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  1. Article ; Online: The RNA interactome in the Hallmarks of Cancer.

    Gabryelska, Marta M / Conn, Simon J

    Wiley interdisciplinary reviews. RNA

    2023  Volume 14, Issue 5, Page(s) e1786

    Abstract: Ribonucleic acid (RNA) molecules are indispensable for cellular homeostasis in healthy and malignant cells. However, the functions of RNA extend well beyond that of a protein-coding template. Rather, both coding and non-coding RNA molecules function ... ...

    Abstract Ribonucleic acid (RNA) molecules are indispensable for cellular homeostasis in healthy and malignant cells. However, the functions of RNA extend well beyond that of a protein-coding template. Rather, both coding and non-coding RNA molecules function through critical interactions with a plethora of cellular molecules, including other RNAs, DNA, and proteins. Deconvoluting this RNA interactome, including the interacting partners, the nature of the interaction, and dynamic changes of these interactions in malignancies has yielded fundamental advances in knowledge and are emerging as a novel therapeutic strategy in cancer. Here, we present an RNA-centric review of recent advances in the field of RNA-RNA, RNA-protein, and RNA-DNA interactomic network analysis and their impact across the Hallmarks of Cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
    MeSH term(s) Humans ; RNA/genetics ; RNA/metabolism ; Neoplasms/genetics ; Proteins/metabolism ; DNA/metabolism
    Chemical Substances RNA (63231-63-0) ; Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2023-04-12
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2634714-3
    ISSN 1757-7012 ; 1757-7004
    ISSN (online) 1757-7012
    ISSN 1757-7004
    DOI 10.1002/wrna.1786
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  2. Article ; Online: Science: priceless, but costly.

    Gabryelska, Marta

    Molecular biology of the cell

    2021  Volume 32, Issue 8, Page(s) 635–637

    Abstract: Working as a researcher is very satisfying. However, it comes with a price. This is a story about growing up as a scientist in the field of molecular biology. Starting as a young, rather naive researcher, I learned, step by step, not only the facts about ...

    Abstract Working as a researcher is very satisfying. However, it comes with a price. This is a story about growing up as a scientist in the field of molecular biology. Starting as a young, rather naive researcher, I learned, step by step, not only the facts about my favorite RNA molecules but also the demands and downsides of academia. Going through my recent "scientific awakening," I fully acknowledged the rules of the game: to write, to publish, to patent, to apply for grants and awards, and finally, to engage in all forms of coscientific endeavors. After going through a divorce, single parenting, immigration, and being scooped, I became a scientist who finally takes her career in her own hands and navigates through, but does not succumb to, the difficulties in science. This is my monument to resilience.
    MeSH term(s) Adult ; Career Choice ; Female ; History, 21st Century ; Humans ; Publishing ; RNA/genetics ; RNA/metabolism ; RNA/physiology ; Research/trends ; Research Personnel ; Science/trends ; Writing
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2021-04-13
    Publishing country United States
    Document type Autobiography ; Historical Article ; Journal Article
    ZDB-ID 1098979-1
    ISSN 1939-4586 ; 1059-1524
    ISSN (online) 1939-4586
    ISSN 1059-1524
    DOI 10.1091/mbc.E20-12-0768
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  3. Article ; Online: Neurotrophins in the Neuropathophysiology, Course, and Complications of Obstructive Sleep Apnea-A Narrative Review.

    Gabryelska, Agata / Turkiewicz, Szymon / Ditmer, Marta / Sochal, Marcin

    International journal of molecular sciences

    2023  Volume 24, Issue 3

    Abstract: Obstructive sleep apnea (OSA) is a disorder characterized by chronic intermittent hypoxia and sleep fragmentation due to recurring airway collapse during sleep. It is highly prevalent in modern societies, and due to its pleiotropic influence on the ... ...

    Abstract Obstructive sleep apnea (OSA) is a disorder characterized by chronic intermittent hypoxia and sleep fragmentation due to recurring airway collapse during sleep. It is highly prevalent in modern societies, and due to its pleiotropic influence on the organism and numerous sequelae, it burdens patients and physicians. Neurotrophins (NTs), proteins that modulate the functioning and development of the central nervous system, such as brain-derived neurotrophic factor (BDNF), have been associated with OSA, primarily due to their probable involvement in offsetting the decline in cognitive functions which accompanies OSA. However, NTs influence multiple aspects of biological functioning, such as immunity. Thus, extensive evaluation of their role in OSA might enlighten the mechanism behind some of its elusive features, such as the increased risk of developing an immune-mediated disease or the association of OSA with cardiovascular diseases. In this review, we examine the interactions between NTs and OSA and discuss their contribution to OSA pathophysiology, complications, as well as comorbidities.
    MeSH term(s) Humans ; Cardiovascular Diseases ; Comorbidity ; Sleep/physiology ; Sleep Apnea, Obstructive ; Sleep Deprivation ; Nerve Growth Factors
    Chemical Substances BDNF protein, human (7171WSG8A2) ; Nerve Growth Factors
    Language English
    Publishing date 2023-01-17
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24031808
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  4. Article: Investigating the Role of BDNF in Insomnia: Current Insights.

