA-DRB1 data of higher resolution were added to the combined score. Patients had higher mean std.GRS than controls (p=7.9×10(-156)), and this score was significantly higher in patients with autoantibodies (shown for both RF and ACPA). Mean std.GRS was also higher in those with two versus one autoantibody (p=3.7×10(-23)) but was similar in patients without autoantibodies and controls (p=0.12). CONCLUSIONS: The GRS was associated with the number of autoantibodies and to both RF and ACPA positivity. ACPA play a more important role than RF with regards to the genetic risk profile, but stratification of patients according to both RF and ACPA may optimise future genetic studies.
Subject(s)
Arthritis, Rheumatoid/genetics , Autoantibodies/immunology , HLA-DRB1 Chains/genetics , Alleles , Arthritis, Rheumatoid/immunology , Case-Control Studies , Female , Genetic Predisposition to Disease , Humans , Male , Peptides, Cyclic/immunology , Rheumatoid Factor/immunology , Risk Assessment , Risk Factors , White PeopleABSTRACT
OBJECTIVE: To evaluate the contribution of the SPP1 rs11439060 and rs9138 polymorphisms, previously reported as autoimmune risk variants, in the rheumatoid arthritis (RA) genetic background according to anti-citrullinated protein antibodies (ACPAs) status of RA individuals. METHODS: We analysed a total of 11,715 RA cases and 26,493 controls from nine independent cohorts; all individuals were genotyped or had imputed genotypes for SPP1 rs11439060 and rs9138. The effect of the SPP1 rs11439060 and rs9138 risk-allele combination on osteopontin (OPN) expression in macrophages and OPN serum levels was investigated. RESULTS: We provide evidence for a distinct contribution of SPP1 to RA susceptibility according to ACPA status: the combination of ≥3 SPP1 rs11439060 and rs9138 common alleles was associated mainly with ACPA negativity (p=1.29×10(-5), ORACPA-negative 1.257 (1.135 to 1.394)) and less with ACPA positivity (p=0.0148, ORACPA-positive 1.072 (1.014 to 1.134)). The ORs between these subgroups (ie, ACPA-positive and ACPA-negative) significantly differed (p=7.33×10(-3)). Expression quantitative trait locus analysis revealed an association of the SPP1 risk-allele combination with decreased SPP1 expression in peripheral macrophages from 599 individuals. To corroborate these findings, we found an association of the SPP1 risk-allele combination and low serum level of secreted OPN (p=0.0157), as well as serum level of secreted OPN correlated positively with ACPA production (p=0.005; r=0.483). CONCLUSIONS: We demonstrate a significant contribution of the combination of SPP1 rs11439060 and rs9138 frequent alleles to risk of RA, the magnitude of the association being greater in patients negative for ACPAs.
Subject(s)
Arthritis, Rheumatoid/genetics , Autoantibodies/immunology , Citrulline/immunology , Osteopontin/genetics , Peptides/immunology , Alleles , Arthritis, Rheumatoid/immunology , Case-Control Studies , Female , Genetic Predisposition to Disease , Haplotypes , Humans , Macrophages/metabolism , Male , Osteopontin/metabolism , Polymorphism, Single NucleotideABSTRACT
Systemic sclerosis (SSc) is complex autoimmune disease affecting the connective tissue; influenced by genetic and environmental components. Recently, we performed the first successful genome-wide association study (GWAS) of SSc. Here, we perform a large replication study to better dissect the genetic component of SSc. We selected 768 polymorphisms from the previous GWAS and genotyped them in seven replication cohorts from Europe. Overall significance was calculated for replicated significant SNPs by meta-analysis of the replication cohorts and replication-GWAS cohorts (3237 cases and 6097 controls). Six SNPs in regions not previously associated with SSc were selected for validation in another five independent cohorts, up to a total of 5270 SSc patients and 8326 controls. We found evidence for replication and overall genome-wide significance for one novel SSc genetic risk locus: CSK [P-value = 5.04 × 10(-12), odds ratio (OR) = 1.20]. Additionally, we found suggestive association in the loci PSD3 (P-value = 3.18 × 10(-7), OR = 1.36) and NFKB1 (P-value = 1.03 × 10(-6), OR = 1.14). Additionally, we strengthened the evidence for previously confirmed associations. This study significantly increases the number of known putative genetic risk factors for SSc, including the genes CSK, PSD3 and NFKB1, and further confirms six previously described ones.
