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  1. Article ; Online: The COVID-19 Pandemic Enhanced Virology Research in Greece.

    Beloukas, Apostolos / Chaintoutis, Serafeim C / Karakasiliotis, Ioannis

    Viruses

    2022  Volume 15, Issue 1

    Abstract: The emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presented an unprecedented public health threat, being the cause of one of the most devastating pandemics in history [ ... ]. ...

    Abstract The emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presented an unprecedented public health threat, being the cause of one of the most devastating pandemics in history [...].
    MeSH term(s) Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; Pandemics ; Greece/epidemiology
    Language English
    Publishing date 2022-12-25
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15010069
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Cellular senescence as a source of SARS‐CoV‐2 quasispecies

    Karakasiliotis, Ioannis / Lagopati, Nefeli / Evangelou, Konstantinos / Gorgoulis, Vassilis G.

    The FEBS Journal. 2023 Mar., v. 290, no. 5 p.1384-1392

    2023  

    Abstract: In‐depth analysis of SARS‐CoV‐2 biology and pathogenesis is rapidly unraveling the mechanisms through which the virus induces all aspects of COVID‐19 pathology. Emergence of hundreds of variants and several important variants of concern has focused ... ...

    Abstract In‐depth analysis of SARS‐CoV‐2 biology and pathogenesis is rapidly unraveling the mechanisms through which the virus induces all aspects of COVID‐19 pathology. Emergence of hundreds of variants and several important variants of concern has focused research on the mechanistic elucidation of virus mutagenesis. RNA viruses evolve quickly either through the error‐prone polymerase or the RNA‐editing machinery of the cell. In this review, we are discussing the links between cellular senescence, a natural aging process that has been recently linked to SARS‐CoV‐2 infection, and virus mutagenesis through the RNA‐editing enzymes APOBEC. The action of APOBEC, enhanced by cellular senescence, is hypothesized to assist the emergence of novel variants, called quasispecies, within a cell or organism. These variants when introduced to the community may lead to the generation of a variant of concern, depending on fitness and transmissibility of the new genome. Such a mechanism of virus evolution may highlight the importance of inhibitors of cellular senescence during SARS‐CoV‐2 clinical treatment.
    Keywords COVID-19 infection ; RNA ; RNA editing ; Severe acute respiratory syndrome coronavirus 2 ; cell senescence ; evolution ; genome ; mutagenesis ; pathogenesis ; viruses
    Language English
    Dates of publication 2023-03
    Size p. 1384-1392.
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note REVIEW
    ZDB-ID 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.16230
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Next-Generation Sequencing Analysis of Mutations in Circulating Tumor DNA from the Plasma of Patients with Head-Neck Cancer Undergoing Chemo-Radiotherapy Using a Pan-Cancer Cell-Free Assay.

    Koukourakis, Michael I / Xanthopoulou, Erasmia / Koukourakis, Ioannis M / Fortis, Sotirios P / Kesesidis, Nikolaos / Kakouratos, Christos / Karakasiliotis, Ioannis / Baxevanis, Constantin N

    Current oncology (Toronto, Ont.)

    2023  Volume 30, Issue 10, Page(s) 8902–8915

    Abstract: Using next-generation sequencing (NGS), we investigated DNA mutations in the plasma tumor cell-free circulating DNA (ctDNA) of 38 patients with inoperable squamous cell head neck cancer (SCHNC) before and after the completion of chemoradiotherapy (CRT). ... ...

    Abstract Using next-generation sequencing (NGS), we investigated DNA mutations in the plasma tumor cell-free circulating DNA (ctDNA) of 38 patients with inoperable squamous cell head neck cancer (SCHNC) before and after the completion of chemoradiotherapy (CRT). Baseline mutations of the
    MeSH term(s) Humans ; Circulating Tumor DNA/genetics ; Neoplasm Recurrence, Local/genetics ; Head and Neck Neoplasms/drug therapy ; Head and Neck Neoplasms/genetics ; Mutation ; High-Throughput Nucleotide Sequencing ; Chemoradiotherapy
    Chemical Substances Circulating Tumor DNA
    Language English
    Publishing date 2023-09-29
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1236972-x
    ISSN 1718-7729 ; 1198-0052
    ISSN (online) 1718-7729
    ISSN 1198-0052
    DOI 10.3390/curroncol30100643
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Circulating Plasma Cell-free DNA (cfDNA) as a Predictive Biomarker for Radiotherapy: Results from a Prospective Trial in Head and Neck Cancer.

