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Koukourakis MI, Xanthopoulou E, Koukourakis IM, Fortis SP, Kesesidis N, Kakouratos C, Karakasiliotis I, Baxevanis CN. 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. Curr Oncol 2023; 30:8902-8915. [PMID: 37887543 PMCID: PMC10604986 DOI: 10.3390/curroncol30100643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
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 TP53 were recorded in 10/38 (26.3%) and persisted in 4/10 patients after CRT. ΤP53 mutations were further detected post CRT in 7/38 additional patients with undetectable mutations at baseline (overall rate 44.7%). Furthermore, 4/38 patients exhibited baseline mutations of the EGFR, AR, FGFR3, and FBXW3, and four new gene mutations were detected after CRT (MTOR, EGFR3, ALK, and SF3B1). Τ4 stage was related with a significantly higher rate of mutations (TP53 and overall). Mutations were observed in 8/30 (26.6%) responders (complete/partial response) vs. in 6/8 (75%) of the rest of the patients (p = 0.03). Significant poorer LRFS was noted for patients with mutations detected before and after CRT (p = 0.02). Patients who had detectable mutations either before or after CRT had significantly worse DMFS (p = 0.04 overall, and p = 0.02 for TP53 mutations). It was concluded that assessment of mutations before and after the end of CRT is essential to characterize patients with a high risk of locoregional recurrence or metastatic progression.
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Affiliation(s)
- Michael I. Koukourakis
- Department of Radiotherapy—Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (E.X.); (C.K.)
| | - Erasmia Xanthopoulou
- Department of Radiotherapy—Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (E.X.); (C.K.)
| | - Ioannis M. Koukourakis
- Radiation Oncology Unit, 1st Department of Radiology, Aretaieion University Hospital, 11528 Athens, Greece;
| | - Sotirios P. Fortis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (S.P.F.); (C.N.B.)
| | - Nikolaos Kesesidis
- Laboratory of Biology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (N.K.); (I.K.)
| | - Christos Kakouratos
- Department of Radiotherapy—Oncology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (E.X.); (C.K.)
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Medical School, Democritus University of Thrace, 68100 Alexandroupolis, Greece; (N.K.); (I.K.)
| | - Constantin N. Baxevanis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, 11522 Athens, Greece; (S.P.F.); (C.N.B.)
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Koukourakis MI, Xanthopoulou E, Koukourakis IM, Fortis SP, Kesesidis N, Karakasiliotis I, Baxevanis CN. Circulating Plasma Cell-free DNA (cfDNA) as a Predictive Biomarker for Radiotherapy: Results from a Prospective Trial in Head and Neck Cancer. Cancer Diagn Progn 2023; 3:551-557. [PMID: 37671311 PMCID: PMC10475926 DOI: 10.21873/cdp.10254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/13/2023] [Indexed: 09/07/2023]
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.
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Affiliation(s)
- Michael I Koukourakis
- Department of Radiotherapy - Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Erasmia Xanthopoulou
- Department of Radiotherapy - Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis M Koukourakis
- Radiation Oncology Unit, 1st Department of Radiology, Aretaieion University Hospital, Athens, Greece
| | - Sotirios P Fortis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, Athens, Greece
| | - Nikolaos Kesesidis
- Laboratory of Biology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Constantin N Baxevanis
- Cancer Immunology and Immunotherapy Center, Cancer Research Center, Saint Savas Cancer Hospital, Athens, Greece
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Katsiari M, Mavroidi A, Kesesidis N, Palla E, Zourla K, Ntorlis K, Konstantinidis K, Laskou M, Strigklis K, Sakkalis A, Nikolaou C, Platsouka ED, Karakasiliotis I, Vrioni G, Tsakris A. Emergence of Clonally-Related South Asian Clade I Clinical Isolates of Candida auris in a Greek COVID-19 Intensive Care Unit. J Fungi (Basel) 2023; 9:jof9020243. [PMID: 36836357 PMCID: PMC9964037 DOI: 10.3390/jof9020243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Candida auris has recently emerged as a multidrug-resistant yeast implicated in various healthcare-associated invasive infections and hospital outbreaks. In the current study, we report the first five intensive care unit (ICU) cases affected by C. auris isolates in Greece, during October 2020-January 2022. The ICU of the hospital was converted to a COVID-19 unit on 25 February 2021, during the third wave of COVID-19 in Greece. Identification of the isolates was confirmed by Matrix Assisted Laser Desorption Ionization Time of Flight mass spectroscopy (MALDI-TOF]. Antifungal susceptibility testing was performed by the EUCAST broth microdilution method. Based on the tentative CDC MIC breakpoints, all five C. auris isolates were resistant to fluconazole (≥32 μg/mL), while three of them exhibited resistance to amphotericin B (≥2 μg/mL). The environmental screening also revealed the dissemination of C. auris in the ICU. Molecular characterization of C. auris clinical and environmental isolates was performed by MultiLocus Sequence Typing (MLST) of a set of four genetic loci, namely ITS, D1/D2, RPB1 and RPB2, encoding for the internal transcribed spacer region (ITS) of the ribosomal subunit, the large ribosomal subunit region and the RNA polymerase II largest subunit, respectively. MLST analysis showed that all isolates possessed identical sequences in the four genetic loci and clustered with the South Asian clade I strains. Additionally, PCR amplification and sequencing of the CJJ09_001802 genetic locus, encoding for the "nucleolar protein 58" that contains clade-specific repeats was performed. Sanger sequence analysis of the TCCTTCTTC repeats within CJJ09_001802 locus also assigned the C. auris isolates to the South Asian clade I. Our study confirms that C. auris is an emerging yeast pathogen in our region, especially in the setting of the ongoing COVID-19 worldwide pandemic. Adherence to strict infection control is needed to restrain further spread of the pathogen.
