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24 pages, 4371 KiB  
Article
Novel Gene-Informed Regional Brain Targets for Clinical Screening for Major Depression
by G. Lorenzo Odierna, Christopher F. Sharpley, Vicki Bitsika, Ian D. Evans and Kirstan A. Vessey
Neurol. Int. 2025, 17(6), 96; https://doi.org/10.3390/neurolint17060096 - 19 Jun 2025
Viewed by 621
Abstract
Background/Objectives: Major Depression (MD) is a common disorder that has significant social and economic impacts. Approximately 30% of all MD patients are refractory to common treatments, representing a major obstacle to managing the impacts of depression. One potential explanation for the incomplete treatment [...] Read more.
Background/Objectives: Major Depression (MD) is a common disorder that has significant social and economic impacts. Approximately 30% of all MD patients are refractory to common treatments, representing a major obstacle to managing the impacts of depression. One potential explanation for the incomplete treatment efficacy in MD is a substantial divergence in the mechanisms and brain networks involved in different subtypes of the disorder. The aim of this study was to identify novel brain regional targets for MD clinical screening using a gene-informed approach. Methods: A new analysis pipeline, called “Analysis Tool for Local Association of Neuronal Transcript Expression” (ATLANTE), was generated and validated. The pipeline identifies brain regions based on the shared high expression of user-generated gene lists; in this study, the pipeline was applied to discover brain regions that may be significant to MD. Results: Nine discrete brain regions of interest to MD were identified, including the temporal pole, anterior transverse temporal gyrus (Heschl’s gyrus), olfactory tubercle, ventral tegmental area, postcentral gyrus, CA1 of the hippocampus, olfactory area, perirhinal gyrus, and posterior insular cortex. The application of network and clustering analyses identified genes of special importance, including, most notably, PRKN. Conclusions: This study provides two major insights. The first is that several brain regions have unique MD-associated genetic architectures, indicating a potential explanation for subtype-specific dysfunction. The second insight is that the PRKN gene, which is strongly associated with Parkinson’s disease, is a key player amongst the MD-associated genes. These findings reveal novel targets for the clinical screening of depression and reinforce a mechanistic connection between MD and Parkinson’s disease. Full article
(This article belongs to the Section Movement Disorders and Neurodegenerative Diseases)
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10 pages, 599 KiB  
Article
Clinical and Genetic Characteristics of Parkinson’s Disease Patients with Substantia Nigra Hyperechogenicity
by Łukasz Milanowski, Piotr Szukało, Małgorzata Kowalska, Alicja Sikorska, Dorota Hoffman-Zacharska and Dariusz Koziorowski
Int. J. Mol. Sci. 2025, 26(12), 5492; https://doi.org/10.3390/ijms26125492 - 8 Jun 2025
Viewed by 453
Abstract
Hyperechogenicity of the substantia nigra (SN) is observed using transcranial ultrasonography in patients with Parkinson’s Disease. In this study, we investigated whether monogenic forms of PD are more prevalent in these patients and clinically defined their characteristics. Eighty-eight PD patients were part of [...] Read more.
Hyperechogenicity of the substantia nigra (SN) is observed using transcranial ultrasonography in patients with Parkinson’s Disease. In this study, we investigated whether monogenic forms of PD are more prevalent in these patients and clinically defined their characteristics. Eighty-eight PD patients were part of the analysis. All patients received clinical diagnoses from experienced movement disorder specialists. Each patient underwent transcranial ultrasonography and genetic testing for mutations in the SNCA, PRKN, LRRK2, DJ1, and PINK1 genes. SN hyperechogenicity was identified in 48 patients. Compared to the non-hyperechogenicity group, these patients did not have monogenic forms of PD more frequently, but they did have REM sleep behavior disorder significantly more often, lived in rural areas, and experienced a later age of disease onset. Our study indicated no association between substantia nigra echogenicity and the presence of mutations in the SNCA, LRRK2, DJ1, PRKN, and PINK1 genes. Hyperechogenicity of the substantia nigra, however, remains a common finding in patients with Parkinson’s Disease, correlating with certain features of the disease. Full article
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8 pages, 992 KiB  
Case Report
Phase Determination and Demonstration of Parental Mosaicism of Intragenic PRKN Deletions Initially Identified by Chromosomal Microarray Analysis
by Lauren A. Choate, Francis Hoffman, Jessica H. Newman, Cassandra Runke, Matthew Webley, Nicole L. Hoppman and Erik C. Thorland
Genes 2025, 16(6), 630; https://doi.org/10.3390/genes16060630 - 24 May 2025
Viewed by 410
Abstract
Background: Autosomal recessive juvenile Parkinson disease (ARJP) is an early-onset neurodegenerative disorder characterized by Parkinsonian motor symptoms with slow progression and preserved cognition. Biallelic pathogenic variants within the PRKN gene are associated with ARJP. Among PRKN pathogenic variants, deletions are a frequent occurrence [...] Read more.
