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Molecular Progression of Genome-Related Diseases

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 30 May 2024 | Viewed by 3216

Special Issue Editors


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Guest Editor
Department Biological, Geological and Environmental Sciences, University of Catania, 95124 Catania, Italy
Interests: genetics; genomics; molecular cytogenetics; chromosomes; nuclear chromatin organization; evolutionary genetics; developmental genetics; forensic genetics; environmental mutagenesis; epigenetics
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Oasi Research Institute—IRCCS, Via Conte Ruggero 73, 94018 Troina, Italy
Interests: Mendelian diseases; neurological diseases; population genetics

Special Issue Information

Dear Colleagues,

Advancements in genomic technologies, such as next-generation sequencing, have revolutionized our ability to unravel the molecular basis of genome-related diseases. By analyzing genetic variations and mutations, the key genes and pathways involved in the development of several diseases have been identified. This knowledge has not only facilitated accurate diagnosis and personalized medicine but also opened avenues for innovative therapies targeting specific genetic aberrations. Our current capacity to rapidly analyze entire exome and genome sequences at an affordable cost has the potential to yield greater benefits, supporting the genetic investigation of complex diseases and generating opportunities which may arise from examining specific and distinct phenotypes.

Despite these significant strides, challenges remain, including the complexity of some genetic diseases and the need for more comprehensive databases to catalog genetic variants and their clinical implications. The definition of gene panels to analyze with NGS for diagnostic purposes is certainly a relevant subject in human health, considering the various diseases with a genetic basis of increasing interest such as, but not limited to, neurological or neuromuscular disorders, cardiomyopathies, and hereditary cancer syndromes and hematological disorders.

For this Special Issue, we invite researchers in the field to publish reviews or original research papers covering recent advances in the use of gene panels to detect mutations/variants related to the diagnosis of complex genetic diseases and improvements related to new tools for genomic analysis. Our aim is to have a Special Issue that presents up-to-date information on genomic analysis systems for complex genetic diseases and serves as a reference to researchers in the field and users of these technologies for diagnostic purposes.

Prof. Dr. Salvatore Saccone
Dr. Francesco Calì
Guest Editors

Manuscript Submission Information

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Keywords

  • next-generation sequencing
  • genetic diseases
  • multifactorial diseases
  • diagnostic tolls
  • human health

Published Papers (4 papers)