Subject(s)
Genetic Predisposition to Disease/genetics , Genome-Wide Association Study/methods , Polymorphism, Single Nucleotide , Protein-Tyrosine Kinases/genetics , Scleroderma, Systemic/genetics , CSK Tyrosine-Protein Kinase , Cohort Studies , Europe , Follow-Up Studies , Genotype , Humans , Interferon Regulatory Factors/genetics , Meta-Analysis as Topic , NF-kappa B p50 Subunit/genetics , Odds Ratio , Risk Factors , beta Karyopherins/genetics , src-Family KinasesABSTRACT
The aim of this study was to determine, through a genome-wide association study (GWAS), the genetic components contributing to different clinical sub-phenotypes of systemic sclerosis (SSc). We considered limited (lcSSc) and diffuse (dcSSc) cutaneous involvement, and the relationships with presence of the SSc-specific auto-antibodies, anti-centromere (ACA), and anti-topoisomerase I (ATA). Four GWAS cohorts, comprising 2,296 SSc patients and 5,171 healthy controls, were meta-analyzed looking for associations in the selected subgroups. Eighteen polymorphisms were further tested in nine independent cohorts comprising an additional 3,175 SSc patients and 4,971 controls. Conditional analysis for associated SNPs in the HLA region was performed to explore their independent association in antibody subgroups. Overall analysis showed that non-HLA polymorphism rs11642873 in IRF8 gene to be associated at GWAS level with lcSSc (Pâ=â2.32×10(-12), ORâ=â0.75). Also, rs12540874 in GRB10 gene (Pâ=â1.27 × 10(-6), ORâ=â1.15) and rs11047102 in SOX5 gene (Pâ=â1.39×10(-7), ORâ=â1.36) showed a suggestive association with lcSSc and ACA subgroups respectively. In the HLA region, we observed highly associated allelic combinations in the HLA-DQB1 locus with ACA (Pâ=â1.79×10(-61), ORâ=â2.48), in the HLA-DPA1/B1 loci with ATA (Pâ=â4.57×10(-76), ORâ=â8.84), and in NOTCH4 with ACA Pâ=â8.84×10(-21), ORâ=â0.55) and ATA (Pâ=â1.14×10(-8), ORâ=â0.54). We have identified three new non-HLA genes (IRF8, GRB10, and SOX5) associated with SSc clinical and auto-antibody subgroups. Within the HLA region, HLA-DQB1, HLA-DPA1/B1, and NOTCH4 associations with SSc are likely confined to specific auto-antibodies. These data emphasize the differential genetic components of subphenotypes of SSc.
Subject(s)
Genetic Predisposition to Disease , Genome-Wide Association Study/methods , Scleroderma, Systemic/genetics , Alleles , Autoantibodies/immunology , Female , Genetic Loci/genetics , Genetic Markers , HLA Antigens/genetics , Humans , Male , Middle Aged , Phenotype , Polymorphism, Single Nucleotide/genetics , Scleroderma, Systemic/classification , Scleroderma, Systemic/immunologyABSTRACT
The escalating use of plastics in agriculture, driven by global population growth and increasing food demand, has concurrently led to a rise in Agricultural Plastic Waste (APW) production. Effective waste management is imperative, prompting this study to address the initial step of management, that is the quantification and localization of waste generated from different production systems in diverse regions. Focused on four Southern European countries (Italy, Spain, Greece, and Portugal) at the regional level, the study uses Geographic Information System (GIS), land use maps, indices tailored to each specific agricultural application and each crop type for plastic waste mapping. Furthermore, after the data was employed, it was validated by relevant stakeholders of the mentioned countries. The study revealed Spain, particularly the Andalusia region, as the highest contributor to APW equal to 324,000 tons per year, while Portugal's Azores region had the lowest estimate equal to 428 tons per year. Significantly, this research stands out as one of the first to comprehensively consider various plastic applications and detailed crop cultivations within the production systems, representing a pioneering effort in addressing plastic waste management in Southern Europe. This can lead further on to the management of waste in this area and the transfer of the scientific proposition to other countries.