Background: Autosomal recessive juvenile Parkinson disease (ARJP) is an early-onset neurodegenerative disorder characterized by Parkinsonian motor symptoms with slow progression and preserved cognition. Biallelic pathogenic variants within the PRKN gene are associated with ARJP. Among PRKN pathogenic variants, deletions are a frequent occurrence and may be identified through chromosomal microarray testing. Methods: Here we present a case with two intragenic PRKN deletions initially identified as a secondary finding using chromosomal microarray. One deletion was paternally inherited and the second initially appeared to be de novo. In addition to microarray which initially identified the two deletions, long-range GAP-PCR and Sanger sequencing were used to further characterize the de novo deletion and phase of the deletions. Results: Molecular characterization of the apparently de novo deletion demonstrated low-level maternal mosaicism of this deletion, thus proving that these deletions are in trans in the proband, yielding a diagnosis of autosomal recessive juvenile Parkinson disease. Conclusions: This case highlights the utility of a diagnostic approach combining microarray, long-range PCR, and Sanger sequencing to establish the phase and confirm biallelic PRKN deletions in a patient with ARJP. Furthermore, these findings highlight the importance of investigating the possibility of parental mosaicism to determine the phase of autosomal recessive variants and establish accurate recurrence risks. Full article
(This article belongs to the Special Issue Clinical Cytogenetics: Current Advances and Future Perspectives)
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14 pages, 5970 KiB  
Article
Impaired Mitophagy Contributes to Pyroptosis in Sarcopenic Obesity Zebrafish Skeletal Muscle
by Xiangbin Tang, Yunyi Zou, Siyuan Yang, Zhanglin Chen, Zuoqiong Zhou, Xiyang Peng and Changfa Tang
Nutrients 2025, 17(10), 1711; https://doi.org/10.3390/nu17101711 - 18 May 2025
Viewed by 665
Abstract
Background: Growing evidence suggests that the prevalence of sarcopenic obesity (SOB) is on the rise across the globe. However, the key molecular mechanisms behind this disease have not been clarified. Methods: In this experiment, we fed zebrafish a high-fat diet (HFD) for 16 [...] Read more.
Background: Growing evidence suggests that the prevalence of sarcopenic obesity (SOB) is on the rise across the globe. However, the key molecular mechanisms behind this disease have not been clarified. Methods: In this experiment, we fed zebrafish a high-fat diet (HFD) for 16 weeks to induce sarcopenic obesity. Results: After a dietary trial, HFD zebrafish exhibited an obese phenotype with skeletal muscle atrophy and decreased swimming capacity. We demonstrated that mitochondrial content and function were abnormal in SOB zebrafish skeletal muscle. These results may be associated with the impairment of mitophagy regulated by the PTEN-induced putative kinase 1 (PINK1)/Parkin (PRKN) pathway. In addition, we also found that NOD-like receptor protein 3 (NLRP3)/gasdermin D (GSDMD) signaling was activated with the upregulation of NLRP3, GSDMD-NT, and mature-IL1β, which indicated that pyroptosis was induced in SOB zebrafish skeletal muscle. Conclusions: Our study identified that impaired mitophagy and pyroptosis were associated with the pathogenesis of SOB. These results could potentially offer novel therapeutic objectives for the treatment of sarcopenic obesity. Full article
(This article belongs to the Special Issue Effects of Diet and Nutrition on Musculoskeletal Health)
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18 pages, 1714 KiB  
Review
The Role of N6-Methyladenosine (m6A) RNA Modification in the Pathogenesis of Parkinson’s Disease
by Yulu Wang, Tianyuan Zhao, Chunsen Yuan and Xuechai Chen
Biomolecules 2025, 15(5), 617; https://doi.org/10.3390/biom15050617 - 23 Apr 2025
Cited by 1 | Viewed by 1053
Abstract
Parkinson’s disease (PD) is a neurodegenerative disease with a high prevalence among the middle-aged and elderly population. The pathogenesis of PD is closely linked to the misfolding and aggregation of α-synuclein, which contributes to the formation of Lewy bodies. These processes are associated [...] Read more.
