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  1. Article ; Online: From powerhouse to regulator: The role of mitoepigenetics in mitochondrion-related cellular functions and human diseases.

    Donato, Luigi / Mordà, Domenico / Scimone, Concetta / Alibrandi, Simona / D'Angelo, Rosalia / Sidoti, Antonina

    Free radical biology & medicine

    2024  Volume 218, Page(s) 105–119

    Abstract: Beyond their crucial role in energy production, mitochondria harbor a distinct genome subject to epigenetic regulation akin to that of nuclear DNA. This paper delves into the nascent but rapidly evolving fields of mitoepigenetics and mitoepigenomics, ... ...

    Abstract Beyond their crucial role in energy production, mitochondria harbor a distinct genome subject to epigenetic regulation akin to that of nuclear DNA. This paper delves into the nascent but rapidly evolving fields of mitoepigenetics and mitoepigenomics, exploring the sophisticated regulatory mechanisms governing mitochondrial DNA (mtDNA). These mechanisms encompass mtDNA methylation, the influence of non-coding RNAs (ncRNAs), and post-translational modifications of mitochondrial proteins. Together, these epigenetic modifications meticulously coordinate mitochondrial gene transcription, replication, and metabolism, thereby calibrating mitochondrial function in response to the dynamic interplay of intracellular needs and environmental stimuli. Notably, the dysregulation of mitoepigenetic pathways is increasingly implicated in mitochondrial dysfunction and a spectrum of human pathologies, including neurodegenerative diseases, cancer, metabolic disorders, and cardiovascular conditions. This comprehensive review synthesizes the current state of knowledge, emphasizing recent breakthroughs and innovations in the field. It discusses the potential of high-resolution mitochondrial epigenome mapping, the diagnostic and prognostic utility of blood or tissue mtDNA epigenetic markers, and the promising horizon of mitochondrial epigenetic drugs. Furthermore, it explores the transformative potential of mitoepigenetics and mitoepigenomics in precision medicine. Exploiting a theragnostic approach to maintaining mitochondrial allostasis, this paper underscores the pivotal role of mitochondrial epigenetics in charting new frontiers in medical science.
    MeSH term(s) Humans ; Epigenesis, Genetic ; Mitochondria/genetics ; Mitochondria/metabolism ; Mitochondria/pathology ; DNA, Mitochondrial/genetics ; DNA, Mitochondrial/metabolism ; DNA Methylation ; Protein Processing, Post-Translational/genetics ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Mitochondrial Diseases/genetics ; Mitochondrial Diseases/metabolism ; Mitochondrial Diseases/pathology ; RNA, Untranslated/genetics ; RNA, Untranslated/metabolism ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/metabolism ; Neurodegenerative Diseases/pathology ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology
    Chemical Substances DNA, Mitochondrial ; Mitochondrial Proteins ; RNA, Untranslated
    Language English
    Publishing date 2024-03-31
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 807032-5
    ISSN 1873-4596 ; 0891-5849
    ISSN (online) 1873-4596
    ISSN 0891-5849
    DOI 10.1016/j.freeradbiomed.2024.03.025
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2109: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article: Investigating the role of imprinted genes in pediatric sporadic brain arteriovenous malformations.

    Scimone, Concetta / Donato, Luigi / Sidoti, Antonina

    Neural regeneration research

    2021  Volume 17, Issue 1, Page(s) 101–102

    Language English
    Publishing date 2021-06-07
    Publishing country India
    Document type Journal Article
    ZDB-ID 2388460-5
    ISSN 1876-7958 ; 1673-5374
    ISSN (online) 1876-7958
    ISSN 1673-5374
    DOI 10.4103/1673-5374.314296
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Investigating G-quadruplex structures in

    Donato, Luigi / Scimone, Concetta / Alibrandi, Simona / Mordà, Domenico / Anchesi, Ivan / Scalinci, Sergio Zaccaria / Rinaldi, Carmela / D'Angelo, Rosalia / Sidoti, Antonina

    Heliyon

    2024  Volume 10, Issue 8, Page(s) e29828

    Abstract: Aims: This pilot study investigates the potential pathogenic role of G-quadruplex (G4) structures in : Main methods: We conducted whole genome amplification experiments and next-generation sequencing to detect the blockade of polymerase activity by ... ...

