scholarly journals Identification of microRNAs Associated With Human Fragile X Syndrome Using Next Generation Sequencing

2021 ◽  
Author(s):  
Maryam Sotoudeh Anvari ◽  
Hamed Vasei ◽  
Hossein Najmabadi ◽  
Reza Shervin Badv ◽  
Akram Gholipour ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Fragile X Syndrome ◽  
Deep Sequencing ◽  
Neurological Disorders ◽  
Fragile X ◽  
Expression Profiles ◽  
Fmr1 Gene ◽  
Blood Samples ◽  
Generation Sequencing ◽  
Potential Biomarkers

Abstract Fragile X syndrome (FXS) is caused by a mutation in the FMR1 gene which can lead to a loss or shortage of the FMR1 protein. This protein interacts with specific miRNAs, and a change can cause a range of neurological disorders. Therefore, miRNAs could act as a novel class of potential biomarkers for common CNS diseases. The aim of this study was to test this theory by exploring the expression profiles of various miRNAs in Iranian FXS patients using deep sequencing-based technologies, and validate the miRNAs affecting expression of the FMR1 gene. Blood samples were taken from 15 patients with FXS (9 males, 6 females) and 12 controls. 25 miRNAs were differentially expressed in individuals with FXS compared to controls. Levels of 9 miRNAs were found to be significantly changed (3 upregulated and 6 downregulated). In FXS patients, the levels of hsa-miR-532-5p, hsa-miR-652-3p and hsa-miR-4797-3p were significantly upregulated while levels of hsa-miR-191-5p, hsa-miR-181-5p, hsa-miR-26a-5p, hsa-miR-30e-5p, hsa-miR-186-5p, and hsa-miR-4797-5p exhibited significant downregulation; and these dysregulations were confirmed by RT‐qPCR. This study present altered miRNA expression in blood samples from FXS patients, which could be used for diagnostic, prognostic, and treatment purposes. Larger studies are required to confirm these preliminary results.

scholarly journals Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Thomas G. Nührenberg ◽  
Marco Cederqvist ◽  
Federico Marini ◽  
Christian Stratz ◽  
Björn A. Grüning ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Next Generation Sequencing ◽  
Platelet Reactivity ◽  
Platelet Rich Plasma ◽  
Expression Profiles ◽  
Bioinformatic Analysis ◽  
Differentially Expressed ◽  
Major Influence ◽  
Next Generation ◽  
Generation Sequencing

Background. Diabetes mellitus (DM) has been associated with increased platelet reactivity as well as increased levels of platelet RNAs in plasma. Here, we sought to evaluate whether the platelet transcriptome is altered in the presence of uncontrolled DM. Methods. Next-generation sequencing (NGS) was performed on platelet RNA for 5 patients with uncontrolled DM (HbA1c 9.0%) and 5 control patients (HbA1c 5.5%) with otherwise similar clinical characteristics. RNA was isolated from leucocyte-depleted platelet-rich plasma. Libraries of platelet RNAs were created separately for long RNAs after ribosomal depletion and for small RNAs from total RNA, followed by next-generation sequencing. Results. Platelets in both groups demonstrated RNA expression profiles characterized by absence of leukocyte-specific transcripts, high expression of well-known platelet transcripts, and in total 6,343 consistently detectable transcripts. Extensive statistical bioinformatic analysis yielded 12 genes with consistently differential expression at a lenient FDR < 0.1, thereof 8 protein-coding genes and 2 genes with known expression in platelets (MACF1 and ITGB3BP). Three of the four differentially expressed noncoding genes were YRNAs (RNY1, RNY3, and RNY4) which were all downregulated in DM. 23 miRNAs were differentially expressed between the two groups. Of the 13 miRNAs with decreased expression in the diabetic group, 8 belonged to the DLK1–DIO3 gene region on chromosome 14q32.2. Conclusions. In this study, uncontrolled DM had a remote impact on different components of the platelet transcriptome. Increased expression of MACF1, together with supporting predicted mRNA-miRNA interactions as well as reduced expression of RNYs in platelets, may reflect subclinical platelet activation in uncontrolled DM.

Roles of ZF5 and CGGBP-20 transcription factors in regulating expression of human FMR1 gene responsible for fragile X-syndrome

2010 ◽  
Vol 4 (1) ◽  
pp. 54-62 ◽  
Author(s):  
P. V. Gulyy ◽  
S. V. Orlov ◽  
E. B. Dizhe ◽  
K. B. Kuteikin-Teplyakov ◽  
I. A. Ignatovich ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Fragile X Syndrome ◽  
Fragile X ◽  
Fmr1 Gene

scholarly journals Analysis of unstable DNA sequence in FMR1 gene in Polish families with fragile X syndrome.