Parkinson’s disease (PD) is a neurodegenerative disease with a high prevalence among the middle-aged and elderly population. The pathogenesis of PD is closely linked to the misfolding and aggregation of α-synuclein, which contributes to the formation of Lewy bodies. These processes are associated with the degeneration of dopaminergic neurons, a key neuropathological change that underlies the motor symptoms of PD. In addition, genetic susceptibility, mitochondrial dysfunction, oxidative stress and neuroinflammation are involved in the progress of the disease. Previous studies indicated that the dysregulation of epigenetic modifications, including DNA methylation and histone acetylation, may be the key pathophysiological factors in PD. N6-methyladenosine (m6A) is a dynamically reversible modification in eukaryotes RNA, and could regulate mRNA degradation, stability, maturation, and translation. Recently, clinical research has shown that the global m6A level is significantly reduced in PD patients as well as the expression changes in m6A-associated proteins. Moreover, the dysregulation of m6A modification was shown to impact dopamine metabolism and damage dopaminergic neurons, indicating that m6A RNA modification may play a critical role in the pathogenesis of PD. In this review, we summarize recent clinical studies on m6A RNA modification in PD patients and discuss the regulatory role of m6A modification in dopamine metabolism and dopaminergic neurons death. Furthermore, based on the different m6A modification databases and prediction websites, we analyzed the potential m6A modification sites on the mRNA of key PD pathogenic genes (SNCA, PRKN, PINK1, and LRRK2) for the first time, aiming to offer new gene targets and perspectives understanding the pathogenesis of PD. Full article
(This article belongs to the Section Molecular Biology)
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18 pages, 1347 KiB  
Article
Population-Specific Differences in Pathogenic Variants of Genes Associated with Monogenic Parkinson’s Disease
by Victor Flores-Ocampo, Amanda Wei-Yin Lim, Natalia S. Ogonowski, Luis M. García-Marín, Jue-Sheng Ong, Dennis Yeow, Claudia Gonzaga-Jauregui, Kishore R. Kumar and Miguel E. Rentería
Genes 2025, 16(4), 454; https://doi.org/10.3390/genes16040454 - 15 Apr 2025
Viewed by 1199
Abstract
Background: Parkinson’s disease (PD) is a genetically complex neurodegenerative disorder. Up to 15% of cases are considered monogenic. However, research on monogenic PD has largely focused on populations of European ancestry, leaving gaps in our understanding of genetic variability in other populations. This [...] Read more.