    Abstract Aims: This pilot study investigates the potential pathogenic role of G-quadruplex (G4) structures in
    Main methods: We conducted whole genome amplification experiments and next-generation sequencing to detect the blockade of polymerase activity by G4 structures. Our specific focus was the
    Key findings: Our data confirmed the obstruction of DNA polymerase enzymes by G4 structures, particularly when stabilized by the compound pyridostatin. This obstruction was evident in the reduced amplification of
    Significance: Our findings suggest that G4 formation in the
    Language English
    Publishing date 2024-04-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2024.e29828
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: How Many Alzheimer-Perusini's Atypical Forms Do We Still Have to Discover?

    Donato, Luigi / Mordà, Domenico / Scimone, Concetta / Alibrandi, Simona / D'Angelo, Rosalia / Sidoti, Antonina

    Biomedicines

    2023  Volume 11, Issue 7

    Abstract: Alzheimer-Perusini's (AD) disease represents the most spread dementia around the world and constitutes a serious problem for public health. It was first described by the two physicians from whom it took its name. Nowadays, we have extensively expanded ... ...

    Abstract Alzheimer-Perusini's (AD) disease represents the most spread dementia around the world and constitutes a serious problem for public health. It was first described by the two physicians from whom it took its name. Nowadays, we have extensively expanded our knowledge about this disease. Starting from a merely clinical and histopathologic description, we have now reached better molecular comprehension. For instance, we passed from an old conceptualization of the disease based on plaques and tangles to a more modern vision of mixed proteinopathy in a one-to-one relationship with an alteration of specific glial and neuronal phenotypes. However, no disease-modifying therapies are yet available. It is likely that the only way to find a few "magic bullets" is to deepen this aspect more and more until we are able to draw up specific molecular profiles for single AD cases. This review reports the most recent classifications of AD atypical variants in order to summarize all the clinical evidence using several discrimina (for example, post mortem neurofibrillary tangle density, cerebral atrophy, or FDG-PET studies). The better defined four atypical forms are posterior cortical atrophy (PCA), logopenic variant of primary progressive aphasia (LvPPA), behavioral/dysexecutive variant and AD with corticobasal degeneration (CBS). Moreover, we discuss the usefulness of such classifications before outlining the molecular-genetic aspects focusing on microglial activity or, more generally, immune system control of neuroinflammation and neurodegeneration.
    Language English
    Publishing date 2023-07-19
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720867-9
    ISSN 2227-9059
    ISSN 2227-9059
    DOI 10.3390/biomedicines11072035
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Bridging Retinal and Cerebral Neurodegeneration: A Focus on Crosslinks between Alzheimer-Perusini's Disease and Retinal Dystrophies.

    Donato, Luigi / Mordà, Domenico / Scimone, Concetta / Alibrandi, Simona / D'Angelo, Rosalia / Sidoti, Antonina

    Biomedicines

    2023  Volume 11, Issue 12

    Abstract: In the early stages of Alzheimer-Perusini's disease (AD), individuals often experience vision-related issues such as color vision impairment, reduced contrast sensitivity, and visual acuity problems. As the disease progresses, there is a connection with ... ...

    Abstract In the early stages of Alzheimer-Perusini's disease (AD), individuals often experience vision-related issues such as color vision impairment, reduced contrast sensitivity, and visual acuity problems. As the disease progresses, there is a connection with glaucoma and age-related macular degeneration (AMD) leading to retinal cell death. The retina's involvement suggests a link with the hippocampus, where most AD forms start. A thinning of the retinal nerve fiber layer (RNFL) due to the loss of retinal ganglion cells (RGCs) is seen as a potential AD diagnostic marker using electroretinography (ERG) and optical coherence tomography (OCT). Amyloid beta fragments (Aβ), found in the eye's vitreous and aqueous humor, are also present in the cerebrospinal fluid (CSF) and accumulate in the retina. Aβ is known to cause tau hyperphosphorylation, leading to its buildup in various retinal layers. However, diseases like AD are now seen as mixed proteinopathies, with deposits of the prion protein (PrP) and α-synuclein found in affected brains and retinas. Glial cells, especially microglial cells, play a crucial role in these diseases, maintaining immunoproteostasis. Studies have shown similarities between retinal and brain microglia in terms of transcription factor expression and morphotypes. All these findings constitute a good start to achieving better comprehension of neurodegeneration in both the eye and the brain. New insights will be able to bring the scientific community closer to specific disease-modifying therapies.
    Language English
    Publishing date 2023-12-08
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720867-9
    ISSN 2227-9059
    ISSN 2227-9059
    DOI 10.3390/biomedicines11123258
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Evidences of PIEZO1 involvement in cerebral cavernous malformation pathogenesis.