1996 ◽  
Vol 43 (2) ◽  
pp. 383-388
Author(s):  
M Milewski ◽  
M Zygulska ◽  
J Bal ◽  
W H Deelen ◽  
E Obersztyn ◽  
...  
Keyword(s):  
Fragile X Syndrome ◽  
Dna Sequence ◽  
Clinical Features ◽  
Fragile Site ◽  
Fragile X ◽  
Fmr1 Gene ◽  
Repeat Number ◽  
Full Mutation ◽  
Cgg Repeats ◽  
Large Expansion

The unstable DNA sequence in the FMR1 gene was analyzed in 85 individuals from Polish families with fragile X syndrome in order to characterize mutations responsible for the disease in Poland. In all affected individuals classified on the basis of clinical features and expression of the fragile site at X(q27.3) a large expansion of the unstable sequence (full mutation) was detected. About 5% (2 of 43) of individuals with full mutation did not express the fragile site. Among normal alleles, ranging in size from 20 to 41 CGG repeats, allele with 29 repeats was the most frequent (37%). Transmission of premutated and fully mutated alleles to the offspring was always associated with size increase. No change in repeat number was found when normal alleles were transmitted.

scholarly journals Profiling Plasma MicroRNA in Nasopharyngeal Carcinoma with Deep Sequencing

2014 ◽  
Vol 60 (5) ◽  
pp. 773-782 ◽  
Author(s):  
Hai-Yun Wang ◽  
Li-Xu Yan ◽  
Qiong Shao ◽  
Sha Fu ◽  
Zi-Chen Zhang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Risk ◽  
Nasopharyngeal Carcinoma ◽  
Deep Sequencing ◽  
Independent Set ◽  
Differentially Expressed ◽  
Low Concentrations ◽  
Plasma Microrna ◽  
Generation Sequencing ◽  
Plasma Mirnas

Abstract BACKGROUND The goal of this study was to establish a plasma microRNA profile by use of next-generation sequencing that could aid in assessment of patient prognosis in nasopharyngeal carcinoma (NPC). METHODS Two panels of NPC patients and healthy controls (HCs) were recruited for this study. We used deep sequencing to screen plasma microRNAs. Differentially expressed microRNAs were verified by quantitative real-time PCR (qPCR). Kaplan–Meier survival analysis with the log-rank test was used to compare overall survival (OS) and progression-free survival (PFS) between groups. RESULTS Twenty-three plasma miRNAs with differential expression levels were selected for qPCR analysis on an independent set including 100 NPC patients and 55 HCs. NPC patients with low concentrations of miR-483–5p and miR-103 had better prognosis for 5-year OS than those with high concentrations (87.5% vs 55.8%, P &lt; 0.001; 80.9% vs 62.3%, P = 0.031). Those with low concentrations of miR-29a and let-7c had poorer prognosis (54.8% vs 82.8%, P = 0.002; 56.3% vs 84.6%, P = 0.001). A 3-signature miRNA integrated with clinical stage was further identified in an independent set. We calculated a prognostic index score and classified patients into low-, medium-, and high-risk groups. Five-year OS among the 3 groups was significantly different (90.9%, 66.7%, and 23.8%; P &lt; 0.001). By multivariate analysis, a high-risk score was the most significantly unfavorable prognostic factor independent of other clinical variables (P &lt; 0.001, hazard ratio = 15.1, 95% CI = 5.2–43.9). CONCLUSIONS Differentially expressed plasma miRNAs as identified by next-generation sequencing can be helpful for predicting survival in NPC patients.

scholarly journals Next-Generation Sequencing and Bioinformatics Protocol for Malaria Drug Resistance Marker Surveillance

2018 ◽  
Vol 62 (4) ◽  
pp. e02474-17 ◽  
Author(s):  
Eldin Talundzic ◽  
Shashidhar Ravishankar ◽  
Julia Kelley ◽  
Dhruviben Patel ◽  
Mateusz Plucinski ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Deep Sequencing ◽  
Artemisinin Resistance ◽  
The United States ◽  
Imported Malaria ◽  
Chloroquine Resistance ◽  
Next Generation ◽  
Content Type ◽  
Generation Sequencing