    Ditmer, Marta / Gabryelska, Agata / Turkiewicz, Szymon / Sochal, Marcin

    Nature and science of sleep

    2023  Volume 15, Page(s) 1045–1060

    Abstract: Insomnia is a common disorder defined as frequent and persistent difficulty initiating, maintaining, or going back to sleep. A hallmark symptom of this condition is a sense of nonrestorative sleep. It is frequently associated with other psychiatric ... ...

    Abstract Insomnia is a common disorder defined as frequent and persistent difficulty initiating, maintaining, or going back to sleep. A hallmark symptom of this condition is a sense of nonrestorative sleep. It is frequently associated with other psychiatric disorders, such as depression, as well as somatic ones, including immunomediated diseases. BDNF is a neurotrophin primarily responsible for synaptic plasticity and proper functioning of neurons. Due to its role in the central nervous system, it might be connected to insomnia of multiple levels, from predisposing traits (neuroticism, genetic/epigenetic factors, etc.) through its influence on different modes of neurotransmission (histaminergic and GABAergic in particular), maintenance of circadian rhythm, and sleep architecture, and changes occurring in the course of mood disturbances, substance abuse, or dementia. Extensive and interdisciplinary evaluation of the role of BDNF could aid in charting new areas for research and further elucidate the molecular background of sleep disorder. In this review, we summarize knowledge on the role of BDNF in insomnia with a focus on currently relevant studies and discuss their implications for future projects.
    Language English
    Publishing date 2023-12-07
    Publishing country New Zealand
    Document type Journal Article ; Review
    ZDB-ID 2587468-8
    ISSN 1179-1608
    ISSN 1179-1608
    DOI 10.2147/NSS.S401271
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  5. Article ; Online: Evaluation of oxidative stress in obstructive sleep apnea and its comorbidities using serum concentrations of oxidized guanine species.

    Turkiewicz, Szymon / Sochal, Marcin / Ditmer, Marta / Gabryelska, Agata

    Polish archives of internal medicine

    2023  Volume 133, Issue 9

    MeSH term(s) Humans ; Oxidative Stress ; Sleep Apnea, Obstructive ; Comorbidity
    Language English
    Publishing date 2023-08-07
    Publishing country Poland
    Document type Journal Article
    ZDB-ID 123500-x
    ISSN 1897-9483 ; 0032-3772
    ISSN (online) 1897-9483
    ISSN 0032-3772
    DOI 10.20452/pamw.16542
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  6. Article ; Online: Global mapping of RNA homodimers in living cells

    Gabryelska, Marta M / Kudla, Grzegorz

    bioRxiv

    Abstract: RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding of RNA homodimerization has been hampered by ... ...

    Abstract RNA homodimerization is important for various physiological processes, including the assembly of membraneless organelles, RNA subcellular localization, and packaging of viral genomes. However, understanding of RNA homodimerization has been hampered by the lack of systematic in vivo detection methods. Here we show that PARIS, COMRADES, and other RNA proximity ligation methods can detect RNA homodimers transcriptome-wide as "overlapping" chimeric reads that contain more than one copy of the same sequence. Analysing published proximity ligation datasets, we show that RNA:RNA homodimers mediated by direct base-pairing interactions are rare across the transcriptome, but highly enriched in specific transcripts, including U8 snoRNA, U2 snRNA and a subset of tRNAs. Analysis of data from virus-infected cells reveals homodimerization of SARS-CoV-2 and Zika genomes, mediated by specific palindromic sequences located within protein-coding regions of N protein in SARS-CoV-2 and NS2A gene in Zika. We speculate that regions of viral genomes involved in homodimerization may constitute effective targets for antiviral therapies.
    Keywords covid19
    Language English
    Publishing date 2021-05-17
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.05.13.444021
    Database COVID19

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  7. Article: The Role of Brain-Derived Neurotrophic Factor in Immune-Related Diseases: A Narrative Review.

    Sochal, Marcin / Ditmer, Marta / Gabryelska, Agata / Białasiewicz, Piotr

    Journal of clinical medicine

    2022  Volume 11, Issue 20

    Abstract: Brain-derived neurotrophic factor (BDNF) is a neurotrophin regulating synaptic plasticity, neuronal excitability, and nociception. It seems to be one of the key molecules in interactions between the central nervous system and immune-related diseases, i.e. ...

    Abstract Brain-derived neurotrophic factor (BDNF) is a neurotrophin regulating synaptic plasticity, neuronal excitability, and nociception. It seems to be one of the key molecules in interactions between the central nervous system and immune-related diseases, i.e., diseases with an inflammatory background of unknown etiology, such as inflammatory bowel diseases or rheumatoid arthritis. Studies show that BDNF levels might change in the tissues and serum of patients during the course of these conditions, e.g., affecting cell survival and modulating pain severity and signaling pathways involving different neurotransmitters. Immune-related conditions often feature psychiatric comorbidities, such as sleep disorders (e.g., insomnia) and symptoms of depression/anxiety; BDNF may be related as well to them as it seems to exert an influence on sleep structure; studies also show that patients with psychiatric disorders have decreased BDNF levels, which increase after treatment. BDNF also has a vital role in nociception, particularly in chronic pain, hyperalgesia, and allodynia, participating in the formation of central hypersensitization. In this review, we summarize the current knowledge on BDNF's function in immune-related diseases, sleep, and pain. We also discuss how BDNF is affected by treatment and what consequences these changes might have beyond the nervous system.
    Language English
    Publishing date 2022-10-12
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm11206023
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  8. Article ; Online: Native Circular RNA Pulldown Method to Simultaneously Profile RNA and Protein Interactions.