    Scimone, Concetta / Donato, Luigi / Alibrandi, Simona / D'Angelo, Rosalia / Sidoti, Antonina

    Microvascular research

    2022  Volume 141, Page(s) 104342

    MeSH term(s) Hemangioma, Cavernous, Central Nervous System/pathology ; Humans ; Ion Channels ; Mutation ; Signal Transduction
    Chemical Substances Ion Channels ; PIEZO1 protein, human
    Language English
    Publishing date 2022-02-14
    Publishing country United States
    Document type Letter
    ZDB-ID 80307-8
    ISSN 1095-9319 ; 0026-2862
    ISSN (online) 1095-9319
    ISSN 0026-2862
    DOI 10.1016/j.mvr.2022.104342
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 746: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article: Human retinal secretome: A cross-link between mesenchymal and retinal cells.

    Donato, Luigi / Scimone, Concetta / Alibrandi, Simona / Scalinci, Sergio Zaccaria / Mordà, Domenico / Rinaldi, Carmela / D'Angelo, Rosalia / Sidoti, Antonina

    World journal of stem cells

    2023  Volume 15, Issue 7, Page(s) 665–686

    Abstract: In recent years, mesenchymal stem cells (MSC) have been considered the most effective source for regenerative medicine, especially due to released soluble paracrine bioactive components and extracellular vesicles. These factors, collectively called the ... ...

    Abstract In recent years, mesenchymal stem cells (MSC) have been considered the most effective source for regenerative medicine, especially due to released soluble paracrine bioactive components and extracellular vesicles. These factors, collectively called the secretome, play crucial roles in immunomodulation and in improving survival and regeneration capabilities of injured tissue. Recently, there has been a growing interest in the secretome released by retinal cytotypes, especially retinal pigment epithelium and Müller glia cells. The latter trophic factors represent the key to preserving morphofunctional integrity of the retina, regulating biological pathways involved in survival, function and responding to injury. Furthermore, these factors can play a pivotal role in onset and progression of retinal diseases after damage of cell secretory function. In this review, we delineated the importance of cross-talk between MSCs and retinal cells, focusing on common/induced secreted factors, during experimental therapy for retinal diseases. The cross-link between the MSC and retinal cell secretomes suggests that the MSC secretome can modulate the retinal cell secretome and vice versa. For example, the MSC secretome can protect retinal cells from degeneration by reducing oxidative stress, autophagy and programmed cell death. Conversely, the retinal cell secretome can influence the MSC secretome by inducing changes in MSC gene expression and phenotype.
    Language English
    Publishing date 2023-07-20
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2583482-4
    ISSN 1948-0210
    ISSN 1948-0210
    DOI 10.4252/wjsc.v15.i7.665
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Editome landscape of CCM-derived endothelial cells

    Scimone, Concetta / Alibrandi, Simona / Donato, L. / Alafaci, Concetta / Germanò, Antonino / Vinci, Sergio L. / D’Angelo, Rosalia / Sidoti, Antonina

    RNA Biology. 2022 Dec. 31, v. 19, no. 1 p.852-865

    2022  

    Abstract: By regulating several phases of gene expression, RNA editing modifications contribute to maintaining physiological RNA expression levels. RNA editing dysregulation can affect RNA molecule half-life, coding/noncoding RNA interaction, alternative splicing, ...