ABSTRACT The recent advances in next-generation sequencing technologies provide a new and effective way of tracking malaria drug-resistant parasites. To take advantage of this technology, an end-to-end Illumina targeted amplicon deep sequencing (TADS) and bioinformatics pipeline for molecular surveillance of drug resistance in P. falciparum, called malaria resistance surveillance (MaRS), was developed. TADS relies on PCR enriching genomic regions, specifically target genes of interest, prior to deep sequencing. MaRS enables researchers to simultaneously collect data on allele frequencies of multiple full-length P. falciparum drug resistance genes (crt, mdr1, k13, dhfr, dhps, and the cytochrome b gene), as well as the mitochondrial genome. Information is captured at the individual patient level for both known and potential new single nucleotide polymorphisms associated with drug resistance. The MaRS pipeline was validated using 245 imported malaria cases that were reported to the Centers for Disease Control and Prevention (CDC). The chloroquine resistance crt CVIET genotype (mutations underlined) was observed in 42% of samples, the highly pyrimethamine-resistant dhps IRN triple mutant in 92% of samples, and the sulfadoxine resistance dhps mutation SGEAA in 26% of samples. The mdr1 NFSND genotype was found in 40% of samples. With the exception of two cases imported from Cambodia, no artemisinin resistance k13 alleles were identified, and 99% of patients carried parasites susceptible to atovaquone-proguanil. Our goal is to implement MaRS at the CDC for routine surveillance of imported malaria cases in the United States and to aid in the adoption of this system at participating state public health laboratories, as well as by global partners.

Impact of Diet and the Gut Microbiome on Neurodegeneration and Regeneration in Neurological Disorders

Neuroforum ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 39-47
Author(s):  
Barbara Gisevius ◽  
Aiden Haghikia ◽  
Sarah Hirschberg
Keyword(s):  
Next Generation Sequencing ◽  
Gut Microbiome ◽  
Neurological Disorders ◽  
Next Generation ◽  
Generation Sequencing

Zusammenfassung Aktuelle Forschungsergebnisse im Bereich neurodegenerativer Erkrankungen deuten vermehrt darauf hin, dass die Ernährung und damit assoziiert die Zusammensetzung des Darm-Mikrobioms einen entscheidenden Einfluss auf die Entstehung und den Verlauf verschiedenster Krankheiten haben. Die sogenannte Darm-Hirn Achse, oder präziser die Darm-Mikrobiom-Hirn Achse hat dadurch deutlich an Aufmerksamkeit gewonnen. Dabei kann der Darm das zentrale Nervensystem auf unterschiedliche Weisen beeinflussen, I) direkt durch bakterielle Bestandteile und Metaboliten von Bakterien, II) durch Manipulation der im Körper zirkulierenden Immunzellen, oder III) durch direkten Kontakt, z. B. über den N. vagus. Fortschritte auf dem Gebiet der Molekularbiologie, wie das Next Generation Sequencing ermöglichen aufgrund ihres hohen Auflösungsvermögens die genaue Identifikation von Bakterien und die Kompositionen ganzer Mikrobiome. Dadurch ist es möglich, die Interaktionen zwischen dem intestinalen Mikrobiom, dem Metabolom und dem Darm- assoziierten Immunsystem detailliert zu erforschen. In dieser Arbeit diskutieren wir den Einfluss des Mikrobioms, der Ernährung und den damit verbundenen Gesundheitszustand auf die Neuroregeneration. Der Fokus liegt dabei auf der Möglichkeit, wie dieses Wissen in Zukunft für therapeutische Zwecke genutzt werden kann.

scholarly journals Targeted Next-Generation Sequencing in Patients with Suggestive X-Linked Intellectual Disability

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 51
Author(s):  
Nekane Ibarluzea ◽  
Ana Belén de la Hoz ◽  
Olatz Villate ◽  
Isabel Llano ◽  
Intzane Ocio ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Next Generation Sequencing ◽  
Fragile X ◽  
Next Generation ◽  
Sequencing Data ◽  
Targeted Next Generation Sequencing ◽  
Biochemical Assays ◽  
History Of ◽  
Male Patients ◽  
Generation Sequencing

X-linked intellectual disability (XLID) is known to contribute up to 10% of intellectual disability (ID) in males and could explain the increased ratio of affected males observed in patients with ID. Over the past decade, next-generation sequencing has clearly stimulated the gene discovery process and has become part of the diagnostic procedure. We have performed targeted next-generation sequencing of 82 XLID genes on 61 non-related male patients with suggestive non-syndromic XLID. These patients were initially referred to the molecular genetics laboratory to exclude Fragile X Syndrome. The cohort includes 47 male patients with suggestive X-linked family history of ID meaning that they had half-brothers or maternal cousins or uncles affected; and 14 male patients with ID and affected brothers whose mothers show skewed X-inactivation. Sequencing data analysis identified 17 candidate variants in 16 patients. Seven families could be re-contacted and variant segregation analysis of the respective eight candidate variants was performed: HUWE1, IQSEC2, MAOA, MED12, PHF8, SLC6A8, SLC9A6, and SYN1. Our results show the utility of targeted next-generation sequencing in unravelling the genetic origin of XLID, especially in retrospective cases. Variant segregation and additional studies like RNA sequencing and biochemical assays also helped in re-evaluating and further classifying the genetic variants found.

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