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Biomedicines
Special Issues
Cellular and Molecular Biology of Neurodegenerative Disorders
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Cellular and Molecular Biology of Neurodegenerative Disorders

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Neurobiology and Clinical Neuroscience".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 4948

Special Issue Editor

Dr. Marta Lualdi

E-Mail Website
Guest Editor
Department of Science and High Technology, University of Insubria, 22100 Como, Italy
Interests: biochemistry; proteomics; systems biology; neurodegeneration; mitochondrial biology; parkinson’s disease
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

I am glad to share with you that I am working as a Guest Editor of the Special Issue entitled “Cellular and Molecular Biology of Neurodegenerative Disorders” in the open access journal Biomedicines. The present topic aims to publish original research articles and reviews in which neurodegenerative diseases are studied at the level of their underlying mechanisms. The major challenge in neurodegeneration research is to find strategies that can contribute to achieving early diagnosis, patients’ classification and stratification, and the development of disease-modifying therapeutic approaches. In this frame, one main objective is to unveil the complex network of cellular and molecular mechanisms that trigger disease onset and progression. Omics techniques, being unbiased and global, represent the most promising strategy to overcome this complexity, also through the use of bioinformatic tools for omics data integration within a “systems biology” perspective.

Dr. Marta Lualdi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Biomedicines is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • neurodegeneration
  • omics
  • biomarkers
  • systems biology
  • disease-modifying therapies

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Review

34 pages, 1583 KiB  
Review
Proteins Associated with Neurodegenerative Diseases: Link to DNA Repair
by Svetlana N. Khodyreva, Nadezhda S. Dyrkheeva and Olga I. Lavrik
Biomedicines 2024, 12(12), 2808; https://doi.org/10.3390/biomedicines12122808 - 11 Dec 2024
Viewed by 1231
Abstract
The nervous system is susceptible to DNA damage and DNA repair defects, and if DNA damage is not repaired, neuronal cells can die, causing neurodegenerative diseases in humans. The overall picture of what is known about DNA repair mechanisms in the nervous system [...] Read more.
The nervous system is susceptible to DNA damage and DNA repair defects, and if DNA damage is not repaired, neuronal cells can die, causing neurodegenerative diseases in humans. The overall picture of what is known about DNA repair mechanisms in the nervous system is still unclear. The current challenge is to use the accumulated knowledge of basic science on DNA repair to improve the treatment of neurodegenerative disorders. In this review, we summarize the current understanding of the function of DNA damage repair, in particular, the base excision repair and double-strand break repair pathways as being the most important in nervous system cells. We summarize recent data on the proteins involved in DNA repair associated with neurodegenerative diseases, with particular emphasis on PARP1 and ND-associated proteins, which are involved in DNA repair and have the ability to undergo liquid–liquid phase separation. Full article
(This article belongs to the Special Issue Cellular and Molecular Biology of Neurodegenerative Disorders)
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Figure 1