Background: Parkinson’s disease (PD) is a genetically complex neurodegenerative disorder. Up to 15% of cases are considered monogenic. However, research on monogenic PD has largely focused on populations of European ancestry, leaving gaps in our understanding of genetic variability in other populations. This study addresses this gap by analysing the allele frequencies of pathogenic and likely pathogenic variants in known monogenic PD genes across eight global populations, using data from the gnomAD database. Methods: We compiled a list of 27 genes associated with Mendelian PD from the Online Mendelian Inheritance in Man (OMIM) database, and identified pathogenic and likely pathogenic variants using ClinVar. We then performed pairwise comparisons of allele frequencies across populations included in the gnomAD database. Variants with significant frequency differences were further assessed using in silico pathogenicity predictions. Results: We identified 81 variants across 17 genes with statistically significant allele frequency differences between at least two populations. Variants in GBA1 were the most prevalent among monogenic PD-related genes, followed by PLA2G6, ATP13A2, VPS13C, and PRKN. GBA1 exhibited the greatest variability in allele frequencies, particularly the NM_000157.4:c.1226A>G (p.Asn409Ser) variant. Additionally, we observed significant population-specific differences in PD-related variants, such as the NM_032409.3:c.1040T>C (p.Leu347Pro) variant in PINK1, which was most prevalent in East Asian populations. Conclusions: Our findings reveal substantial population-specific differences in the allele frequencies of pathogenic variants linked to monogenic PD, emphasising the need for broader genetic studies beyond European populations. These insights have important implications for PD research, genetic screening, and understanding the pathogenesis of PD in diverse populations. Full article
(This article belongs to the Special Issue Genetics of Parkinson’s Disease Around the World)
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18 pages, 762 KiB  
Article
Next Generation Sequencing Analysis in Patients Affected by Parkinson’s Disease and Correlation Between Genotype and Phenotype in Selected Clinical Cases
by Andrea Pilotto, Mattia Carini, Roberto Bresciani, Eugenio Monti, Fabiana Ferrari, Maria Antonia De Francesco, Alessandro Padovani and Giorgio Biasiotto
Int. J. Mol. Sci. 2025, 26(6), 2397; https://doi.org/10.3390/ijms26062397 - 7 Mar 2025
Viewed by 1059
Abstract
Parkinson’s Disease (PD) is the most frequent movement disorder and is second only to Alzheimer’s Disease as the most frequent neurodegenerative pathology. Early onset Parkinson’s disease (EOPD) is less common and may be characterized by genetic predisposition. NGS testing might be useful in [...] Read more.
Parkinson’s Disease (PD) is the most frequent movement disorder and is second only to Alzheimer’s Disease as the most frequent neurodegenerative pathology. Early onset Parkinson’s disease (EOPD) is less common and may be characterized by genetic predisposition. NGS testing might be useful in the diagnostic assessment of these patients. A panel of eight genes (SNCA, PRKN, PINK1, DJ1, LRRK2, FBXO7, GBA1 and HFE) was validated and used as a diagnostic tool. A total of 38 in sequence EOPD patients of the Parkinson’s Disease Unit of our Hospital Institution were tested. In addition, the number of the hexanucleotide repeats of the C9ORF72 gene and the frequency of main HFE mutations were evaluated. Six patients were carriers of likely pathogenic mutations in heterozygosity in the analyzed genes, one of them presented mutations in association and another had a complex genetic background. Their clinical symptoms were correlated with their genotypes. In the cohort of patients, only the p.Cys282Tyr of HFE was significantly decreased in the dominant model and allele contrast comparison. Only one patient with one allele of C9ORF72 containing 10 repeats was identified and clinically described. The clinical signs of sporadic and monogenic PD are often very similar; for this reason, it is fundamental to correlate genotypes and phenotypes, as we tried to describe here, to better classify PD patients with the aim to deepen our knowledge in the molecular mechanisms involved and collaborate in reaching a personalized management and treatment. Full article
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21 pages, 2753 KiB  
Article
Genetic Variants Associated with Suspected Neonatal Hypoxic Ischaemic Encephalopathy: A Study in a South African Context
by Caroline J. Foden, Kevin Durant, Juanita Mellet, Fourie Joubert, Jeanne van Rensburg, Khomotso Masemola, Sithembiso C. Velaphi, Firdose L. Nakwa, Alan R. Horn, Shakti Pillay, Gugu Kali, Melantha Coetzee, Daynia E. Ballot, Thumbiko Kalua, Carina Babbo and Michael S. Pepper
Int. J. Mol. Sci. 2025, 26(5), 2075; https://doi.org/10.3390/ijms26052075 - 27 Feb 2025
Cited by 1 | Viewed by 975
Abstract
Neonatal encephalopathy suspected to be due to hypoxic ischaemic encephalopathy (NESHIE) carries the risk of death or severe disability (cognitive defects and cerebral palsy). Previous genetic studies on NESHIE have predominantly focused on exomes or targeted genes. The objective of this study was [...] Read more.