ABSTRACT
OBJECTIVE: To analyze the association of the severity of the menopausal symptoms with musculoskeletal pain in Portuguese postmenopausal women. METHODS: A cross-sectional, observational study was conducted on 167 women (63.85 ± 9.36 years). The Menopause Rating Scale was used to evaluate the menopausal symptoms severity, while the Nordic Musculoskeletal Questionnaire was employed to assess the localization of the musculoskeletal pain, and multi-located pain was determined if two or more body regions were affected. Depression (Hospital Anxiety and Depression Scale), age, body mass index (BMI) and physical activity level were considered as potential confounders. RESULTS: A greater severity of the somato-vegetative menopausal symptoms was related to the prevention from usual activities because of pain in the neck, shoulders, elbows, wrists/hands and knees (R2 of Nagelkerke = 0.064, 0.043, 0.074, 0.045 and 0.045, respectively). Associations were also observed between greater age and pain in the knees, ankles and feet (R2 of Nagelkerke = 0.036 and 0.034, respectively), and being physically inactive with upper back pain (R2 of Nagelkerke = 0.060). Higher depressive symptoms were linked to pain in the hip/thighs and knees (R2 of Nagelkerke = 0.067 and 0.085, respectively), as well as being physically inactive was related ton in the neck (R2 of Nagelkerke = 0.053). Only a greater BMI was related to multi-located pain in the last 7 days (R2 of Nagelkerke = 0.041). CONCLUSIONS: The findings of our study showed that, taking into account possible confounders, greater severity of the menopausal symptoms at a somatic-vegetative level was associated with more anatomical regions with musculoskeletal pain.
Subject(s)
Musculoskeletal Pain , Humans , Female , Musculoskeletal Pain/epidemiology , Musculoskeletal Pain/etiology , Postmenopause , Cross-Sectional Studies , Portugal/epidemiology , Menopause , Surveys and QuestionnairesABSTRACT
The main source of vitamin D results from skin sunlight exposure. Vitamin D deficiency (VDD) is linked to several adverse events during pregnancy. While performing a cross-sectional study with 886 pregnant women in Elda (Spain) from September 2019 to July 2020 to determine the association of VDD with gestational diabetes mellitus in relation to body mass index, a strict lockdown (SL) due to the COVID-19 pandemic was declared from 15 March 2020 to 15 May 2020. To determine if VDD prevalence in the local population of pregnant women was influenced by SL, a retrospective cross-sectional study was conducted to estimate the prevalence odds ratio (POR) for the association of VDD and SL. A crude logistic regression model was calculated, and then further adjusted by the biweekly measured vitamin D-specific UVB dose in our geographical area. The POR during SL was 4.0 (95%CI = 2.7-5.7), with a VDD prevalence of 77.8% in the quarantine period. Our results revealed that VDD prevalence in pregnant women was influenced by SL. This valuable information could guide us in future if public officials order the population to stay indoors for any given reason.
Subject(s)
COVID-19 , Vitamin D Deficiency , Humans , Female , Pregnancy , Pregnant Women , Retrospective Studies , Cross-Sectional Studies , Pandemics , COVID-19/epidemiology , COVID-19/prevention & control , Communicable Disease Control , Vitamin D Deficiency/epidemiology , Vitamin D , Vitamins , PrevalenceABSTRACT
Background: The aging of population is leading to the investigation of new options to achieve healthy aging. One of these options is high-intensity interval training (HIIT), although its effects on body composition and muscle strength are currently unclear. The objective of this systematic review is to examine the scientific publications on the effects of HIIT on the body composition and muscle strength of middle-aged and older adults. Methods: The search was carried out in the PubMed, Cochrane Plus, Web of Science, CINAHL and SciELO databases without limitation of publication dates. The literature search, data extraction and systematic review were performed following the PRISMA standards and the risk of bias of the selected studies was assessed using the Cochrane Collaboration Risk-of-Bias. Results: Initially 520 publications were identified, out of which a total of 8 articles were finally selected to be included in this systematic review. Improvements in body composition were seen in six of the selected items and an increase in muscle strength in seven of the eight. Regarding physical function, improvements were found in both gait speed and balance. Conclusions: This systematic review found that HIIT is effective in improving body composition and increasing muscle strength. However, when comparing HIIT to moderate-intensity continuous training, it is not clear that HIIT is more beneficial; a firm conclusion cannot be drawn due to the scarcity of published studies, their variety in methodology and the ambiguity of their results, so it is suggested to carry out more research in this area.