Figure 1
<p>DNA repair pathways and typical repaired lesions (italicized).</p> Full article ">Figure 2
<p>Base excision repair (BER) mechanisms. Base excision repair is performed by short patch (SP-BER) or long patch (LP-BER). Damaged bases are removed by monofunctional (UNG, TDG, SMUG1, MBD4, MPG, MUTYH) and bifunctional (NTH1, OGG1, NEIL1, NEIL2, NEIL3) DNA glycosylases. AP (apurinic/apyrimidinic) sites remaining after the action of monofunctional glycosylases are incised by apurinic/apyrimidinic endonuclease 1 (APE1). dRP (5′ deoxyribose phosphate) is removed by the 5′dRP lyase activity of DNA polymerase β (Polβ), followed by Polβ-catalysed incorporation of a dNMP (SP-BER). The resulting nick is sealed by DNA ligase 3 (Lig3)-XRCC1. Oxidized DNA bases are processed by bifunctional DNA glycosylases, which remove the base and cut into the DNA backbone, creating the nick with 3′ α,β-4-hydroxypentene-2-al (PUA) or phosphate (P). The 3′ PUA residue and the 3′ P group are removed by APE1 and polynucleotide kinase phosphatase (PNKP), respectively. In LP-BER, a 2 to 13 nucleotide patch is synthesized by Polδ/ε (or Polβ) with the assistance of PCNA. A resulting 5′ flap is removed by flap endonuclease 1 (FEN1), and the final ligation step is performed by DNA ligase 1 (Lig1). Red arrow indicates the newly incorporated nucleotide(s); red and yellow ovals indicate the damaged base and AP site, respectively.</p> Full article ">Figure 3
<p><b>Nonhomologous end-joining (NHEJ) mechanisms</b>. NHEJ occurs via classical (C-NHEJ) or alternative (Alt-NHEJ) pathways. Alt-NHEJ is subdivided into microhomology-mediated end-joining (MMEJ) and single-strand annealing (SSA) pathways. In C-NHEJ, DSB recognition is carried out by the Ku70/Ku80 protein, followed by recruitment of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs), PNKP, and nucleases (WRN or Artemis) or tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA polymerases (Polμ or Polλ) to process the ends as required. DNA ligase 4 (Lig4) rejoins DNA ends in the presence of XRCC4, XLF/Cernunnos proteins. In MMEJ, PARP1 performs recognition and recruits MRN (Mre11/Rad50/Nbs1) and CtIP for short-end resection. After microhomology-mediated annealing of the DNA chains, ERCC1/XPF nuclease trims the gaps. Gaps are filled by Polθ or Polβ, and nicks are sealed by Lig1 or Lig3/XRCC1. In SSA, after long-end resection, RAD52-mediated annealing and ERCC1/XPF-mediated flap trimming followed by DNA synthesis (Polθ), Lig1 seals the nicks. Red arrows indicate unpaired regions of DNA strands.</p> Full article ">
21 pages, 1871 KiB  
Review
Role of Microbiota-Derived Hydrogen Sulfide (H2S) in Modulating the Gut–Brain Axis: Implications for Alzheimer’s and Parkinson’s Disease Pathogenesis
by Constantin Munteanu, Gelu Onose, Mariana Rotariu, Mădălina Poștaru, Marius Turnea and Anca Irina Galaction
Biomedicines 2024, 12(12), 2670; https://doi.org/10.3390/biomedicines12122670 - 23 Nov 2024
Viewed by 1505
Abstract
Microbiota-derived hydrogen sulfide (H2S) plays a crucial role in modulating the gut–brain axis, with significant implications for neurodegenerative diseases such as Alzheimer’s and Parkinson’s. H2S is produced by sulfate-reducing bacteria in the gut and acts as a critical signaling [...] Read more.
Microbiota-derived hydrogen sulfide (H2S) plays a crucial role in modulating the gut–brain axis, with significant implications for neurodegenerative diseases such as Alzheimer’s and Parkinson’s. H2S is produced by sulfate-reducing bacteria in the gut and acts as a critical signaling molecule influencing brain health via various pathways, including regulating inflammation, oxidative stress, and immune responses. H2S maintains gut barrier integrity at physiological levels and prevents systemic inflammation, which could impact neuroinflammation. However, as H2S has a dual role or a Janus face, excessive H2S production, often resulting from gut dysbiosis, can compromise the intestinal barrier and exacerbate neurodegenerative processes by promoting neuroinflammation and glial cell dysfunction. This imbalance is linked to the early pathogenesis of Alzheimer’s and Parkinson’s diseases, where the overproduction of H2S exacerbates beta-amyloid deposition, tau hyperphosphorylation, and alpha-synuclein aggregation, driving neuroinflammatory responses and neuronal damage. Targeting gut microbiota to restore H2S homeostasis through dietary interventions, probiotics, prebiotics, and fecal microbiota transplantation presents a promising therapeutic approach. By rebalancing the microbiota-derived H2S, these strategies may mitigate neurodegeneration and offer novel treatments for Alzheimer’s and Parkinson’s diseases, underscoring the critical role of the gut–brain axis in maintaining central nervous system health. Full article
(This article belongs to the Special Issue Cellular and Molecular Biology of Neurodegenerative Disorders)
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Figure 1

