1,721,015 research outputs found
What's Wrong in a Jump? Prediction and Validation of Splice Site Variants
Full text linkAlternative splicing (AS) is a crucial process to enhance gene expression driving organ-ism development. Interestingly, more than 95% of human genes undergo AS, producing multiple protein isoforms from the same transcript. Any alteration (e.g., nucleotide substitutions, insertions, and deletions) involving consensus splicing regulatory sequences in a specific gene may result in the production of aberrant and not properly working proteins. In this review, we introduce the key steps of splicing mechanism and describe all different types of genomic variants affecting this process (splicing variants in acceptor/donor sites or branch point or polypyrimidine tract, exonic, and deep intronic changes). Then, we provide an updated approach to improve splice variants detection. First, we review the main computational tools, including the recent Machine Learn-ing-based algorithms, for the prediction of splice site variants, in order to characterize how a genomic variant interferes with splicing process. Next, we report the experimental methods to vali-date the predictive analyses are defined, distinguishing between methods testing RNA (tran-scriptomics analysis) or proteins (proteomics experiments). For both prediction and validation steps, benefits and weaknesses of each tool/procedure are accurately reported, as well as sugges-tions on which approaches are more suitable in diagnostic rather than in clinical research. © 2021 by the author. Licensee MDPI, Basel, Switzerland
Antisense Oligonucleotides (ASOs) in Motor Neuron Diseases: A Road to Cure in Light and Shade
Full text linkAntisense oligonucleotides (ASOs) are short oligodeoxynucleotides designed to bind to specific regions of target mRNA. ASOs can modulate pre-mRNA splicing, increase levels of functional proteins, and decrease levels of toxic proteins. ASOs are being developed for the treatment of motor neuron diseases (MNDs), including spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS) and spinal and bulbar muscular atrophy (SBMA). The biggest success has been the ASO known as nusinersen, the first effective therapy for SMA, able to improve symptoms and slow disease progression. Another success is tofersen, an ASO designed to treat ALS patients with SOD1 gene mutations. Both ASOs have been approved by the FDA and EMA. On the other hand, ASO treatment in ALS patients with the C9orf72 gene mutation did not show any improvement in disease progression. The aim of this review is to provide an up-to-date overview of ASO research in MNDs, from preclinical studies to clinical trials and, where available, regulatory approval. We highlight the successes and failures, underline the strengths and limitations of the current ASO research, and suggest possible approaches that could lead to more effective treatments
Opposite effects of beta amyloid on endothelial cell survival: role of fibroblast growth factor-2 (FGF-2)
No full textAmyloid beta-peptides (Abeta) aggregate during Alzheimer's disease contributing to the development of the pathology. At micromolar concentration Abeta is toxic and accumulates in neurons and in the vasculature. However, Abeta is found at nanomolar concentrations in the plasma of healthy individuals and is also produced by endothelial cells. Here, we investigate the dual role exerted by Abeta(1-40) on endothelial cell functions. Coronary vascular endothelial cells were utilized to study whether Abeta affects endothelial cell growth and its action was compared with the effect of fibroblast growth factor-2 (FGF-2). In a range from 5 to 100 nM, Abeta(1-40) concentration-dependently increased cell growth, whereas higher concentrations of Abeta(1-40) reduced cell number compared to control. At nanomolar concentration of the peptide Abeta(1-40) also stimulated FGF-2mRNA expression and protein production, which was negatively affected by micromolar concentration of the peptide. The dual role observed on endothelial cell growth, was mediated by FGF-2 biodisponibility. In fact, neutralizing anti-FGF-2 antibody inhibited Abeta(1-40)-induced ERK1/2 phosphorylation at 50 nM. 5 muM inhibited ERK1/2 activation over control and this was reflected by diminished cell growth which was recovered by exogenous FGF-2 administration. These results suggest that low Abeta concentrations stimulate endothelial cells to acquire an angiogenic phenotype through interaction with endogenous FGF-2 and induction of its synthesis. In contrast, accumulation of Abeta results toxic for endothelial cells and at these concentrations Abeta peptide looses its ability to prime FGF-2 cycle. This may be a fundamental pathological event which might contribute to the worsening of the pathology
Autosomal dominant familial neurohypophyseal diabetes insipidus caused by a novel missense mutation in AVP gene in a large Italian kindred
Full text linkPurpose Familial neurohypophysial diabetes insipidus (FNDI), commonly caused by autosomal dominant arginine vasopressin (AVP) mutations, is a rare condition in which vasopressin fails in regulating body's level of water with final polyuria and polydipsia. Genetic testing in familial cases of FNDI should be carry out to ensure adequate treatments and avoid disease manifestations especially in infants. Methods In this study, we investigated three-generations of a large Italian family with clinical diagnosis of familial central diabetes insipidus for the presence of potential pathogenic mutations in the AVP gene. Results We identified a heterozygous missense mutation (c.154 T > A; p.C52S) in AVP gene in all affected members studied of a large Italian family. In silico tools were used to investigate the pathogenic role of the mutation and three-dimensional protein structure predicted that the p.C52S impairs disulfide bridges formation resulting in misfolding of the protein. Conclusions This is the first study that identified a novel missense p.C52S mutation as causative of central diabetes insipidus in a large Italian pedigree. © 2021, The Author(s)
miRNA Targets: From Prediction Tools to Experimental Validation
