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  1. Article ; Online: The landscape of histone modifications in epigenomics since 2020.

    Shirvaliloo, Milad

    Epigenomics

    2023  Volume 14, Issue 23, Page(s) 1465–1477

    Abstract: Histone proteins are a primary component of chromatin; therefore, any modifications to their structure are anticipated to affect the behavior of our genetic material, which is manifested in the form of phenotypic changes at a molecular, cellular or ... ...

    Abstract Histone proteins are a primary component of chromatin; therefore, any modifications to their structure are anticipated to affect the behavior of our genetic material, which is manifested in the form of phenotypic changes at a molecular, cellular or organic level. The majority of histone modifications are of either methylation or acetylation type that regulate gene expression. Though, not all of these modifications are concerned with the direct regulation of gene transcription. Throughout its 13-year run,
    MeSH term(s) Humans ; Histones/genetics ; Histones/metabolism ; Histone Code ; Epigenomics ; Chromatin/genetics ; Protein Processing, Post-Translational ; Acetylation ; Epigenesis, Genetic
    Chemical Substances Histones ; Chromatin
    Language English
    Publishing date 2023-01-30
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2537199-X
    ISSN 1750-192X ; 1750-1911
    ISSN (online) 1750-192X
    ISSN 1750-1911
    DOI 10.2217/epi-2022-0437
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: LncRNA H19 promotes tumor angiogenesis in smokers by targeting anti-angiogenic miRNAs.

    Shirvaliloo, Milad

    Epigenomics

    2023  Volume 15, Issue 2, Page(s) 61–73

    Abstract: A key concept in drug discovery is the identification of candidate therapeutic targets such as long noncoding RNAs (lncRNAs) because of their extensive involvement in neoplasms, and impressionability by smoking. Induced by exposure to cigarette smoke, ... ...

    Abstract A key concept in drug discovery is the identification of candidate therapeutic targets such as long noncoding RNAs (lncRNAs) because of their extensive involvement in neoplasms, and impressionability by smoking. Induced by exposure to cigarette smoke, lncRNA H19 targets and inactivates miR-29, miR-30a, miR-107, miR-140, miR-148b, miR-199a and miR-200, which control the rate of angiogenesis by inhibiting BiP,
    MeSH term(s) Male ; Humans ; MicroRNAs/genetics ; RNA, Long Noncoding/genetics ; Carcinoma, Squamous Cell ; Carcinoma, Non-Small-Cell Lung ; Smokers ; Cell Line, Tumor ; Mouth Neoplasms ; Lung Neoplasms ; Adenocarcinoma ; Head and Neck Neoplasms ; Cell Proliferation/genetics
    Chemical Substances MicroRNAs ; RNA, Long Noncoding ; Mirn140 microRNA, human
    Language English
    Publishing date 2023-02-19
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2537199-X
    ISSN 1750-192X ; 1750-1911
    ISSN (online) 1750-192X
    ISSN 1750-1911
    DOI 10.2217/epi-2022-0145
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The unfavorable clinical outcome of COVID-19 in smokers is mediated by H3K4me3, H3K9me3 and H3K27me3 histone marks.

    Shirvaliloo, Milad

    Epigenomics

    2022  Volume 14, Issue 3, Page(s) 153–162

    Abstract: Smoking could predispose individuals to a more severe COVID-19 by upregulating a particular gene known ... ...