Figure 1
<p>The dysbiosis-associated overproduction of H<sub>2</sub>S is proposed as a contributing factor in the progression of neurodegenerative diseases, where neuroinflammation plays a pivotal role. At the same time, H<sub>2</sub>S can have positive effects in a concentration-dependent manner.</p> Full article ">Figure 2
<p>Illustrative interplay between diet, gut microbiota, and their metabolites in the context of neurodegenerative diseases, particularly Alzheimer’s and Parkinson’s. Diet shapes the gut microbial composition, including diverse groups such as Clostridium, Desulfovibrio, and Prevotella, responsible for metabolic activities with systemic impacts. Microbes metabolize dietary components into various products, including hydrogen sulfide (H<sub>2</sub>S) via sulfate reduction and short-chain fatty acids (SCFAs) like acetate, propionate, and butyrate from fiber fermentation. These metabolites influence gut permeability and barrier integrity, with butyrate supporting the gut lining. At the same time, excess H<sub>2</sub>S may compromise it, leading to a “leaky gut” and the release of inflammatory lipopolysaccharides (LPSs) into circulation. SCFAs and other microbial metabolites reach the brain through the bloodstream and vagus nerve, potentially promoting neuroinflammation—a known factor in neurodegeneration. The figure highlights how disruptions in gut microbiota balance can affect brain health, linking gut dysbiosis and altered barrier function to neurodegenerative disease risk and suggesting that therapeutic interventions targeting the gut may help mitigate these diseases.</p> Full article ">Figure 3
<p>Bidirectional gut–brain axis, highlighting interactions among the hypothalamic–pituitary–adrenal (HPA) axis, gut microbiota, circulatory system, and neural pathways. The HPA axis produces cortisol, affecting immune cells, gut epithelium, and enteric muscles. Gut microbes modulate brain function via metabolites like short-chain fatty acids (SCFAs), neurotransmitters, and tryptophan metabolism. H<sub>2</sub>S was found to regulate mucosal integrity, support the anti-inflammatory environment of the gut, and maintain the protective mucus layer.</p> Full article ">
29 pages, 951 KiB  
Review
The Relevance of Spinal Muscular Atrophy Biomarkers in the Treatment Era
by Marianna Maretina, Valeria Koroleva, Lyudmila Shchugareva, Andrey Glotov and Anton Kiselev
Biomedicines 2024, 12(11), 2486; https://doi.org/10.3390/biomedicines12112486 - 30 Oct 2024
Viewed by 1668
Abstract
Spinal muscular atrophy (SMA) is a severe neuromuscular disorder that currently has an approved treatment for all forms of the disease. Previously, biomarkers were primarily used for diagnostic purposes, such as detecting the presence of the disease or determining a specific clinical type [...] Read more.
Spinal muscular atrophy (SMA) is a severe neuromuscular disorder that currently has an approved treatment for all forms of the disease. Previously, biomarkers were primarily used for diagnostic purposes, such as detecting the presence of the disease or determining a specific clinical type of SMA. Currently, with the availability of therapy, biomarkers have become more valuable due to their potential for prognostic, predictive, and pharmacodynamic applications. This review describes the most promising physiological, functional, imaging and molecular biomarkers for SMA, derived from different patients’ tissues. The review summarizes information about classical biomarkers that are already used in clinical practice as well as fresh findings on promising biomarkers that have been recently disclosed. It highlights the usefulness, limitations, and strengths of each potential biomarker, indicating the purposes for which each is best suited and when combining them may be most beneficial. Full article
(This article belongs to the Special Issue Cellular and Molecular Biology of Neurodegenerative Disorders)
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Figure 1

Figure 1
<p>The origin of prospective SMA biomarkers in human organism. Informative biomarker measures can be derived from different tissues. Molecular biomarkers are determined in blood, CSF, and patient-derived cell cultures. Electrophysiological and imaging biomarkers reflect muscle and nerve state. Functional biomarkers are obtained from physiological tests.</p> Full article ">
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