    Gabryelska, Marta M / Webb, Stuart T / Lin, He / Gantley, Laura / Kirk, Kirsty / Liu, Ryan / Stringer, Brett W / Conn, Vanessa M / Conn, Simon J

    Methods in molecular biology (Clifton, N.J.)

    2024  Volume 2765, Page(s) 299–309

    Abstract: Circular RNAs (circRNAs) are a widespread, cell-, tissue-, and disease-specific class of largely non-coding RNA transcripts. These single-stranded, covalently-closed transcripts arise through non-canonical splicing of pre-mRNA, a process called back- ... ...

    Abstract Circular RNAs (circRNAs) are a widespread, cell-, tissue-, and disease-specific class of largely non-coding RNA transcripts. These single-stranded, covalently-closed transcripts arise through non-canonical splicing of pre-mRNA, a process called back-splicing. Back-splicing results in circRNAs which are distinguishable from their cognate mRNA as they possess a unique sequence of nucleic acids called the backsplice junction (BSJ). CircRNAs have been shown to play key functional roles in various cellular contexts and achieve this through their interaction with other macromolecules, particularly other RNA molecules and proteins. To elucidate the molecular mechanisms underlying circRNA function, it is necessary to identify these interacting partners. Herein, we present an optimized strategy for the simultaneous purification of the circRNA interactome within eukaryotic cells, allowing the identification of both circRNA-RNA and circRNA-protein interactions.
    MeSH term(s) RNA, Circular ; RNA/genetics ; RNA Precursors ; RNA, Messenger/genetics ; Eukaryotic Cells
    Chemical Substances RNA, Circular ; RNA (63231-63-0) ; RNA Precursors ; RNA, Messenger
    Language English
    Publishing date 2024-02-21
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3678-7_16
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  9. Article: Evaluation of cognitive and psychomotor faculties in relation to mood-related symptoms under the conditions of sleep deprivation.

    Sochal, Marcin / Ditmer, Marta / Białasiewicz, Piotr / Turkiewicz, Szymon / Karuga, Filip Franciszek / Gabryelska, Agata

    Frontiers in psychiatry

    2023  Volume 14, Page(s) 1332831

    Abstract: Introduction: Deprivation of sleep (DS) has been associated with changes in mood and cognitive function, rapidly but transiently improving the severity of depression symptoms. However, it remains unclear whether there are differences in performance ... ...

    Abstract Introduction: Deprivation of sleep (DS) has been associated with changes in mood and cognitive function, rapidly but transiently improving the severity of depression symptoms. However, it remains unclear whether there are differences in performance between DS responders and non-responders. The relationship between DS, mood, cognitive, and psychomotor function is also poorly understood.
    Methods: Participants (
    Results: All participants exhibited increased response speed to visual triggers after DS compared to baseline (
    Conclusion: RE tend to maintain or improve cognitive function after DS, oppositely to NR. Vigilance in particular might be tightly associated with changes in depression symptoms after DS. Future studies should examine the biological basis behind the response to sleep loss.
    Language English
    Publishing date 2023-12-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564218-2
    ISSN 1664-0640
    ISSN 1664-0640
    DOI 10.3389/fpsyt.2023.1332831
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  10. Article ; Online: Relation between serum interleukin 33 concentration, depressive symptoms, and sleep quality in inflammatory bowel disease.

    Sochal, Marcin / Ditmer, Marta / Małecka-Wojciesko, Ewa / Gabryelska, Agata / Talar-Wojnarowska, Renata / Białasiewicz, Piotr

    Polish archives of internal medicine

    2023  Volume 133, Issue 9

    MeSH term(s) Humans ; Depression/blood ; Depression/etiology ; Depression/genetics ; Depression/metabolism ; Inflammatory Bowel Diseases/blood ; Inflammatory Bowel Diseases/complications ; Inflammatory Bowel Diseases/genetics ; Inflammatory Bowel Diseases/metabolism ; Interleukin-33/blood ; Interleukin-33/genetics ; Interleukin-33/metabolism ; Sleep/genetics ; Sleep/physiology ; Sleep Quality ; Dyssomnias/blood ; Dyssomnias/etiology ; Dyssomnias/genetics ; Dyssomnias/metabolism
    Chemical Substances Interleukin-33 ; IL33 protein, human
    Language English
    Publishing date 2023-08-25
    Publishing country Poland
    Document type Journal Article
    ZDB-ID 123500-x
    ISSN 1897-9483 ; 0032-3772
    ISSN (online) 1897-9483
    ISSN 0032-3772
    DOI 10.20452/pamw.16549
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