Subject(s)
High-Intensity Interval Training , Body Composition/physiology , High-Intensity Interval Training/methods , Muscle Strength/physiologyABSTRACT
Sjögren's disease is a complex autoimmune disease with twelve established susceptibility loci. This genome-wide association study (GWAS) identifies ten novel genome-wide significant (GWS) regions in Sjögren's cases of European ancestry: CD247, NAB1, PTTG1-MIR146A, PRDM1-ATG5, TNFAIP3, XKR6, MAPT-CRHR1, RPTOR-CHMP6-BAIAP6, TYK2, SYNGR1. Polygenic risk scores yield predictability (AUROC = 0.71) and relative risk of 12.08. Interrogation of bioinformatics databases refine the associations, define local regulatory networks of GWS SNPs from the 95% credible set, and expand the implicated gene list to >40. Many GWS SNPs are eQTLs for genes within topologically associated domains in immune cells and/or eQTLs in the main target tissue, salivary glands.
Subject(s)
Genome-Wide Association Study , Sjogren's Syndrome , Genetic Predisposition to Disease , Humans , Polymorphism, Single Nucleotide , Sjogren's Syndrome/geneticsABSTRACT
In addition to the standard set of chromosomes (A), about 15% of eukaryote genomes carry B chromosomes. In most cases, B chromosomes behave as genomic parasites being detrimental for the individuals carrying them and prospering in natural populations because of transmission advantages (drive). B chromosomes are mostly made up of repetitive DNA sequences, especially ribosomal DNA (rDNA), satellite DNA and mobile elements. In only two cases have B chromosomes been shown to carry protein-coding genes. Although some B chromosomes seem to have derived from interspecific hybridisation, the most likely source of B chromosomes is the host genome itself, but the specific A chromosome being the B ancestor has not been identified in any B-containing species. Here, we provide strong evidence for B chromosome ancestry in the migratory locust, based on the location of genes for the H3 and H4 histones in the B chromosome and a single A chromosome pair (i.e. the eighth in order of decreasing size). The high DNA sequence similarity of A and B chromosome H3-H4 genes supports B-origin from chromosome 8. The higher variation shown by B sequences, compared to A sequences, suggests that B chromosome sequences are most likely inactive and thus less subjected to purifying selection. Estimates of time of divergence for histone genes from A and B chromosomes suggest that B chromosomes are quite old (>750,000 years), showing the B-chromosome ability to persist in natural populations for long periods of time.
Subject(s)
Chromosomes/genetics , Evolution, Molecular , Genes, Insect , Histones/genetics , Locusta migratoria/genetics , Animals , Cloning, Molecular , DNA, Ribosomal/genetics , Female , In Situ Hybridization, Fluorescence , Male , Molecular Sequence Data , Phylogeny , Sequence Analysis, DNA , Time FactorsABSTRACT
OBJECTIVE: To identify the genetic variants that affect gene expression (expression quantitative trait loci [eQTLs]) in systemic sclerosis (SSc) and to investigate their role in the pathogenesis of the disease. METHODS: We performed an eQTL analysis using whole-blood sequencing data from 333 SSc patients and 524 controls and integrated them with SSc genome-wide association study (GWAS) data. We integrated our findings from expression modeling, differential expression analysis, and transcription factor binding site enrichment with key clinical features of SSc. RESULTS: We detected 49,123 validated cis-eQTLs from 4,539 SSc-associated single-nucleotide polymorphisms (SNPs) (PGWAS < 10-5 ). A total of 1,436 genes were within 1 Mb of the 4,539 SSc-associated SNPs. Of those 1,436 genes, 565 were detected as having ≥1 eQTL with an SSc-associated SNP. We developed a strategy to prioritize disease-associated genes based on their expression variance explained by SSc eQTLs (r2 > 0.05). As a result, 233 candidates were identified, 134 (58%) of them associated with hallmarks of SSc and 105 (45%) of them differentially expressed in the blood cells, skin, or lung tissue of SSc patients. Transcription factor binding site analysis revealed enriched motifs of 24 transcription factors (5%) among SSc eQTLs, 5 of which were found to be differentially regulated in the blood cells (ELF1 and MGA), skin (KLF4 and ID4), and lungs (TBX4) of SSc patients. Ten candidate genes (4%) can be targeted by approved medications for immune-mediated diseases, of which only 3 have been tested in clinical trials in patients with SSc. CONCLUSION: The findings of the present study indicate a new layer to the molecular complexity of SSc, contributing to a better understanding of the pathogenesis of the disease.