Neonatal encephalopathy suspected to be due to hypoxic ischaemic encephalopathy (NESHIE) carries the risk of death or severe disability (cognitive defects and cerebral palsy). Previous genetic studies on NESHIE have predominantly focused on exomes or targeted genes. The objective of this study was to identify genetic variants associated with moderate–severe NESHIE through whole-genome, unbiased analysis. Variant filtering and prioritization were performed, followed by association testing both on a case–control basis and to compare the grades of severity and/or progression. Association testing on neonates with NESHIE (N = 172) and ancestry-matched controls (N = 288) produced 71 significant genetic variants (false discovery rate corrected p-value < 6.2 × 10−4), all located in non-coding regions and not previously implicated in NESHIE. Disease-associated variants in non-coding regions are considered to affect regulatory functions, possibly by modifying gene expression, promoters, enhancers, or DNA structure. The most significant variant was at position 6:162010973 in the Parkin RBR E3 ubiquitin protein ligase (PRKN) intron. Intronic variants were also identified in genes involved in inflammatory processes (SLCO3A1), DNA repair (ZGRF1), synaptogenesis (CNTN5), haematopoiesis (ASXL2), and the transcriptional response to hypoxia (PADI4). Ten variants were associated with a higher severity or lack of improvement in NESHIE, including one in ADAMTS3, which encodes a procollagen amino protease with a role in angiogenesis and lymphangiogenesis. This analysis represents one of the first efforts to analyze whole-genome data to investigate the genetic complexity of NESHIE in diverse ethnolinguistic groups of African origin and provides direction for further study. Full article
(This article belongs to the Special Issue Genetic and Molecular Susceptibility in Human Diseases: 2nd Edition)
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17 pages, 7358 KiB  
Article
Disrupted Mitochondrial Dynamics Impair Corneal Epithelial Healing in Neurotrophic Keratopathy
by Mengyi Jin, Zeyu Liu, Ruize Shi, Ya Deng, Jingwei Lin, Yuting Zhang, Lexin Lin, Yanzi Wang, Yunyi Shi, Cheng Li and Zuguo Liu
Int. J. Mol. Sci. 2025, 26(3), 1290; https://doi.org/10.3390/ijms26031290 - 3 Feb 2025
Cited by 1 | Viewed by 1623
Abstract
Neurotrophic keratopathy (NK) is a degenerative corneal disease characterized by impaired corneal sensitivity and epithelial repair that is often linked to sensory nerve dysfunction. To establish a clinically relevant model and explore the mechanisms underlying NK pathogenesis, we developed a novel mouse model [...] Read more.
Neurotrophic keratopathy (NK) is a degenerative corneal disease characterized by impaired corneal sensitivity and epithelial repair that is often linked to sensory nerve dysfunction. To establish a clinically relevant model and explore the mechanisms underlying NK pathogenesis, we developed a novel mouse model through partial transection of the ciliary nerve. This approach mimics the progressive nature of NK, reproducing key clinical features such as corneal epithelial defects, reduced sensitivity, diminished tear secretion, and delayed wound healing. Using this model, we investigated how disruptions in mitochondrial dynamics contribute to corneal epithelial dysfunction and impaired repair in NK. Our findings revealed substantial disruptions in mitochondrial dynamics, including reduced expression of fusion proteins (OPA1), downregulation of fission regulators (FIS1 and MFF), and impaired mitochondrial transport, as evidenced by decreased expression of Rhot1 and Kif5b. Additionally, the downregulation of mitophagy-related genes (Pink1 and Prkn) contributed to the accumulation of dysfunctional mitochondria, leading to DNA damage and impaired corneal epithelial repair. These mitochondrial abnormalities were accompanied by increased γH2AX staining, indicative of DNA double-strand breaks and cellular stress. This study highlights the pivotal role of mitochondrial dynamics in corneal epithelial health and repair, suggesting that therapeutic strategies aimed at restoring mitochondrial function, enhancing mitophagy, and mitigating oxidative stress may offer promising avenues for treating NK. Full article
(This article belongs to the Section Molecular Neurobiology)
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27 pages, 12788 KiB  
Article
A Multi-Omics Analysis of a Mitophagy-Related Signature in Pan-Cancer
by Nora Agir, Ilias Georgakopoulos-Soares and Apostolos Zaravinos
Int. J. Mol. Sci. 2025, 26(2), 448; https://doi.org/10.3390/ijms26020448 - 7 Jan 2025
Cited by 1 | Viewed by 1543
Abstract
Mitophagy, an essential process within cellular autophagy, has a critical role in regulating key cellular functions such as reproduction, metabolism, and apoptosis. Its involvement in tumor development is complex and influenced by the cellular environment. Here, we conduct a comprehensive analysis of a [...] Read more.