    Koukourakis, Michael I / Xanthopoulou, Erasmia / Koukourakis, Ioannis M / Fortis, Sotirios P / Kesesidis, Nikolaos / Karakasiliotis, Ioannis / Baxevanis, Constantin N

    Cancer diagnosis & prognosis

    2023  Volume 3, Issue 5, Page(s) 551–557

    Abstract: Background/aim: The plasma levels of cell-free DNA (cfDNA) in cancer patients increase due to rapid cancer cell proliferation and death. Therefore, cfDNA can be used to study specific tumor-DNA features. In addition, the non-specific cfDNA concentration ...

    Abstract Background/aim: The plasma levels of cell-free DNA (cfDNA) in cancer patients increase due to rapid cancer cell proliferation and death. Therefore, cfDNA can be used to study specific tumor-DNA features. In addition, the non-specific cfDNA concentration may be an important biomarker of cancer prognosis.
    Patients and methods: We prospectively examined the predictive role of cfDNA levels and the kinetics in the outcome of chemo-radiotherapy (CRT) in a cohort of 47 patients with locally advanced squamous cell head-neck cancer (SCHNC) treated with definitive chemo-radiotherapy.
    Results: Increased cfDNA levels after therapy completion (after/before treatment ratio; A/B-ratio >1) were found in 26/47 patients (55.3%). Locally advanced T4-stage was significantly associated with higher cfDNA levels after CRT (3.3 ng/μl in T4-stage vs. 1.3 ng/μl in T1-3 stages, p=0.007). Patients who responded to CRT (partial/complete response) had significantly lower cfDNA levels before therapy (mean values 1.2 ng/μl vs. 2.7 ng/μl, p=0.03). A significantly worse locoregional progression-free survival in patients with an A/B-ratio >1 was documented (p=0.01; hazard ratio 3.5, 95%CI=1.2-9.7). This was also confirmed in multivariate analysis, where the A/B-ratio was an independent predictive variable of locoregional relapse (p=0.03, hazard ratio 3.9, 95%CI=1.2-13).
    Conclusion: High post-CRT cfDNA levels could be an early biomarker for the immediate recruitment of patients with SCHNC in consolidation chemo-immunotherapy protocols.
    Language English
    Publishing date 2023-09-03
    Publishing country Greece
    Document type Journal Article
    ISSN 2732-7787
    ISSN (online) 2732-7787
    DOI 10.21873/cdp.10254
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Cellular senescence as a source of SARS-CoV-2 quasispecies.

    Karakasiliotis, Ioannis / Lagopati, Nefeli / Evangelou, Konstantinos / Gorgoulis, Vassilis G

    The FEBS journal

    2021  Volume 290, Issue 5, Page(s) 1384–1392

    Abstract: In-depth analysis of SARS-CoV-2 biology and pathogenesis is rapidly unraveling the mechanisms through which the virus induces all aspects of COVID-19 pathology. Emergence of hundreds of variants and several important variants of concern has focused ... ...

    Abstract In-depth analysis of SARS-CoV-2 biology and pathogenesis is rapidly unraveling the mechanisms through which the virus induces all aspects of COVID-19 pathology. Emergence of hundreds of variants and several important variants of concern has focused research on the mechanistic elucidation of virus mutagenesis. RNA viruses evolve quickly either through the error-prone polymerase or the RNA-editing machinery of the cell. In this review, we are discussing the links between cellular senescence, a natural aging process that has been recently linked to SARS-CoV-2 infection, and virus mutagenesis through the RNA-editing enzymes APOBEC. The action of APOBEC, enhanced by cellular senescence, is hypothesized to assist the emergence of novel variants, called quasispecies, within a cell or organism. These variants when introduced to the community may lead to the generation of a variant of concern, depending on fitness and transmissibility of the new genome. Such a mechanism of virus evolution may highlight the importance of inhibitors of cellular senescence during SARS-CoV-2 clinical treatment.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/genetics ; Quasispecies ; Viruses/genetics ; Cellular Senescence/genetics ; RNA
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2021-11-08
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2173655-8
    ISSN 1742-4658 ; 1742-464X
    ISSN (online) 1742-4658
    ISSN 1742-464X
    DOI 10.1111/febs.16230
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Embryonic Cell-free DNA in Spent Culture Medium: A Non-invasive Tool for Aneuploidy Screening of the Corresponding Embryos.