    Abstract By regulating several phases of gene expression, RNA editing modifications contribute to maintaining physiological RNA expression levels. RNA editing dysregulation can affect RNA molecule half-life, coding/noncoding RNA interaction, alternative splicing, and circular RNA biogenesis. Impaired RNA editing has been observed in several pathological conditions, including cancer and Alzheimer’s disease. No data has been published yet on the editome profile of endothelial cells (ECs) isolated from human cerebral cavernous malformation (CCM) lesions. Here, we describe a landscape of editome modifications in sporadic CCM-derived ECs (CCM-ECs) by comparing editing events with those observed in human brain microvascular endothelial cells (HBMECs). With a whole transcriptome-based variant calling pipeline, we identified differential edited genes in CCM-ECs that were enriched in pathways related to angiogenesis, apoptosis and cell survival, inflammation and, in particular, to thrombin signalling mediated by protease-activated receptors and non-canonical Wnt signalling. These pathways, not yet associated to CCM development, could be a novel field for further investigations on CCM molecular mechanisms. Moreover, enrichment analysis of differentially edited miRNAs suggested additional small noncoding transcripts to consider for development of targeted therapies.
    Keywords abnormal development ; angiogenesis ; apoptosis ; biogenesis ; brain ; cell viability ; circular RNA ; gene expression ; half life ; humans ; inflammation ; landscapes ; microRNA ; non-coding RNA ; thrombin ; Cerebral cavernous malformation ; editome profile ; protease-activated receptor signalling ; RNA sequencing analysis ; differentially edited genes
    Language English
    Dates of publication 2022-1231
    Size p. 852-865.
    Publishing place Taylor & Francis
    Document type Article ; Online
    ZDB-ID 2159587-2
    ISSN 1555-8584
    ISSN 1555-8584
    DOI 10.1080/15476286.2022.2091306
    Database NAL-Catalogue (AGRICOLA)

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  9. Article: Oxidative Stress and the Neurovascular Unit.

    Rinaldi, Carmela / Donato, Luigi / Alibrandi, Simona / Scimone, Concetta / D'Angelo, Rosalia / Sidoti, Antonina

    Life (Basel, Switzerland)

    2021  Volume 11, Issue 8

    Abstract: The neurovascular unit (NVU) is a relatively recent concept that clearly describes the relationship between brain cells and their blood vessels. The components of the NVU, comprising different types of cells, are so interrelated and associated with each ... ...

    Abstract The neurovascular unit (NVU) is a relatively recent concept that clearly describes the relationship between brain cells and their blood vessels. The components of the NVU, comprising different types of cells, are so interrelated and associated with each other that they are considered as a single functioning unit. For this reason, even slight disturbances in the NVU could severely affect brain homeostasis and health. In this review, we aim to describe the current state of knowledge concerning the role of oxidative stress on the neurovascular unit and the role of a single cell type in the NVU crosstalk.
    Language English
    Publishing date 2021-07-29
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life11080767
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: New evaluation methods of read mapping by 17 aligners on simulated and empirical NGS data: an updated comparison of DNA- and RNA-Seq data from Illumina and Ion Torrent technologies.

    Donato, Luigi / Scimone, Concetta / Rinaldi, Carmela / D'Angelo, Rosalia / Sidoti, Antonina

    Neural computing & applications

    2021  Volume 33, Issue 22, Page(s) 15669–15692

    Abstract: During the last (15) years, improved omics sequencing technologies have expanded the scale and resolution of various biological applications, generating high-throughput datasets that require carefully chosen software tools to be processed. Therefore, ... ...

    Abstract During the last (15) years, improved omics sequencing technologies have expanded the scale and resolution of various biological applications, generating high-throughput datasets that require carefully chosen software tools to be processed. Therefore, following the sequencing development, bioinformatics researchers have been challenged to implement alignment algorithms for next-generation sequencing reads. However, nowadays selection of aligners based on genome characteristics is poorly studied, so our benchmarking study extended the "state of art" comparing 17 different aligners. The chosen tools were assessed on empirical human DNA- and RNA-Seq data, as well as on simulated datasets in human and mouse, evaluating a set of parameters previously not considered in such kind of benchmarks. As expected, we found that each tool was the best in specific conditions. For Ion Torrent single-end RNA-Seq samples, the most suitable aligners were CLC and BWA-MEM, which reached the best results in terms of efficiency, accuracy, duplication rate, saturation profile and running time. About Illumina paired-end osteomyelitis transcriptomics data, instead, the best performer algorithm, together with the already cited CLC, resulted Novoalign, which excelled in accuracy and saturation analyses. Segemehl and DNASTAR performed the best on both DNA-Seq data, with Segemehl particularly suitable for exome data. In conclusion, our study could guide users in the selection of a suitable aligner based on genome and transcriptome characteristics. However, several other aspects, emerged from our work, should be considered in the evolution of alignment research area, such as the involvement of artificial intelligence to support cloud computing and mapping to multiple genomes.
    Supplementary information: The online version contains supplementary material available at 10.1007/s00521-021-06188-z.
    Language English
    Publishing date 2021-06-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 1480526-1
    ISSN 1433-3058 ; 0941-0643
    ISSN (online) 1433-3058
    ISSN 0941-0643
    DOI 10.1007/s00521-021-06188-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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