    Abstract Smoking could predispose individuals to a more severe COVID-19 by upregulating a particular gene known as
    MeSH term(s) Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; COVID-19/diagnosis ; COVID-19/genetics ; COVID-19/metabolism ; COVID-19/virology ; Cathepsin D/genetics ; Cathepsin D/metabolism ; Cathepsin L/genetics ; Cathepsin L/metabolism ; Dioxygenases/genetics ; Dioxygenases/metabolism ; Epigenesis, Genetic ; Histone Demethylases/genetics ; Histone Demethylases/metabolism ; Histones/genetics ; Histones/metabolism ; Humans ; Interleukin-6/genetics ; Interleukin-6/metabolism ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Methylation ; Neuropilin-1/genetics ; Neuropilin-1/metabolism ; Neuropilin-2/genetics ; Neuropilin-2/metabolism ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Protein Processing, Post-Translational ; Receptor, Angiotensin, Type 1/genetics ; Receptor, Angiotensin, Type 1/metabolism ; Receptors, Prostaglandin E/genetics ; Receptors, Prostaglandin E/metabolism ; Risk Factors ; SARS-CoV-2/genetics ; SARS-CoV-2/growth & development ; SARS-CoV-2/metabolism ; Smoking/genetics ; Smoking/metabolism ; Smoking/pathology ; Virus Internalization
    Chemical Substances AGTR1 protein, human ; Histones ; IL6 protein, human ; Interleukin-6 ; Membrane Transport Proteins ; NRP1 protein, human ; Neuropilin-2 ; Nuclear Proteins ; Protein Isoforms ; Receptor, Angiotensin, Type 1 ; Receptors, Prostaglandin E ; SLC6A20 protein, human ; histone H3 trimethyl Lys4 ; neuropilin-2, human ; Neuropilin-1 (144713-63-3) ; Dioxygenases (EC 1.13.11.-) ; Histone Demethylases (EC 1.14.11.-) ; RIOX2 protein, human (EC 1.14.11.-) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; CTSL protein, human (EC 3.4.22.15) ; Cathepsin L (EC 3.4.22.15) ; CTSD protein, human (EC 3.4.23.5) ; Cathepsin D (EC 3.4.23.5)
    Language English
    Publishing date 2022-01-13
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2537199-X
    ISSN 1750-192X ; 1750-1911
    ISSN (online) 1750-192X
    ISSN 1750-1911
    DOI 10.2217/epi-2021-0476
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Epigenomics in COVID-19; the link between DNA methylation, histone modifications and SARS-CoV-2 infection.

    Shirvaliloo, Milad

    Epigenomics

    2021  Volume 13, Issue 10, Page(s) 745–750

    MeSH term(s) COVID-19/genetics ; COVID-19/immunology ; COVID-19/virology ; Chromosomes, Human, X ; DNA Methylation ; Epigenomics ; Histone Code ; Humans ; Immunity, Innate ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/physiology ; Virus Internalization
    Language English
    Publishing date 2021-04-20
    Publishing country England
    Document type Editorial
    ZDB-ID 2537199-X
    ISSN 1750-192X ; 1750-1911
    ISSN (online) 1750-192X
    ISSN 1750-1911
    DOI 10.2217/epi-2021-0057
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Targeting the SARS-CoV-2 3CL

    Shirvaliloo, Milad

    Future cardiology

    2021  Volume 17, Issue 5, Page(s) 765–768

    MeSH term(s) COVID-19/virology ; Cyclic GMP/metabolism ; Humans ; Phosphodiesterase 5 Inhibitors/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/metabolism ; COVID-19 Drug Treatment
    Chemical Substances Phosphodiesterase 5 Inhibitors ; Cyclic GMP (H2D2X058MU)
    Language English
    Publishing date 2021-02-12
    Publishing country England
    Document type Editorial
    ZDB-ID 2274267-0
    ISSN 1744-8298 ; 1479-6678
    ISSN (online) 1744-8298
    ISSN 1479-6678
    DOI 10.2217/fca-2020-0201
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6836: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  6. Article ; Online: The blood-gas barrier in COVID-19: an overview of the effects of SARS-CoV-2 infection on the alveolar epithelial and endothelial cells of the lung.

    Shirvaliloo, Milad

    Tissue barriers

    2021  Volume 9, Issue 4, Page(s) 1937013

    Abstract: Blood-gas barrier (BGB) or alveolar-capillary barrier is the primary tissue barrier affected by coronavirus disease 2019 (COVID-19). Comprising alveolar epithelial cells (AECs), endothelial cells (ECs) and the extracellular matrix (ECM) in between, the ... ...

    Abstract Blood-gas barrier (BGB) or alveolar-capillary barrier is the primary tissue barrier affected by coronavirus disease 2019 (COVID-19). Comprising alveolar epithelial cells (AECs), endothelial cells (ECs) and the extracellular matrix (ECM) in between, the BGB is damaged following the action of multiple pro-inflammatory cytokines during acute inflammation. The infection of AECs and ECs with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen behind COVID-19, triggers an inflammatory response at the BGB, inducing the release of interleukin 1 (IL-1), IL-6, tumor necrosis factor alpha (TNF-α), transforming growth factor beta (TGF-β), high mobility group box 1 (HMGB1), matrix metalloproteinases (MMPs), intercellular adhesion molecule-1 (ICAM-1) and platelet activating factor (PAF). The end result is the disassembly of adherens junctions (AJs) and tight junctions (TJs) in both AECs and ECs, AEC hyperplasia, EC pyroptosis, ECM remodeling and deposition of fibrin clots in the alveolar capillaries, leading to disintegration and thickening of the BGB, and ultimately, hypoxia. This commentary seeks to provide a brief account of how the BGB might become affected in COVID-19.
    MeSH term(s) Alveolar Epithelial Cells/metabolism ; Alveolar Epithelial Cells/pathology ; Blood-Air Barrier/metabolism ; Blood-Air Barrier/pathology ; COVID-19/metabolism ; COVID-19/pathology ; Humans ; Microvessels/metabolism ; Microvessels/pathology ; Pulmonary Gas Exchange
    Language English
    Publishing date 2021-07-07
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2168-8370
    ISSN (online) 2168-8370
    DOI 10.1080/21688370.2021.1937013
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  7. Article ; Online: Epigenetic memory in breast cancer: electrochemical biosensor-based tracing of histone H3 acetylation inheritance.

