Genome-Wide Identification and Functional Classification of Tomato (Solanum lycopersicum) Aldehyde Dehydrogenase (ALDH) Gene Superfamily

Background:Recent studies underlined the crucial role of DNA methylation in several autoimmune diseases by altering gene expression profiles, thus influencing disease severity. Yet, aberrant methylation patterns in monocytes, key players in the pathogenesis of APS patients, has not been evaluated.Objectives:To analyze the genome-wide DNA methylation profile of monocytes from APS patients and its relationship with the cardiovascular (CV) pathology. 2. To evaluate the role of antiphospholipid antibodies (aPL) in the regulation of this process.Methods:Thirty-three APS patients and 15 healthy donors (HD) were included in the study. Monocytes were isolated from peripheral blood by positive immunomagnetic selection. The Illumina Infinium Methylation EPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs (TSS1500, TSS200, 5UTR, 3UTR, first exon, intergenic, gene body). Beta values (β) estimating methylation levels were obtained at each CpG site, and differentially methylated genes (DMG) between APS and HD were identified. Functional classification of that genes was carried out by gene ontology analysis (PANTHER database). Gene expression of selected DMG genes was evaluated by RT-PCR. CV-risk parameters, including carotid intima-media thickness (CIMT) and microvascular endothelial function were further assessed, and correlation/association studies were developed with clinical and analytical variables. The effects of aPLs were also evaluated byin vitrostudies.Results:Genome-wide DNA methylation analysis identified 813 DMG, including 279 hypomethylated and 534 hypermethylated. Functional classification of these genes revealed signatures associated with biological processes and pathways related to their clinical profile, including immune response, adhesion, oxidative stress and vascular signaling. Correlation and association studies showed that the methylation levels of genes related to immune response were associated with the CV-risk score, aGAPSS (CCR2, TXLNB, GLIPR), type of thrombosis (SIGLEC11, COLEC11, LRRC16A, AHSA1, TRIL) and aPL titers (CLEC4G, RGS4, HLA-DPA1, GBP6, RAET1E, HLA-G, HLA-DPA1, HLA-H, TXLNB). Besides, methylation levels of DMG related to vascular signaling and adhesion processes were associated with the presence of thrombotic recurrences (VEGFA, MAPK14, ITGA8, EPCAM, PCDHA6, DLG1) as well as with traditional CV-risk factor such as hypertension and dyslipidemia (ITGA11, DSCAM, CLEC4F, CDH4, LTBP2, PCDHB14). In addition, methylation levels of DMG genes related to oxidative stress (GP2, PGD, ADH1) were associated with microvascular endothelial dysfunction. An altered mRNA expression of some of those genes with aberrant methylation and related to increased CV-risk and thrombotic recurrences in APS was also identified. Both, abnormal methylation and transcription levels of several genes were further associated with a pathological increase of the CIMT. Finally, in vitro studies supported the role of aPLs as key players in the altered methylation and transcriptomic profiles of APS patients.Conclusion:APS patients showed an impaired methylation profile in monocytes of genes associated with clinical features of the disease, including aPL titers, CV risk, thrombotic recurrences, endothelial dysfunction and early atherosclerosis. These results offered a map to the monocytes methylome and shed light on the pathophysiology of APS, paving the way for the development of new, more effective biomarkers and therapeutics.Acknowledgments:Funded by ISCIII (PI18/0837 and RIER RD16/0012/0015) co-funded with FEDER.Disclosure of Interests:Carlos Perez-Sanchez: None declared, Alejandra M. Patiño-Trives: None declared, Maria A Aguirre: None declared, Pérez Sánchez Laura: None declared, María Luque-Tévar: None declared, Iván Arias de la Rosa: None declared, Carmen Torres-Granados: None declared, Maria del Carmen Abalos-Aguilera: None declared, Pedro Seguí Azpilcueta: None declared, Javier Rodríguez: None declared, Esteban Ballester: None declared, Nuria Barbarroja Puerto Grant/research support from: ROCHE and Pfizer., Speakers bureau: ROCHE and Celgene., Eduardo Collantes Estevez Grant/research support from: ROCHE and Pfizer, Speakers bureau: ROCHE, Lilly, Bristol and Celgene, Chary Lopez-Pedrera Grant/research support from: ROCHE and Pfizer.

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Objective and parametric methods used in functional classification disabled swimmers

Physiotherapy ◽

10.2478/physio-2013-0022 ◽

2013 ◽

Vol 21 (3) ◽

Cited By ~ 1

Author(s):

Natalia Uścinowicz ◽

Wojciech Seidel ◽

Paweł Zostawa ◽

Sebastian Klich

Keyword(s):

Medical Diagnosis ◽

Olympic Games ◽

Objective Evaluation ◽

Subjective Assessment ◽

Fair Play ◽

Functional Classification ◽

Kinematic Parameters ◽

Athletes With Disabilities ◽

Rule Out

AbstractThe recent Olympic Games in London incited much interest in the competition of disabled athletes. Various people connected with swimming, including coaches and athletes, have speculated about the fairness of competitions of disabled athletes. A constant problem are the subjective methods of classification in disabled sport. Originally, athletes with disabilities were classified according to medical diagnosis. Due to the injustice which still affects the competitors, functional classification was created shortly after. In the present review, the authors show the anomalies in the structure of the classification. The presented discovery led to the suggestion to introduce objective methods, thanks to which it would be no longer necessary to rely on the subjective assessment of the classifier. According to the authors, while using objective methods does not completely rule out the possibility of fraud by disabled athletes in the classification process, it would certainly reduce their incidence. Some of the objective methods useful for the classification of disabled athletes are: posturography, evaluation of the muscle parameters, electrogoniometric assessment, surface electromyography, and analysis of kinematic parameters. These methods have provide objective evaluation in the diagnostic sense but only if they are used in tandem. The authors demonstrate the undeniable benefits of using objective methods. Unfortunately, there are not only advantages of such solution, there also several drawbacks to be found. The conclusion of the article is the statement by the authors that it is right to use objective methods which allow to further the most important rule in sport: fair-play.

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Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽

10.3390/genes12010023 ◽

2020 ◽

Vol 12 (1) ◽

pp. 23

Author(s):

Antt Htet Wai ◽

Muhammad Waseem ◽

A B M Mahbub Morshed Khan ◽

Ujjal Kumar Nath ◽

Do Jin Lee ◽

...

Keyword(s):

Abiotic Stress ◽

Gene Family ◽

Stress Tolerance ◽

Solanum Lycopersicum ◽

Expression Profiling ◽

Abiotic Stress Tolerance ◽

Dependent Manner ◽

Solanum Lycopersicum L ◽

Genome Wide ◽

Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

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