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Neurodegenerative Disease: From Molecular Basis to Therapy, 3rd Edition
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Neurodegenerative Disease: From Molecular Basis to Therapy, 3rd Edition

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: 31 January 2025 | Viewed by 954

Special Issue Editor

Dr. Claudia Ricci

E-Mail Website
Guest Editor
Department of Medical, Surgical and Neurological Sciences, University of Siena, Siena, Italy
Interests: molecular biology; neurogenetics; motor neuron diseases; amyotrophic lateral sclerosis; gene variants; gene regulation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Neurodegenerative diseases are a heterogeneous group of disorders, largely age-dependent, affecting the central nervous system and eventually leading to neurodegeneration. The prevalence of these diseases is increasing, partly due to the aging population, with a consequent growing economic burden on healthcare systems. The current treatments are mostly symptomatic, without affecting the underlying cause of disease, and have no or only slight effects on disease progression.

Recent advancements in neurobiology and neurogenetics have provided valuable insights into the pathogenesis of neurodegenerative diseases. This has paved the way for the development of molecularly targeted therapies, which are able to pause or slow the fundamental pathological processes that cause neuronal damage and consequent cognitive and motor dysfunctions. In some cases, neurodegenerative diseases are caused by genetic variants and/or cellular pathway dysregulation. Some mechanisms common to several neurodegenerative conditions have been identified, such as the presence of misfolded protein aggregates, the abnormal accumulation of proteins, RNA toxicity, or translational products from the expansion of repeats within genes. As advances are made in understanding critical aspects of the underlying molecular pathophysiology, therapeutic strategies continue to evolve. Among these, gene therapy is attracting great interest due to the possibility to deliver functional genetic material to cells to correct a defective gene.

This Special Issue aims to provide an updated overview of the advancements in the research on neurodegenerative diseases, from the understanding of the molecular bases to the development of new therapies. Contributions related but not limited to Alzheimer's disease and other types of dementia, Parkinson's disease and motor neuron diseases are welcome, including original research articles and full and short reviews.

Dr. Claudia Ricci
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • neurodegenerative diseases
  • molecular biology
  • neurogenetics
  • pathogenesis
  • therapy
  • personalized medicine

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Published Papers (1 paper)

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Research

24 pages, 3265 KiB  
Article
A Map of Transcriptomic Signatures of Different Brain Areas in Alzheimer’s Disease
by Riccardo Rocco Ferrari, Valentina Fantini, Maria Garofalo, Rosalinda Di Gerlando, Francesca Dragoni, Bartolo Rizzo, Erica Spina, Michele Rossi, Chiara Calatozzolo, Xhulja Profka, Mauro Ceroni, Antonio Guaita, Annalisa Davin, Stella Gagliardi and Tino Emanuele Poloni
Int. J. Mol. Sci. 2024, 25(20), 11117; https://doi.org/10.3390/ijms252011117 - 16 Oct 2024
Viewed by 670
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder that progressively involves brain regions with an often-predictable pattern. Damage to the brain appears to spread and worsen with time, but the molecular mechanisms underlying the region-specific distribution of AD pathology at different stages of the [...] Read more.
Alzheimer’s disease (AD) is a neurodegenerative disorder that progressively involves brain regions with an often-predictable pattern. Damage to the brain appears to spread and worsen with time, but the molecular mechanisms underlying the region-specific distribution of AD pathology at different stages of the disease are still under-investigated. In this study, a whole-transcriptome analysis was carried out on brain samples from the hippocampus (HI), temporal and parietal cortices (TC and PC, respectively), cingulate cortex (CG), and substantia nigra (SN) of six subjects with a definite AD diagnosis and three healthy age-matched controls in duplicate. The transcriptomic results showed a greater number of differentially expressed genes (DEGs) in the TC (1571) and CG (1210) and a smaller number of DEGs in the HI (206), PC (109), and SN (60). Furthermore, the GSEA showed a difference between the group of brain areas affected early (HI and TC) and the group of areas that were subsequently involved (PC, CG, and SN). Notably, in the HI and TC, there was a significant downregulation of shared DEGs primarily involved in synaptic transmission, while in the PC, CG, and SN, there was a significant downregulation of genes primarily involved in protein folding and trafficking. The course of AD could follow a definite time- and severity-related pattern that arises from protein misfolding, as observed in the PC, CG, and SN, and leads to synaptic impairment, as observed in the HI and TC. Therefore, a map of the molecular and biological processes involved in AD pathogenesis may be traced. This could aid in the discovery of novel biological targets in order to develop effective and well-timed therapeutic approaches. Full article
(This article belongs to the Special Issue Neurodegenerative Disease: From Molecular Basis to Therapy, 3rd Edition)
►▼ Show Figures