    Youshanlui, Mahya Ahmadpour / Shirvaliloo, Milad

    Epigenomics

    2023  Volume 15, Issue 3, Page(s) 111–114

    MeSH term(s) Humans ; Female ; Histones/genetics ; Histones/metabolism ; Breast Neoplasms/genetics ; Epigenetic Memory ; Acetylation ; Epigenesis, Genetic ; Biosensing Techniques
    Chemical Substances Histones
    Language English
    Publishing date 2023-04-05
    Publishing country England
    Document type Editorial
    ZDB-ID 2537199-X
    ISSN 1750-192X ; 1750-1911
    ISSN (online) 1750-192X
    ISSN 1750-1911
    DOI 10.2217/epi-2023-0061
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Epigenetic cues regulating airway development in human lung organoids: Polycomb repressive complex 2 and altered chromatin accessibility determine cell fate.

    Shirvaliloo, Milad / Akhavan-Sigari, Reza

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology

    2023  Volume 37, Issue 4, Page(s) e22868

    Abstract: Today, human organoids are becoming an integrated part of genomics and epigenomics, as they provide a platform that can be used for the definite study of molecular and cellular mechanisms occurring at different stages of development, particularly ... ...

    Abstract Today, human organoids are becoming an integrated part of genomics and epigenomics, as they provide a platform that can be used for the definite study of molecular and cellular mechanisms occurring at different stages of development, particularly organogenesis, within the human body. Airway development is a complex process heavily influenced by epigenetic regulatory mechanisms in response to environmental changes, and as such, human lung organoids are an indispensable asset for further exploration of these mechanisms as a mode of transition from human in vitro to human ex vivo studies. Cultured primarily in compounds mimicking the extracellular matrix, such as Matrigel, these lung organoids have helped us to come to a better understanding of the role of polycomb repressive complex 2 (PRC2) and enhancer of zeste homolog 2 (EZH2) in lung epithelial cell differentiation and airway development, which was first reported in the FASEB journal in 2019. The following is an extended account of how the histone methylation-regulating PRC2 comes to play in the molding of the human bronchial tree, along with further epigenetic insights based on more recently developed human lung organoids.
    MeSH term(s) Humans ; Polycomb Repressive Complex 2/genetics ; Epigenomics ; Cues ; Enhancer of Zeste Homolog 2 Protein/metabolism ; Cell Differentiation ; Epigenesis, Genetic ; Chromatin/genetics ; Lung/metabolism ; Organoids/metabolism
    Chemical Substances Polycomb Repressive Complex 2 (EC 2.1.1.43) ; Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43) ; Chromatin
    Language English
    Publishing date 2023-03-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 639186-2
    ISSN 1530-6860 ; 0892-6638
    ISSN (online) 1530-6860
    ISSN 0892-6638
    DOI 10.1096/fj.202201666R
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2266: 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)
    Zs.MO 296: Show issues

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  9. Article ; Online: Symptomatology and microbiology of the gastrointestinal tract in post-COVID conditions.

    Norouzi Masir, Mohamad / Shirvaliloo, Milad

    JGH open : an open access journal of gastroenterology and hepatology

    2022  

    Abstract: Post-COVID conditions, also known as post-acute sequelae of SARS-CoV-2 (PASC), refer to the persistence of symptoms in COVID-19 long-haulers. Various manifestations of post-COVID conditions are general symptoms and/or manifestations of damage in multiple ...