Subject(s)
Gene Expression Regulation/genetics , Scleroderma, Systemic/genetics , Adult , Aged , Basic Helix-Loop-Helix Transcription Factors/genetics , Female , Genetic Association Studies , Humans , Inhibitor of Differentiation Proteins/genetics , Kruppel-Like Factor 4 , Kruppel-Like Transcription Factors/genetics , Male , Middle Aged , Molecular Targeted Therapy , Nuclear Proteins/genetics , Polymorphism, Single Nucleotide , Quantitative Trait Loci , T-Box Domain Proteins/genetics , Transcription Factors/geneticsABSTRACT
Primary Sjögren's syndrome (SS) is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The etiology of SS is complex with environmental triggers and genetic factors involved. By conducting an integrated multi-omics study, we confirmed a vast coordinated hypomethylation and overexpression effects in IFN-related genes, what is known as the IFN signature. Stratified and conditional analyses suggest a strong interaction between SS-associated HLA genetic variation and the presence of Anti-Ro/SSA autoantibodies in driving the IFN epigenetic signature and determining SS. We report a novel epigenetic signature characterized by increased DNA methylation levels in a large number of genes enriched in pathways such as collagen metabolism and extracellular matrix organization. We identified potential new genetic variants associated with SS that might mediate their risk by altering DNA methylation or gene expression patterns, as well as disease-interacting genetic variants that exhibit regulatory function only in the SS population. Our study sheds new light on the interaction between genetics, autoantibody profiles, DNA methylation and gene expression in SS, and contributes to elucidate the genetic architecture of gene regulation in an autoimmune population.
Subject(s)
Autoantibodies , Epigenomics , Gene Expression Regulation/genetics , Gene Expression/genetics , Genetic Variation , HLA Antigens/genetics , Interferons/genetics , Sjogren's Syndrome/genetics , Sjogren's Syndrome/immunology , DNA Methylation/genetics , Female , Humans , Male , Sjogren's Syndrome/etiologyABSTRACT
(1) Background: The objective of the present study was to determine the ability of the SARC-F questionnaire to identify individuals at risk of falling among middle-aged and older community-dwelling postmenopausal women. (2) Methods: An analytical cross-sectional study was conducted on 157 women (70.80 ± 8.37 years). The SARC-F questionnaire was used to screen for risk of sarcopenia. Fear of falling and balance confidence, as measured by the Falls Efficacy Scale-International (FES-I) and the Activities-Specific balance Scale-16 items (ABC-16) respectively, were used to assess risk of falling. Anxiety and depression (Hospital Anxiety and Depression Scale), fatigue (Fatigue Severity Scale), body mass index, waist-to-hip ratio, and sleep duration were also determined. (3) Results: Logistic regression showed that higher risk of falling as assessed by FES-I was associated with higher SARC-F scores (OR = 1.656), anxiety levels (OR = 1.147), and age (OR = 1.060), while increased SARC-F scores (OR = 1.612), fatigue (OR = 1.044), and shorter sleep duration (OR = 0.75) were related to ABC-16 scores. In addition, a SARC-F cutoff of 1.50 (83.33% sensitivity and 59.13% specificity) and 3.50 (44.44% sensitivity and 89.26% specificity) were shown to be able to discriminate participants at risk of falling according to the FES-I and the ABC-16, respectively. (4) Conclusions: our results show that SARC-F is an independent predictor of the risk of falling among middle-aged and older community-dwelling postmenopausal women.