Mitophagy, an essential process within cellular autophagy, has a critical role in regulating key cellular functions such as reproduction, metabolism, and apoptosis. Its involvement in tumor development is complex and influenced by the cellular environment. Here, we conduct a comprehensive analysis of a mitophagy-related gene signature, composed of PRKN, PINK1, MAP1LC3A, SRC, BNIP3L, BECN1, and OPTN, across various cancer types, revealing significant differential expression patterns associated with molecular subtypes, stages, and patient outcomes. Pathway analysis revealed a complex interplay between the expression of the signature and potential effects on the activity of various cancer-related pathways in pan-cancer. Immune infiltration analysis linked the mitophagy signature with certain immune cell types, particularly OPTN with immune infiltration in melanoma. Methylation patterns correlated with gene expression and immune infiltration. Mutation analysis also showed frequent alterations in PRKN (34%), OPTN (21%), PINK1 (28%), and SRC (15%), with implications for the tumor microenvironment. We also found various correlations between the expression of the mitophagy-related genes and sensitivity in different drugs, suggesting that targeting this signature could improve therapy efficacy. Overall, our findings underscore the importance of mitophagy in cancer biology and drug resistance, as well as its potential for informing treatment strategies. Full article
(This article belongs to the Special Issue Data Science in Cancer Genomics and Precision Medicine: 2nd Edition)
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10 pages, 274 KiB  
Commentary
The α-Synuclein Seeding Amplification Assay for Parkinson’s Disease
by Ling-Xiao Yi, Eng King Tan and Zhi Dong Zhou
Int. J. Mol. Sci. 2025, 26(1), 389; https://doi.org/10.3390/ijms26010389 - 4 Jan 2025
Cited by 2 | Viewed by 2295
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disease in the world. Currently, PD is incurable, and the diagnosis of PD mainly relies on clinical manifestations. The central pathological event in PD is the abnormal aggregation and deposition of misfolded α-synuclein (α-Syn) [...] Read more.
Parkinson’s disease (PD) is the second most common neurodegenerative disease in the world. Currently, PD is incurable, and the diagnosis of PD mainly relies on clinical manifestations. The central pathological event in PD is the abnormal aggregation and deposition of misfolded α-synuclein (α-Syn) protein aggregates in the Lewy body (LB) in affected brain areas. Behaving as a prion-like seeding, the misfolded α-syn protein can induce and facilitate the aggregation of native unfolded α-Syn protein to aggravate α-Syn protein aggregation, leading to PD progression. Recently, in a blood-based α-Syn seeding amplification assay (SAA), Kluge et al. identified pathological α-Syn seeding activity in PD patients with Parkin (PRKN) gene variants. Additionally, pathological α-syn seeding activity was also identified in sporadic PD and PD patients with Leucine-rich repeat kinase 2 (LRRK2) or glucocerebrosidase (GBA) gene variants. Principally, the α-Syn SAA can be used to detect pathological α-Syn seeding activity, which will significantly enhance PD diagnosis, progression monitoring, prognosis prediction, and anti-PD therapy. The significance and future strategies of α-Syn SAA protocol are highlighted and proposed, whereas challenges and limitations of the assay are discussed. Full article
15 pages, 1125 KiB  
Review
Alpha-Synuclein Effects on Mitochondrial Quality Control in Parkinson’s Disease
by Lydia Shen and Ulf Dettmer
Biomolecules 2024, 14(12), 1649; https://doi.org/10.3390/biom14121649 - 22 Dec 2024
Cited by 4 | Viewed by 2372
Abstract
The maintenance of healthy mitochondria is essential for neuronal survival and relies upon mitochondrial quality control pathways involved in mitochondrial biogenesis, mitochondrial dynamics, and mitochondrial autophagy (mitophagy). Mitochondrial dysfunction is critically implicated in Parkinson’s disease (PD), a brain disorder characterized by the progressive [...] Read more.
