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Advanced Molecular Diagnostic Approaches for Neurodevelopmental Disorders: Applications and Future Perspectives

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

Deadline for manuscript submissions: closed (20 April 2026) | Viewed by 7877

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Dr. Barbara Lombardo

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Guest Editor

Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", 80131 Napoli, Italy
Interests: genetic; biochemistry; molecular biology; neurodevelopmental disorders; array CGH and NGS
Special Issues, Collections and Topics in MDPI journals

Dr. Michele Pinelli

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Department of Molecular Medicine and Medical Biotechnology, University Federico II, 80131 Naples, Italy
Interests: human genetic; medical genetics; rare disease; genomics; next generation sequencing; mutation

Special Issue Information

Dear Colleagues,

In recent years, molecular diagnostic technologies, such as array CGH and NGS, have become more important in the clinical field thanks to the availability of highly sensitive, which allow to detect molecular alterations with a higher resolution, accuracy, and specificity. Since it has been demonstrated a strong genetic basis for neurodevelopmental disorders (NDDs), research of this condition as improved. The application of these advanced methods for patients with NDDs could provide interesting insights into their pathophysiology, the relationship between specific molecular findings and various symptom domains, suggesting the presence of shared molecular pathways underlying specific clinical signs. This would allow to explain the comorbidity of these conditions and could open new avenues to identify possible new molecular targets. In this perspective, therefore, could be better to understand and define not only the mechanisms underlying the onset of the disease, but also to design new therapeutic strategies.

Dr. Barbara Lombardo
Dr. Michele Pinelli
Guest Editors

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Keywords

neurodevelopmental disorders
array CGH
NGS

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Published Papers (5 papers)

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Research

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17 pages, 466 KB

Open AccessArticle

Using Whole Exome Sequencing to Identify Genetic Causes of Neurodevelopmental Disorders in a Cohort of 11 Patients: A Single Center Experience

by Marton Tompa, Gabriella Sinko, Judit Mally, Judit Karteszi and Bernadette Kalman

Int. J. Mol. Sci. 2025, 26(20), 10176; https://doi.org/10.3390/ijms262010176 - 20 Oct 2025

Viewed by 1744

Abstract

Neurodevelopmental disorders (NDDs) represent a heterogeneous group of diseases with a variety of clinical presentations related to different genetic, epigenetic, and environmental etiologies. Numerous pathogenic variants have been identified by comprehensive genetic approaches such as next-generation sequencing and chromosomal microarray analyses. This study included eleven pediatric patients with NDDs who were referred to our Molecular Medicine (MM) unit for further diagnostic workup. Whole exome sequencing (WES) was performed, and data were analyzed as part of a contracted service with the National Genomic Center and iBioScience LTD. Likely pathogenic single nucleotide variants in genes DDX3X c.869C>A, p.S290* and CNOT1 c.920delG, p.G307Afs*32 in two patients, and pathogenic copy number variants in the 16p11.2 (16:29,690,418-30,200,285)x3 and 16p12.1-p11.2 (16:27,078,317-29,001,333)x3 regions in a third patient with NDDs were identified. In a fourth patient, the c.6839A>G, p.Gln2280Arg variant of uncertain significance was found in the NIPBL gene. Altogether, our study has revealed four novel variants in genes previously linked to NDDs. Identification of genetic causes of NDDs not only promotes establishing a more precise diagnosis and improves our understanding of disease pathogenesis but may also provide better means for developing preventive measures for the recurrence of this serious condition. Full article

(This article belongs to the Special Issue Advanced Molecular Diagnostic Approaches for Neurodevelopmental Disorders: Applications and Future Perspectives)

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17 pages, 6847 KB

Open AccessArticle

Genetic and Pathogenic Overlaps Between Autism Spectrum Disorder and Alzheimer’s Disease: Evolutionary Features and Opportunities for Drug Repurposing

by Ekaterina A. Trifonova, Anna A. Pashchenko, Roman A. Ivanov, Alex V. Kochetov and Sergey A. Lashin

Int. J. Mol. Sci. 2025, 26(20), 10066; https://doi.org/10.3390/ijms262010066 - 16 Oct 2025

Cited by 1 | Viewed by 2438

Abstract

Autism spectrum disorder (ASD) and Alzheimer’s disease (AD) are neurodevelopmental and neurodegenerative disorders, respectively. While exome sequencing is routinely employed during the early stages of ASD diagnosis, it rarely influences therapeutic strategies. To address this gap, we have reconstructed and analyzed the gene networks linking autism spectrum disorders, Alzheimer’s disease, and mTOR signaling. In addition, we have performed a phylostratigraphic analysis that reveals similarities and differences in the evolution of both ASD and Alzheimer’s disease predisposition genes. We have shown that almost half of the genes predisposing to autism and two-fifths of the genes predisposing to Alzheimer’s disease are directly related to the mTOR signaling pathway. Analysis of Phylostratigraphic Age Index (PAI) value distributions revealed a significant enrichment of evolutionarily ancient genes in both ASD- and AD-related gene sets. When studying the distribution of ASD predisposition genes by Divergence Index (DI) values, a significant enrichment with genes having extremely low DI = 0 has been found. Such low DI values indicate that most likely these genes are under stabilizing selection. Using the ANDVisio tool, both pharmacological and natural mTOR regulators with potential for ASD treatment were selected, such as propofol, dexamethasone, celecoxib, statins, berberine, resveratrol, quercetin, myricetin, mio-inositol, and several amino acids. Full article

(This article belongs to the Special Issue Advanced Molecular Diagnostic Approaches for Neurodevelopmental Disorders: Applications and Future Perspectives)