Full text linkMicroRNAs (miRNAs) are post-transcriptional regulators of gene expression in both animals and plants. By pairing to microRNA responsive elements (mREs) on target mRNAs, miRNAs play gene-regulatory roles, producing remarkable changes in several physiological and pathological processes. Thus, the identification of miRNA-mRNA target interactions is fundamental for discovering the regulatory network governed by miRNAs. The best way to achieve this goal is usually by computational prediction followed by experimental validation of these miRNA-mRNA interactions. This review summarizes the key strategies for miRNA target identification. Several tools for computational analysis exist, each with different approaches to predict miRNA targets, and their number is constantly increasing. The major algorithms available for this aim, including Machine Learning methods, are discussed, to provide practical tips for familiarizing with their assumptions and understanding how to interpret the results. Then, all the experimental procedures for verifying the authenticity of the identified miRNA-mRNA target pairs are described, including High-Throughput technologies, in order to find the best approach for miRNA validation. For each strategy, strengths and weaknesses are discussed, to enable users to evaluate and select the right approach for their interests. © 2020 by the authors
Editorial: Non-Syndromic Familial Non-Medullary Thyroid Carcinoma: Clinical and Genetic Update
Full text linkClinical significance of type 2 iodothyronine deiodinase polymorphism
No full textIntroduction: Biological activity of thyroid hormones (TH) is regulated by enzymes known as deiodinases. The most important is represented by the type 2 deiodinase (D2), which is the main T4-activating enzyme, ubiquitous in human tissues and therefore essential in many metabolic processes. A single nucleotide polymorphism (SPN) of D2, known as Thr92Ala (rs225014), has been reported in the general population while other polymorphisms are less frequently described. Areas covered: Several authors investigated the potential metabolic effect of these polymorphisms in the general population and in specific groups of patients. Thr92Ala polymorphism was mainly studied in patients with autoimmune or surgical hypothyroidism and in patients with physical/psychological disorders that could be related to an overt hypothyroidism. Susceptibility to develop more severe type 2 diabetes or insulin resistance has also been evaluated. Commentary: There is an increasing evidence that the presence of D2 polymorphisms may play a pivotal role in a better definition and customized therapeutic approach of patients with hypothyroidism and/or type 2 diabetes, suggesting that these patients should be screened for D2 polymorphisms. Nevertheless, further research should be performed in order to clarify the association between D2 polymorphisms, metabolic alterations and clinical conditions of the carrier patients
Familial non-medullary thyroid cancer: a critical review
Full text linkBackground: Familial non-medullary thyroid carcinoma (FNMTC), mainly of papillary histotype (FPTC), is defined by the presence of the disease in two or more first-degree relatives in the absence of other known familial syndromes. With the increasing incidence of PTC in the recent years, the familial form of the disease has also become more common than previously reported and constitutes nearly 10% of all thyroid cancers. Many aspects of FNMTC are debated, concerning both clinical and genetic aspects. Several studies reported that, in comparison with sporadic PTCs, FPTCs are more aggressive at disease presentation, while other authors reported no differences in the clinical behavior of sporadic and familial PTCs. For this reason, recent guidelines do not recommend screening of family members of patients with diagnosis of differentiated thyroid cancer (DTC). FNMTC is described as a polygenic disorder associated with multiple low- to moderate-penetrance susceptibility genes and incomplete penetrance. At the moment, the genetic factors contributing to the development of FNMTC remain poorly understood, though many putative genes have been proposed in the recent years. Purpose: Based on current literature and our experience with FNMTC, in this review, we critically discussed the most relevant controversies, including its definition, the genetic background and some clinical aspects as screening and treatment
Telomeres and thyroid cancer
No full textTelomeres are specialized structures at the ends of chromosomes, consisting of hundreds of repeated hexanucleotides (TTAGGG)n. Genetic integrity is partly maintained by the architecture of telomeres and it is gradually lost as telomeres progressively shorten with each cell replication, due to incomplete lagging DNA strand synthesis and oxidative damage. Telomerase is a reverse transcriptase enzyme that counteracts telomere shortening by adding telomeric repeats to the G-rich strand. It is composed of a telomerase RNA component and a protein component, telomerase reverse transcriptase. In the absence of telomerase or when the activity of the enzyme is low compared to the replicative erosion, apoptosis is triggered. Patients who have inherited genetic defects in telomere maintenance seem to have an increased risk of developing familial benign diseases or malignant diseases. At the somatic level, telomerase is reactivated in the majority of human carcinomas, suggesting that telomerase reactivation is a critical step for cancerogenesis.
In sporadic thyroid carcinoma telomerase activity is detectable in nearly 50% of thyroid cancer tissues and some authors proposed that the detection of telomerase activity may be used for differentiating between benign and malignant thyroid tumours. Recently a germline alteration of telomere-telomerase complex has been identified in patients with familial papillary thyroid cancer, characterized by short telomeres and increased expression and activity of telomerase compared to patients with sporadic papillary thyroid cancer.
In this report, we will review the role of telomere-telomerase complex in sporadic and familial thyroid cancer
HABP2 G534E variation in familial non-medullary thyroid cancer: an Italian series
No full textIntroduction: Thyroid cancer may have a familial predisposition and may occur in the context of hereditary syndromes or as isolated tumor. Recently, the G534E variant in the HABP2 gene has been suggested as causative mutation for familial thyroid cancer, but other studies gave contradictory results. Methods: We have analyzed the G534E variant in an Italian series of 63 familial thyroid cancer patients and 41 unaffected family members with end-point PCR, DHPLC and direct sequencing. Results: All samples analyzed displayed a pattern typical of the homozygous wild type revealing the absence of the G534E variant. Conclusion: In this study, HABP2 G534E variant is not correlated with the familial form of PTC
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