The maintenance of healthy mitochondria is essential for neuronal survival and relies upon mitochondrial quality control pathways involved in mitochondrial biogenesis, mitochondrial dynamics, and mitochondrial autophagy (mitophagy). Mitochondrial dysfunction is critically implicated in Parkinson’s disease (PD), a brain disorder characterized by the progressive loss of dopaminergic neurons in the substantia nigra. Consequently, impaired mitochondrial quality control may play a key role in PD pathology. This is affirmed by work indicating that genes such as PRKN and PINK1, which participate in multiple mitochondrial processes, harbor PD-associated mutations. Furthermore, mitochondrial complex-I-inhibiting toxins like MPTP and rotenone are known to cause Parkinson-like symptoms. At the heart of PD is alpha-synuclein (αS), a small synaptic protein that misfolds and aggregates to form the disease’s hallmark Lewy bodies. The specific mechanisms through which aggregated αS exerts its neurotoxicity are still unknown; however, given the vital role of both αS and mitochondria to PD, an understanding of how αS influences mitochondrial maintenance may be essential to elucidating PD pathogenesis and discovering future therapeutic targets. Here, the current knowledge of the relationship between αS and mitochondrial quality control pathways in PD is reviewed, highlighting recent findings regarding αS effects on mitochondrial biogenesis, dynamics, and autophagy. Full article
(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)
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14 pages, 3499 KiB  
Article
High Mitophagy and Low Glycolysis Predict Better Clinical Outcomes in Acute Myeloid Leukemias
by Amreen Salwa, Alessandra Ferraresi, Letizia Vallino, Chinmay Maheshwari, Riccardo Moia, Gianluca Gaidano and Ciro Isidoro
Int. J. Mol. Sci. 2024, 25(21), 11527; https://doi.org/10.3390/ijms252111527 - 27 Oct 2024
Cited by 1 | Viewed by 1858
Abstract
Acute myeloid leukemia (AML) emerges as one of the most common and fatal leukemias. Treatment of the disease remains highly challenging owing to profound metabolic rewiring mechanisms that confer plasticity to AML cells, ultimately resulting in therapy resistance. Autophagy, a highly conserved lysosomal-driven [...] Read more.
Acute myeloid leukemia (AML) emerges as one of the most common and fatal leukemias. Treatment of the disease remains highly challenging owing to profound metabolic rewiring mechanisms that confer plasticity to AML cells, ultimately resulting in therapy resistance. Autophagy, a highly conserved lysosomal-driven catabolic process devoted to macromolecular turnover, displays a dichotomous role in AML by suppressing or promoting disease development and progression. Glycolytic metabolism represents a pivotal strategy for AML cells to sustain increasing energy needs related to uncontrolled growth during disease progression. In this study, we tested the hypothesis that a high glycolytic rate and low autophagy flux could represent an advantage for AML cell proliferation and thus be detrimental for patient’s prognosis, and vice versa. TCGA in silico analysis of the AML cohort shows that the high expression of MAP1LC3B (along with that of BECN1 and with low expression of p62/SQSTM1) and the high expression of BNIP3 (along with that of PRKN and of MAP1LC3B), which together are indicative of increased autophagy and mitophagy, correlate with better prognosis. On the other hand, the high expression of glycolytic markers HK2, PFKM, and PKM correlates with poor prognosis. Most importantly, the association of a low expression of glycolytic markers with a high expression of autophagy–mitophagy markers conferred the longest overall survival for AML patients. Transcriptomic analysis showed that this combined signature correlates with the downregulation of a subset of genes required for the differentiation of myeloid cells, lactate/pyruvate transporters, and cell cycle progression, in parallel with the upregulation of genes involved in autophagy/lysosomal trafficking and proteolysis, anti-tumor responses like beta-interferon production, and positive regulation of programmed cell death. Taken together, our data support the view that enhanced autophagy-mitophagy flux together with low glycolytic rate predisposes AML patients to a better clinical outcome, suggesting that autophagy inducers and glucose restrictors may hold potential as adjuvant therapeutics for improving AML management. Full article
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20 pages, 5773 KiB  
Article
Structural and Functional Characterization of the Most Frequent Pathogenic PRKN Substitution p.R275W
by Bernardo A. Bustillos, Liam T. Cocker, Mathew A. Coban, Caleb A. Weber, Jenny M. Bredenberg, Paige K. Boneski, Joanna Siuda, Jaroslaw Slawek, Andreas Puschmann, Derek P. Narendra, Neill R. Graff-Radford, Zbigniew K. Wszolek, Dennis W. Dickson, Owen A. Ross, Thomas R. Caulfield, Wolfdieter Springer and Fabienne C. Fiesel
Cells 2024, 13(18), 1540; https://doi.org/10.3390/cells13181540 - 13 Sep 2024
Cited by 2 | Viewed by 2121
Abstract
Mutations in the PINK1 and PRKN genes are the most frequent genetic cause of early-onset Parkinson disease. The pathogenic p.R275W substitution in PRKN is the most frequent substitution observed in patients, and thus far has been characterized mostly through overexpression models that suggest [...] Read more.