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18 pages, 866 KB

Open AccessArticle

BDNF Val66Met Genotype, DNA Methylation, mRNA, and Protein Levels as Potential Blood-Based Biomarkers for Dementia and Cognitive Decline

by Lucija Tudor, Alja Videtic Paska, Marcela Konjevod, Nikola Balic, Matea Nikolac Perkovic, Suzana Uzun, Barbara Vuic, Tina Milos, Gordana Nedic Erjavec, Ninoslav Mimica, Katarina Kouter, Nela Pivac and Dubravka Svob Strac

Int. J. Mol. Sci. 2025, 26(18), 8987; https://doi.org/10.3390/ijms26188987 - 15 Sep 2025

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Abstract

Brain-derived neurotrophic factor (BDNF) plays a crucial role in cognitive functions and dementia. In individuals with mild cognitive impairment (MCI) and dementia, we have investigated BDNF Val66Met genotype distribution, peripheral BDNF DNA methylation, mRNA and protein levels, and cognitive performance using the Mini-Mental State Examination (MMSE) and Clock Drawing Test (CDT). Lower BDNF_IV1 methylation had predictive value for dementia. Patients with mild-to-moderate dementia had lower levels of BDNF_IV2 methylation, whereas patients with severe dementia had higher levels than the MCI group, while BDNF_IV2 methylation positively correlated with CDT scores. An insignificant decline in BDNF mRNA levels in dementia patients positively correlated with significantly lower BDNF plasma levels, especially pronounced in severe dementia patients. BDNF mRNA and protein levels were positively correlated with CDT and MMSE scores, respectively. BDNF Val66Met polymorphism was associated with methylation of the BDNF_IX amplicon, but not with methylation in BDNF promoters I and IV, peripheral BDNF gene and protein expression, MMSE and CDT scores, or dementia. Methylation at the BDNF Val66Met site was positively correlated with overall BDNF_IX methylation and methylation at 5 BDNF_IX CpG loci but negatively correlated with methylation of BDNF_IV1, BDNF_IV3, and BDNF_I1 amplicons. Further studies should evaluate the translational potential of these peripheral BDNF-based biomarkers for dementia. Full article

(This article belongs to the Special Issue Advanced Molecular Diagnostic Approaches for Neurodevelopmental Disorders: Applications and Future Perspectives)

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Review

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27 pages, 2799 KB

Open AccessReview

The Regulatory Potential of Long Non-Coding RNAs in Bipolar Disorder

by Siqi Li, Yuhan Fu, Zhenzhen Wang, Yan Zhang, Tao Sun and Nan Miao

Int. J. Mol. Sci. 2026, 27(7), 3099; https://doi.org/10.3390/ijms27073099 - 28 Mar 2026

Viewed by 693

Abstract

Bipolar disorder (BD) is characterized by mood swings between mania and depression, sharing overlapping symptomatic and genetic risk factors with other mood disorders. Long non-coding RNAs (lncRNAs) show specific spatiotemporal precision in distinct cell types in the human brain, and understanding the precise mechanisms of lncRNAs in mood switching in BD is fundamental to deciphering the key molecular networks underlying BD diagnosis and therapy. In this review, we summarize the classification of BD subtypes, the differences between BD and multiple mood disorders, and the functional potential of lncRNAs in BD. Future studies of these lncRNAs will facilitate the development of RNA-based diagnosis for BD. Full article

(This article belongs to the Special Issue Advanced Molecular Diagnostic Approaches for Neurodevelopmental Disorders: Applications and Future Perspectives)

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42 pages, 4069 KB

Open AccessReview

Regeneration-Associated Factors in the Regulation of Adult and Post-Traumatic Neurogenesis in the Forebrain of Fish and Other Vertebrates

by Evgeniya V. Pushchina and Eva I. Zharikova

Int. J. Mol. Sci. 2026, 27(1), 247; https://doi.org/10.3390/ijms27010247 - 25 Dec 2025

Viewed by 689

Abstract

This review summarizes a growing collection of data on adult neurogenesis in various vertebrate species, with a focus on teleost fish and mammals. Teleost fish serve as exceptional models for studying the dynamics of the cell cycle and the functions of adult neural stem progenitor cells (aNSPCs) throughout the central nervous system (CNS). New information about the characteristics of cells in various areas of the telencephalon of non-model objects—juvenile masu salmon Oncorhynchus masou and chum salmon Oncorhynchus keta—during postembryonic ontogenesis and after traumatic injury expands the current understanding of the issue. The expression of molecular markers of adult-type glial precursors in the model zebrafish and non-model objects, juveniles O. masou and O. keta, was presented. Immunohistochemical (IHC) verification of BrdU and PCNA made it possible to identify a population of rapidly and slowly proliferating cells in the pallium of intact O. masou and after traumatic brain injury (TBI). In salmonids, unlike in mammals, progenitor cells are able to differentiate into neurons after injury. The expression of vimentin and GFAP in the aNSCPs has functional specificity. A comparative analysis of the expression of Pax transcription factors in various vertebrates and juveniles O. masou is presented. Pax genes maintain cells in an undifferentiated state and ensure the spatiotemporal formation of mature cell types in changing developing neurogenic niches. The functions of glutamine synthetase (GS) and H₂S in the brains of vertebrates and juvenile chum salmon under intact conditions and after TBI are characterized. In fish, unlike mammals, as a result of TBI, neuronal conduction is restored in the injury area, whereas in mammals the regenerative process is complicated by neuroinflammation and culminates in the formation of a glial scar. Full article

(This article belongs to the Special Issue Advanced Molecular Diagnostic Approaches for Neurodevelopmental Disorders: Applications and Future Perspectives)

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