    Sialakouma, Afrodite / Karakasiliotis, Ioannis / Ntala, Vaia / Nikolettos, Nikolaos / Asimakopoulos, Byron

    In vivo (Athens, Greece)

    2021  Volume 35, Issue 6, Page(s) 3449–3457

    Abstract: Background/aim: Preimplantation genetic testing (PGT) for chromosomal screening, based on embryo biopsy, has significant limitations. Cell-free DNA (cf-DNA) has been detected in spent culture medium (SCM), opening new horizons for the development of non- ...

    Abstract Background/aim: Preimplantation genetic testing (PGT) for chromosomal screening, based on embryo biopsy, has significant limitations. Cell-free DNA (cf-DNA) has been detected in spent culture medium (SCM), opening new horizons for the development of non-invasive PGT (ni-PGT). In this study, we evaluated the diagnostic performance of ni-PGT for aneuploidy (niPGT-A), comparing the results of trophectoderm biopsies (TE) and respective SCM from individually cultured embryos via Next Generation Sequencing (NGS).
    Materials and methods: Forty fresh embryos were analyzed. TE and SCM from blastocysts were collected and analyzed.
    Results: We detected cfDNA in 100% of samples tested. The overall concordance rate between the ni-PGT-A and PGT-A was 27/33 (81.8%). The full concordance rate was 21/33 (63.6%). The aneuploidy agreement was 91.66%, and the euploidy agreement was 76.19%.
    Conclusion: We found a good accordance between TE and SCM analysis, suggesting that niPGT-A could be a reliable alternative for chromosomal abnormalities assessment of in vitro cultured embryos.
    MeSH term(s) Aneuploidy ; Blastocyst ; Cell-Free Nucleic Acids/genetics ; Female ; Genetic Testing ; Humans ; Pregnancy ; Preimplantation Diagnosis
    Chemical Substances Cell-Free Nucleic Acids
    Language English
    Publishing date 2021-11-12
    Publishing country Greece
    Document type Journal Article
    ZDB-ID 807031-3
    ISSN 1791-7549 ; 0258-851X
    ISSN (online) 1791-7549
    ISSN 0258-851X
    DOI 10.21873/invivo.12645
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: West Nile Disease Symptoms and Comorbidities: A Systematic Review and Analysis of Cases.

    Bampali, Maria / Konstantinidis, Konstantinos / Kellis, Emmanouil E / Pouni, Theodoti / Mitroulis, Ioannis / Kottaridi, Christine / Mathioudakis, Alexander G / Beloukas, Apostolos / Karakasiliotis, Ioannis

    Tropical medicine and infectious disease

    2022  Volume 7, Issue 9

    Abstract: West Nile virus (WNV) is a mosquito-borne flavivirus that has emerged as a major cause of viral encephalitis and meningitis, rarely leading to death. Several risk factors have been discussed in the past concerning the severity of the disease, while few ... ...

    Abstract West Nile virus (WNV) is a mosquito-borne flavivirus that has emerged as a major cause of viral encephalitis and meningitis, rarely leading to death. Several risk factors have been discussed in the past concerning the severity of the disease, while few reports have focused on precipitating conditions that determine of WNV-related death. Studies on cohorts of patients suffering of West Nile disease (WND) usually encompass low numbers of deceased patients as a result of the rarity of the event. In this systematic review and critical analysis of 428 published case studies and case series, we sought to evaluate and highlight critical parameters of WND-related death. We summarized the symptoms, comorbidities, and treatment strategies related to WND in all published cases of patients that included clinical features. Symptoms such as altered mental status and renal problems presented increased incidence among deceased patients, while these patients presented increased cerebrospinal fluid (CSF) glucose. Our analysis also highlights underestimated comorbidities such as pulmonary disease to act as precipitating conditions in WND, as they were significantly increased amongst deceased patients. CSF glucose and the role of pulmonary diseases need to be revaluated either retrospectively or prospectively in WND patient cohorts, as they may be linked to increased mortality risk.
    Language English
    Publishing date 2022-09-08
    Publishing country Switzerland
    Document type Journal Article ; Review
    ISSN 2414-6366
    ISSN (online) 2414-6366
    DOI 10.3390/tropicalmed7090236
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Next-Generation Sequencing of microRNAs in Small Abdominal Aortic Aneurysms: MiR-24 as a Biomarker.