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Affiliation(s)
- Maria Katsiari
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Angeliki Mavroidi
- Department of Microbiology, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Nikolaos Kesesidis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Eleftheria Palla
- Department of Microbiology, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Konstantina Zourla
- Department of Microbiology, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Kyriakos Ntorlis
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Konstantinos Konstantinidis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Maria Laskou
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | | | - Anastasios Sakkalis
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Charikleia Nikolaou
- Intensive Care Unit, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Evangelia D. Platsouka
- Department of Microbiology, Konstantopouleio-Patission General Hospital, 14233 Athens, Greece
| | - Ioannis Karakasiliotis
- Laboratory of Biology, Department of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Georgia Vrioni
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 75 MikrasAsias Street, 11527 Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 75 MikrasAsias Street, 11527 Athens, Greece
- Correspondence: ; Tel.: +30-210-7462011
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Panagiotopoulos A, Tseliou M, Karakasiliotis I, Kotzampasi D, Daskalakis V, Kesesidis N, Notas G, Lionis C, Kampa M, Pirintsos S, Sourvinos G, Castanas E. p-cymene impairs SARS-CoV-2 and Influenza A (H1N1) viral replication: In silico predicted interaction with SARS-CoV-2 nucleocapsid protein and H1N1 nucleoprotein. Pharmacol Res Perspect 2021; 9:e00798. [PMID: 34128351 PMCID: PMC8204097 DOI: 10.1002/prp2.798] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023] Open
Abstract
Therapeutic regimens for the COVID-19 pandemics remain unmet. In this line, repurposing of existing drugs against known or predicted SARS-CoV-2 protein actions have been advanced, while natural products have also been tested. Here, we propose that p-cymene, a natural monoterpene, can act as a potential novel agent for the treatment of SARS-CoV-2-induced COVID-19 and other RNA-virus-induced diseases (influenza, rabies, Ebola). We show by extensive molecular simulations that SARS-CoV-2 C-terminal structured domain contains a nuclear localization signal (NLS), like SARS-CoV, on which p-cymene binds with low micromolar affinity, impairing nuclear translocation of this protein and inhibiting viral replication, as verified by preliminary in vitro experiments. A similar mechanism may occur in other RNA-viruses (influenza, rabies and Ebola), also verified in vitro for influenza, by interaction of p-cymene with viral nucleoproteins, and structural modification of their NLS site, weakening its interaction with importin A. This common mechanism of action renders therefore p-cymene as a possible antiviral, alone, or in combination with other agents, in a broad spectrum of RNA viruses, from SARS-CoV-2 to influenza A infections.
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Affiliation(s)
| | - Melpomeni Tseliou
- Laboratory of Clinical VirologySchool of MedicineUniversity of CreteHeraklionGreece
| | - Ioannis Karakasiliotis
- Laboratory of BiologySchool of MedicineDemocritus University of ThraceAlexandroupolisGreece
| | - Danai‐Maria Kotzampasi
- Laboratory of Experimental EndocrinologySchool of MedicineUniversity of CreteHeraklionGreece
| | - Vangelis Daskalakis
- Department of Chemical EngineeringCyprus University of TechnologyLimassolCyprus
| | - Nikolaos Kesesidis
- Laboratory of BiologySchool of MedicineDemocritus University of ThraceAlexandroupolisGreece
| | - George Notas
- Laboratory of Experimental EndocrinologySchool of MedicineUniversity of CreteHeraklionGreece
| | - Christos Lionis
- Clinic of Social and Family MedicineSchool of MedicineUniversity of CreteHeraklionGreece
- Nature Crete PharmaceuticalsHeraklionGreece
| | - Marilena Kampa
- Laboratory of Experimental EndocrinologySchool of MedicineUniversity of CreteHeraklionGreece
- Nature Crete PharmaceuticalsHeraklionGreece
| | - Stergios Pirintsos
- Nature Crete PharmaceuticalsHeraklionGreece
- Department of BiologyUniversity of CreteHeraklionGreece
- Botanical GardenUniversity of CreteRethymnonGreece
| | - George Sourvinos
- Laboratory of Clinical VirologySchool of MedicineUniversity of CreteHeraklionGreece
- Nature Crete PharmaceuticalsHeraklionGreece
| | - Elias Castanas
- Laboratory of Experimental EndocrinologySchool of MedicineUniversity of CreteHeraklionGreece
- Nature Crete PharmaceuticalsHeraklionGreece
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