Mutations in the PINK1 and PRKN genes are the most frequent genetic cause of early-onset Parkinson disease. The pathogenic p.R275W substitution in PRKN is the most frequent substitution observed in patients, and thus far has been characterized mostly through overexpression models that suggest a possible gain of toxic misfunction. However, its effects under endogenous conditions are largely unknown. We used patient fibroblasts, isogenic neurons, and post-mortem human brain samples from carriers with and without PRKN p.R275W to assess functional impact. Immunoblot analysis and immunofluorescence were used to study mitophagy activation, and mitophagy execution was analyzed by flow cytometry of the reporter mitoKeima. The functional analysis was accompanied by structural investigation of PRKN p.R275W. We observed lower PRKN protein in fibroblasts with compound heterozygous p.R275W mutations. Isogenic neurons showed an allele-dose dependent decrease in PRKN protein. Lower PRKN protein levels were accompanied by diminished phosphorylated ubiquitin and decreased MFN2 modification. Mitochondrial degradation was also allele-dose dependently impaired. Consistently, PRKN protein levels were drastically reduced in human brain samples from p.R275W carriers. Finally, structural simulations showed significant changes in the closed form of PRKN p.R275W. Our data suggest that under endogenous conditions the p.R275W mutation results in a loss-of-function by destabilizing PRKN. Full article
(This article belongs to the Section Autophagy)
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16 pages, 4610 KiB  
Article
Preservation of Mitochondrial Function by SkQ1 in Skin Fibroblasts Derived from Patients with Leber’s Hereditary Optic Neuropathy Is Associated with the PINK1/PRKN-Mediated Mitophagy
by Jin Xu, Yan Li, Shun Yao, Xiuxiu Jin, Mingzhu Yang, Qingge Guo, Ruiqi Qiu and Bo Lei
Biomedicines 2024, 12(9), 2020; https://doi.org/10.3390/biomedicines12092020 - 4 Sep 2024
Cited by 1 | Viewed by 1669
Abstract
Increased or altered mitochondrial ROS production in the retinal ganglion cells is regarded as the chief culprit of the disease-causing Leber’s hereditary optic neuropathy (LHON). SkQ1 is a rechargeable mitochondria-targeted antioxidant with high specificity and efficiency. SkQ1 has already been used to treat [...] Read more.
Increased or altered mitochondrial ROS production in the retinal ganglion cells is regarded as the chief culprit of the disease-causing Leber’s hereditary optic neuropathy (LHON). SkQ1 is a rechargeable mitochondria-targeted antioxidant with high specificity and efficiency. SkQ1 has already been used to treat LHON patients, and a phase 2a randomized clinical trial of SkQ1 has demonstrated improvements in eyesight. However, the underlying mechanism of SkQ1 in LHON remains unclear. This study aimed to assess the effects and molecular mechanism of SkQ1 in the preservation of mitochondrial function using skin fibroblasts derived from LHON patients. Our study found that SkQ1 could reduce ROS production and stabilize the mitochondrial membrane. Mechanistically, through network pharmacology and molecular docking, we identified the key targets of SkQ1 as SOD2 and PINK1, which play crucial roles in redox and mitophagy. SkQ1 interacted with PINK1 and downregulated its expression to balance mitochondrial homeostasis. Collectively, the findings of our study reveal that by regulating PINK1/PRKN-mediated mitophagy, SkQ1 preserves mitochondrial function in LHON fibroblasts. The data indicate that SkQ1 may be a novel therapeutic intervention to prevent the progression of LHON. Full article
(This article belongs to the Section Cell Biology and Pathology)
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