    Tasopoulou, Kalliopi-Maria / Karakasiliotis, Ioannis / Argyriou, Christos / Bampali, Maria / Tsaroucha, Alexandra K / Dovrolis, Nikolas / Christaina, Eleni / Georgiadis, George S

    Annals of vascular surgery

    2023  Volume 99, Page(s) 366–379

    Abstract: Background: Small abdominal aortic aneurysms (AAAs) are asymptomatic but can potentially lead to rupture if left undetected. To date, there is a lack of simple nonradiologic routine tests available for diagnosing AAAs. MicroRNAs (miRNAs) have been ... ...

    Abstract Background: Small abdominal aortic aneurysms (AAAs) are asymptomatic but can potentially lead to rupture if left undetected. To date, there is a lack of simple nonradiologic routine tests available for diagnosing AAAs. MicroRNAs (miRNAs) have been proven to be good-quality biomarkers in several diseases, including AAA.
    Methods: An attempt to identify a panel of circulating miRNAs with differential expression in AAAs via next-generation sequencing (NGS) was performed in serum samples: small AAAs (n = 3), large AAAs (n = 3), and controls (n = 3). For miR-24, validation with real-time polymerase chain reaction (PCR) was undertaken in a larger group (n = 80).
    Results: In the NGS study, 23 miRNAs were identified as differentially expressed (with statistical significance) in small AAAs in comparison with controls. Among them, miR-24 showed the largest upregulation with 23-fold change (log2FC 4.5, P = 0.024). For large AAAs compared with controls, and small AAAs compared with large AAAs, a panel of 33 and 131 miRNAs showed statistically significant differential expression, respectively. Based on the results of the NGS stage, a literature search was performed, and information regarding AAA pathogenesis, coronary artery disease, and peripheral arterial disease was documented where applicable: miR-24, miR-103, miR-193a, miR-486, miR-582, and miR-3663. Of these 6 miRNAs, miR-24 was chosen for further validation with real-time PCR. Additionally, in the NGS study analysis, 17 miRNAs were common between the small-large AAAs, small AAAs-controls, and large AAAs-controls comparisons: miR-7846, miR-3195, miR-486-2, miR-3194, miR-5589, miR-1538, miR-3178, miR-4771-1, miR-5695, miR-6504, miR-1908, miR-6823, miR-3159, miR-23a, miR-7853, miR-496, and miR-193a. Interestingly, in the validation stage with real-time PCR, miR-24 was found downregulated in small and large AAAs compared with controls (fold-changes: 0.27, P = 0.015 and 0.15, P = 0.005, respectively). No correlation was found between average Ct values, aneurysm diameter, and patients' age.
    Conclusions: Our findings further highlight the importance of miR-24 as a potential biomarker as well as a therapeutic target for abdominal aneurysmal disease. Future research and validation of a panel of miRNAs for AAA would aid in diagnosis and discrimination between diseases with overlapping pathogeneses.
    MeSH term(s) Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Treatment Outcome ; Aortic Aneurysm, Abdominal/diagnostic imaging ; Aortic Aneurysm, Abdominal/genetics ; Biomarkers ; High-Throughput Nucleotide Sequencing
    Chemical Substances MicroRNAs ; Biomarkers ; MIRN24 microRNA, human ; MIRN496 microRNA, human ; MIRN582 microRNA, human
    Language English
    Publishing date 2023-11-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1027366-9
    ISSN 1615-5947 ; 0890-5096
    ISSN (online) 1615-5947
    ISSN 0890-5096
    DOI 10.1016/j.avsg.2023.09.065
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Dissecting the Species-Specific Virome in

    Konstantinidis, Konstantinos / Bampali, Maria / de Courcy Williams, Michael / Dovrolis, Nikolas / Gatzidou, Elisavet / Papazilakis, Pavlos / Nearchou, Andreas / Veletza, Stavroula / Karakasiliotis, Ioannis

    Frontiers in microbiology

    2022  Volume 13, Page(s) 802577

    Abstract: Biting midges ( ...

    Abstract Biting midges (
    Language English
    Publishing date 2022-03-07
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.802577
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Hepatocellular carcinoma: from hepatocyte to liver cancer stem cell.

    Karakasiliotis, Ioannis / Mavromara, Penelope

    Frontiers in physiology

    2015  Volume 6, Page(s) 154

    Language English
    Publishing date 2015-05-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564217-0
    ISSN 1664-042X
    ISSN 1664-042X
    DOI 10.3389/fphys.2015.00154
    Database MEDical Literature Analysis and Retrieval System OnLINE

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