    Abstract Post-COVID conditions, also known as post-acute sequelae of SARS-CoV-2 (PASC), refer to the persistence of symptoms in COVID-19 long-haulers. Various manifestations of post-COVID conditions are general symptoms and/or manifestations of damage in multiple organs. Besides, SARS-CoV-2 can involve the gastrointestinal tract, resulting in sequelae such as diarrhea, abdominal pain, nausea, anorexia, vomiting, constipation, abdominal distension, acid reflux, and/or gastrointestinal bleeding. Previous investigations point to SARS-CoV-2 entry into enterocytes enhances by the angiotensin-converting enzyme 2 (ACE2) receptors. Interestingly, ACE2 receptors are abundantly expressed in the gut, implying infection with SARS-CoV-2 might occur through this route as well as in the respiratory tract. According to mounting evidence, SARS-CoV-2 RNA has been identified in fecal specimens of patients with COVID-19 during and beyond the acute phase. In addition, studies have shown gut microbiome composition is altered in patients with PASC, hence, another putative mechanism linked to gastrointestinal symptoms is gut dysbiosis. The presence of the gut-lung axis in COVID-19 might have major implications for disease pathogenesis and treatment. This review discussed the prevalence of gastrointestinal symptoms and pathophysiology underlying possible infection of the gut in patients with PASC. Also, SARS-COV-2 induced NLRP3 inflammasome-dependent inflammatory pathways are briefly addressed.
    Language English
    Publishing date 2022-08-25
    Publishing country Australia
    Document type Journal Article ; Review
    ISSN 2397-9070
    ISSN (online) 2397-9070
    DOI 10.1002/jgh3.12811
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  10. Article ; Online: Expression and promoter methylation of mitogen-activated protein kinase 1 in tumor and marginal cells of breast cancer.

    Goldoost, Solmaz / Zarredar, Habib / Asadi, Milad / Shirvaliloo, Milad / Raeisi, Mortaza

    Breast disease

    2023  Volume 42, Issue 1, Page(s) 437–445

    Abstract: Aim: In the present study, we sought to explore potential differences in the expression and promoter methylation of mitogen-activated protein kinase 1 (MAPK1) between tumor and marginal cells of breast cancer lesions.: Methods: A total of 50 randomly ...

    Abstract Aim: In the present study, we sought to explore potential differences in the expression and promoter methylation of mitogen-activated protein kinase 1 (MAPK1) between tumor and marginal cells of breast cancer lesions.
    Methods: A total of 50 randomly selected patients with breast cancer (BCa) undergoing needle biopsy were enrolled. Clinical specimens containing both tumor and marginal cells were collected and preserved. After DNA extraction using specific primers, MAPK1 mRNA and promoter methylation were measured with spectrophotometry at 260/280 nm absorption wavelengths. To deliver a comparative analysis, data from The Cancer Genome Atlas (TCGA) program regarding breast cancer (BRCA), were downloaded from Xena Functional Genomics Explorer and separately analyzed. The suitability of MAPK1 expression and promoter methylation as biomarkers for BCa was analyzed with receiver operating characteristic (ROC) curves.
    Results: We found a positive correlation between tumor stage and MAPK1 expression (P-value: 0.029) in BCa. Likewise, MAPK1 expression was significantly associated with lymph node metastasis (P-value: 0.018). There was a significant difference in the expression of MAPK1 mRNA between tumor and marginal cells of BCa and BRCA (P-value < 0.001). However, we did not find any statistically significant difference in MAPK1 promoter methylation between tumor and marginal cells of both BCa and BRCA. With an area under the curve (AUC) of 0.71, the diagnostic accuracy of MAPK1 expression in BCa and BRCA was validated. However, MAPK1 promoter methylation was not found to be a suitable biomarker.
    Conclusion: Our findings suggest that while MAPK1 expression, might be a promising biomarker for evaluating oncogenic activity in patients suspected of BCa. We were not able to detect a prognostic/diagnostic role for MAPK1 promoter methylation.
    MeSH term(s) Humans ; Female ; Breast Neoplasms/pathology ; DNA Methylation ; Mitogen-Activated Protein Kinase 1/genetics ; Mitogen-Activated Protein Kinase 1/metabolism ; Biomarkers ; RNA, Messenger/metabolism ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism
    Chemical Substances Mitogen-Activated Protein Kinase 1 (EC 2.7.11.24) ; Biomarkers ; RNA, Messenger ; Biomarkers, Tumor
    Language English
    Publishing date 2023-12-22
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 639267-2
    ISSN 1558-1551 ; 0888-6008
    ISSN (online) 1558-1551
    ISSN 0888-6008
    DOI 10.3233/BD-230001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2294: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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