Figure 1

Figure 1
<p>Hippocampus. (<b>A</b>) PCA of DEGs in the HI of AD subjects in comparison with those of the CTRL subjects; AD subjects and CTRL subjects were separated into two distinct groups, suggesting a substantial difference between the two groups from a statistical point of view. (<b>B</b>) Volcano plot of DEGs between AD and CTRL subjects. Genes were plotted in order to emphasize both statistical significance (<span class="html-italic">p</span>-value) and magnitude of change (Log<sub>2</sub> fold change). Genes whose deregulation was the most statistically significant and that had a large fold change are represented with red dots. (<b>C</b>) GO-enriched terms in the HI of AD vs. CTRL for biological processes, molecular functions (<b>D</b>), and cellular components (<b>E</b>). The dots in each category may vary in color and dimension; a color that tends toward red indicates a higher statistical significance, while large dots indicate a higher number of genes of that specific enrichment term that were deregulated in the analyzed sample in comparison with the original GO classification.</p> Full article ">Figure 2
<p>Temporal cortex. (<b>A</b>) PCA of DEGs in the TC of AD subjects in comparison with CTRL subjects. AD subjects and CTRL subjects were separated into two distinct groups, suggesting a substantial difference between the two groups from a statistical point of view. (<b>B</b>) Volcano plot of DEGs between AD and CTRL subjects. Genes were plotted in order to emphasize both statistical significance (<span class="html-italic">p</span>-value) and magnitude of change (Log<sub>2</sub> fold change). Genes whose deregulation was most statistically significant and that had a large fold change are represented by red dots; (<b>C</b>) GO-enriched terms in the TC of AD vs. CTRL for biological processes, molecular functions (<b>D</b>), and cellular components (<b>E</b>). The dots in each category may vary in color and dimension; a color that tends toward red indicates greater statistical significance, while large dots indicate a higher number of genes of that specific enrichment term that were deregulated in the analyzed sample in comparison with the original GO classification.</p> Full article ">Figure 3
<p>Parietal cortex. (<b>A</b>) PCA of DEGs in the PC of AD subjects in comparison with CTRL subjects. In this case, the separation between AD subjects and CTRL subjects was less defined, suggesting a minor difference between the two groups from a statistical point of view. (<b>B</b>) Volcano plot of DEGs between AD and CTRL subjects. Genes were plotted in order to emphasize both statistical significance (<span class="html-italic">p</span>-value) and the magnitude of change (Log<sub>2</sub> fold change). Genes whose deregulation was most statistically significant and those with a large fold change are represented by red dots. (<b>C</b>) Interaction network for the PC obtained through STRING. The two nodes are represented by <span class="html-italic">HSPH1</span> and <span class="html-italic">DNAJB1</span>. Interactions between the two nodes were determined using curated datasets and experimental determinations. (<b>D</b>) GO-enriched terms in the PC of AD vs. CTRL for biological processes, molecular functions (<b>E</b>), and cellular components (<b>F</b>). The dots in each category may vary in color and dimension; a color that tends toward red indicates a greater statistical significance, while large dots indicate a higher number of genes of that specific enrichment term that were deregulated in the analyzed sample in comparison with the original GO classification. In this case, the reduced number of DEGs observed in the PC resulted in a less defined enrichment analysis with a minor degree of statistical significance.</p> Full article ">Figure 4
<p>Cingulate gyrus. (<b>A</b>) PCA of DEGs in the CG of AD subjects compared with the CTRL subjects. In this case, the separation between AD subjects and CTRL subjects was less defined, suggesting a minor difference between the two groups from a statistical point of view. (<b>B</b>) Volcano plot of DEGs between the AD and CTRL subjects. Genes were plotted in order to emphasize both statistical significance (<span class="html-italic">p</span>-value) and the magnitude of change (Log<sub>2</sub> fold change). Genes whose deregulation was most statistically significant and those that had a large fold change are represented by red dots. (<b>C</b>) GO-enriched terms in the CG of AD vs. CTRL for biological processes, molecular functions (<b>D</b>), and cellular components (<b>E</b>). Dots in each category may vary in color and dimension; a color that tends toward red indicates a higher statistical significance, while large dots indicate a higher number of genes of that specific enrichment term that were deregulated in the analyzed sample in comparison with the original GO classification.</p> Full article ">Figure 5
<p>Substantia nigra. (<b>A</b>) PCA of DEGs in the SN of AD subjects in comparison with CTRL subjects. AD subjects and CTRL subjects were separated into two distinct groups, suggesting a substantial difference between the two groups from a statistical point of view. (<b>B</b>) Volcano plot of DEGs between the AD and CTRL subjects. Genes were plotted in order to emphasize both statistical significance (<span class="html-italic">p</span>-value) and the magnitude of change (Log<sub>2</sub> fold change). Genes whose deregulation was most statistically significant and those that had a large fold change are represented by red dots. (<b>C</b>) GO-enriched terms in the SN of AD vs. CTRL for biological processes, molecular functions (<b>D</b>), and cellular components (<b>E</b>). Dots in each category may vary in color and dimension; a color that tends toward red indicates a higher statistical significance, while large dots indicate a higher number of genes of that specific enrichment term that were deregulated in the analyzed sample in comparison with the original GO classification.</p> Full article ">Figure 6
<p>Brain areas of AD subjects were clustered according to the deregulation of the same class of enrichment terms. (<b>A</b>) Venn diagram of DEGs across the analyzed brain areas in AD subjects. The selection of DEGs was made by considering protein-coding genes with an adjusted <span class="html-italic">p</span> value of ≤0.05. The Venn diagrams referring to the overlapping of GO enrichment terms resulted from the STRING functional enrichment analysis: (<b>B</b>) GO biological process terms; (<b>C</b>) GO molecular function terms; and (<b>D</b>) GO cellular component terms.</p> Full article ">
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