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Research

19 pages, 4565 KiB  
Article
Novel Acetamide-Based HO-1 Inhibitor Counteracts Glioblastoma Progression by Interfering with the Hypoxic–Angiogenic Pathway
by Agata Grazia D’Amico, Grazia Maugeri, Luca Vanella, Valeria Consoli, Valeria Sorrenti, Francesca Bruno, Concetta Federico, Antonino Nicolò Fallica, Valeria Pittalà and Velia D’Agata
Int. J. Mol. Sci. 2024, 25(10), 5389; https://doi.org/10.3390/ijms25105389 - 15 May 2024
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Abstract
Glioblastoma multiforme (GBM) represents the deadliest tumor among brain cancers. It is a solid tumor characterized by uncontrolled cell proliferation generating the hypoxic niches in the cancer core. By inducing the transcription of hypoxic inducible factor (HIF), hypoxia triggers many signaling cascades responsible [...] Read more.
Glioblastoma multiforme (GBM) represents the deadliest tumor among brain cancers. It is a solid tumor characterized by uncontrolled cell proliferation generating the hypoxic niches in the cancer core. By inducing the transcription of hypoxic inducible factor (HIF), hypoxia triggers many signaling cascades responsible for cancer progression and aggressiveness, including enhanced expression of vascular endothelial growth factor (VEGF) or antioxidant enzymes, such as heme oxygenase-1 (HO-1). The present work aimed to investigate the link between HO-1 expression and the hypoxic microenvironment of GBM by culturing two human glioblastoma cell lines (U87MG and A172) in the presence of a hypoxic mimetic agent, deferoxamine (DFX). By targeting hypoxia-induced HO-1, we have tested the effect of a novel acetamide-based HO-1 inhibitor (VP18/58) on GBM progression. Results have demonstrated that hypoxic conditions induced upregulation and nuclear expression of HO-1 in a cell-dependent manner related to malignant phenotype. Moreover, our data demonstrated that the HO-1 inhibitor counteracted GBM progression by modulating the HIFα/HO-1/VEGF signaling cascade in cancer cells bearing more malignant phenotypes. Full article
(This article belongs to the Special Issue Molecular Progression of Genome-Related Diseases)
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13 pages, 1399 KiB  
Article
APOE ε2-Carriers Are Associated with an Increased Risk of Primary Angle-Closure Glaucoma in Patients of Saudi Origin
by Altaf A. Kondkar, Taif A. Azad, Tahira Sultan, Tanvir Khatlani, Abdulaziz A. Alshehri, Rakesh Radhakrishnan, Glenn P. Lobo, Ehab Alsirhy, Faisal A. Almobarak, Essam A. Osman and Saleh A. Al-Obeidan
Int. J. Mol. Sci. 2024, 25(8), 4571; https://doi.org/10.3390/ijms25084571 - 22 Apr 2024
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Abstract
This study investigated the association between apolipoprotein E (APOE) gene polymorphisms (rs429358 and rs7412) and primary angle-closure glaucoma (PACG) and pseudoexfoliation glaucoma (PXG) in a Saudi cohort. Genotyping of 437 DNA samples (251 controls, 92 PACG, 94 PXG) was conducted using [...] Read more.
This study investigated the association between apolipoprotein E (APOE) gene polymorphisms (rs429358 and rs7412) and primary angle-closure glaucoma (PACG) and pseudoexfoliation glaucoma (PXG) in a Saudi cohort. Genotyping of 437 DNA samples (251 controls, 92 PACG, 94 PXG) was conducted using PCR-based Sanger sequencing. The results showed no significant differences in the allele and genotype frequencies of rs429358 and rs7412 between the PACG/PXG cases and controls. Haplotype analysis revealed ε3 as predominant, followed by ε4 and ε2 alleles, with no significant variance in PACG/PXG. However, APOE genotype analysis indicated a significant association between ε2-carriers and PACG (odds ratio = 4.82, 95% CI 1.52–15.26, p = 0.007), whereas no notable association was observed with PXG. Logistic regression confirmed ε2-carriers as a significant predictor for PACG (p = 0.008), while age emerged as significant for PXG (p < 0.001). These findings suggest a potential role of ε2-carriers in PACG risk within the Saudi cohort. Further validation and larger-scale investigations are essential to elucidate the precise role of APOE in PACG pathogenesis and progression. Full article
(This article belongs to the Special Issue Molecular Progression of Genome-Related Diseases)
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18 pages, 2274 KiB  
Article
Whole Exome Sequencing as a First-Line Molecular Genetic Test in Developmental and Epileptic Encephalopathies
by Luigi Vetri, Francesco Calì, Salvatore Saccone, Mirella Vinci, Natalia Valeria Chiavetta, Marco Carotenuto, Michele Roccella, Carola Costanza and Maurizio Elia
Int. J. Mol. Sci. 2024, 25(2), 1146; https://doi.org/10.3390/ijms25021146 - 17 Jan 2024
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Abstract
Developmental and epileptic encephalopathies (DEE) are severe neurodevelopmental disorders characterized by recurrent, usually early-onset, epileptic seizures accompanied by developmental impairment often related to both underlying genetic etiology and abnormal epileptiform activity. Today, next-generation sequencing technologies (NGS) allow us to sequence large portions of [...] Read more.
Developmental and epileptic encephalopathies (DEE) are severe neurodevelopmental disorders characterized by recurrent, usually early-onset, epileptic seizures accompanied by developmental impairment often related to both underlying genetic etiology and abnormal epileptiform activity. Today, next-generation sequencing technologies (NGS) allow us to sequence large portions of DNA quickly and with low costs. The aim of this study is to evaluate the use of whole-exome sequencing (WES) as a first-line molecular genetic test in a sample of subjects with DEEs characterized by early-onset drug-resistant epilepsies, associated with global developmental delay and/or intellectual disability (ID). We performed 82 WESs, identifying 35 pathogenic variants with a detection rate of 43%. The identified variants were highlighted on 29 different genes including, 3 new candidate genes (KCNC2, STXBP6, DHRS9) for DEEs never identified before. In total, 23 out of 35 (66%) de novo variants were identified. The most frequently identified type of inheritance was autosomal dominant de novo (60%) followed by autosomal recessive in homozygosity (17%) and heterozygosity (11%), autosomal dominant inherited from parental mosaicism (6%) and X-linked dominant de novo (6%). The most frequent mutations identified were missense (75%) followed by frameshift deletions (16%), frameshift duplications (5%), and splicing mutations (3%). Considering the results obtained in the present study we support the use of WES as a form of first-line molecular genetic testing in DEEs. Full article
(This article belongs to the Special Issue Molecular Progression of Genome-Related Diseases)
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12 pages, 5257 KiB  
Article
STXBP6 Gene Mutation: A New Form of SNAREopathy Leads to Developmental Epileptic Encephalopathy
by Mirella Vinci, Carola Costanza, Rosanna Galati Rando, Simone Treccarichi, Salvatore Saccone, Marco Carotenuto, Michele Roccella, Francesco Calì, Maurizio Elia and Luigi Vetri
Int. J. Mol. Sci. 2023, 24(22), 16436; https://doi.org/10.3390/ijms242216436 - 17 Nov 2023
Cited by 2 | Viewed by 939
Abstract
Syntaxin-binding protein 6 (STXBP6), also known as amysin, is an essential component of the SNAP receptor (SNARE) complex and plays a crucial role in neuronal vesicle trafficking. Mutations in genes encoding SNARE proteins are often associated with a broad spectrum of neurological conditions [...] Read more.
Syntaxin-binding protein 6 (STXBP6), also known as amysin, is an essential component of the SNAP receptor (SNARE) complex and plays a crucial role in neuronal vesicle trafficking. Mutations in genes encoding SNARE proteins are often associated with a broad spectrum of neurological conditions defined as “SNAREopathies”, including epilepsy, intellectual disability, and neurodevelopmental disorders such as autism spectrum disorders. The present whole exome sequencing (WES) study describes, for the first time, the occurrence of developmental epileptic encephalopathy and autism spectrum disorders as a result of a de novo deletion within the STXBP6 gene. The truncated protein in the STXBP6 gene leading to a premature stop codon could negatively modulate the synaptic vesicles’ exocytosis. Our research aimed to elucidate a plausible, robust correlation between STXBP6 gene deletion and the manifestation of developmental epileptic encephalopathy. Full article
(This article belongs to the Special Issue Molecular Progression of Genome-Related Diseases)
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