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Kolenda T, Graczyk Z, Żarska B, Łosiewski W, Smolibowski M, Wartecki A, Kozłowska-Masłoń J, Guglas K, Florczak A, Kazimierczak U, Teresiak A, Lamperska K. SRY-Related Transcription Factors in Head and Neck Squamous Cell Carcinomas: In Silico Based Analysis. Curr Issues Mol Biol 2023; 45:9431-9449. [PMID: 38132438 PMCID: PMC10742289 DOI: 10.3390/cimb45120592] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/23/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth leading cancer and the fifth cause of cancer-related deaths worldwide with a poor 5-year survival. SOX family genes play a role in the processes involved in cancer development such as epithelial-mesenchymal transition (EMT), the maintenance of cancer stem cells (CSCs) and the regulation of drug resistance. We analyzed the expression of SOX2-OT, SOX6, SOX8, SOX21, SOX30 and SRY genes in HNSCC patients using the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets, to assess their biological role and their potential utility as biomarkers. We demonstrated statistically significant differences in expression between normal and primary tumor tissues for SOX6, SOX8, SOX21 and SOX30 genes and pointed to SOX6 as the one that met the independent diagnostic markers criteria. SOX21 or SRY alone, or the panel of six SRY-related genes, could be used to estimate patient survival. SRY-related genes are positively correlated with immunological processes, as well as with keratinization and formation of the cornified envelope, and negatively correlated with DNA repair and response to stress. Moreover, except SRY, all analyzed genes were associated with a different tumor composition and immunological profiles. Based on validation results, the expression of SOX30 is higher in HPV(+) patients and is associated with patients' survival. SRY-related transcription factors have vast importance in HNSCC biology. SOX30 seems to be a potential biomarker of HPV infection and could be used as a prognostic marker, but further research is required to fully understand the role of SOX family genes in HNSCC.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
| | - Zuzanna Graczyk
- Department of Cancer Immunology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland (A.W.); (A.F.)
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Barbara Żarska
- Department of Cancer Immunology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland (A.W.); (A.F.)
| | - Wojciech Łosiewski
- Department of Cancer Immunology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland (A.W.); (A.F.)
| | - Mikołaj Smolibowski
- Department of Cancer Immunology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland (A.W.); (A.F.)
| | - Adrian Wartecki
- Department of Cancer Immunology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland (A.W.); (A.F.)
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Anna Florczak
- Department of Cancer Immunology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland (A.W.); (A.F.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Garbary 15, 61-688 Poznan, Poland
| | - Urszula Kazimierczak
- Department of Cancer Immunology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland (A.W.); (A.F.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Garbary 15, 61-688 Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
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Kozłowska-Masłoń J, Guglas K, Kolenda T, Lamperska K, Makałowska I. miRNA in head and neck squamous cell carcinomas: promising but still distant future of personalized oncology. Rep Pract Oncol Radiother 2023; 28:681-697. [PMID: 38179293 PMCID: PMC10764040 DOI: 10.5603/rpor.96666] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/24/2023] [Indexed: 01/06/2024] Open
Abstract
Head and neck squamous cell carcinoma is one of the most common and fatal cancers worldwide. Lack of appropriate preventive screening tests, late detection, and high heterogeneity of these tumors are the main reasons for the unsatisfactory effects of therapy and, consequently, unfavorable outcomes for patients. An opportunity to improve the quality of diagnostics and treatment of this group of cancers are microRNAs (miRNAs) - molecules with a great potential both as biomarkers and therapeutic targets. This review aims to present the characteristics of these short non-coding RNAs (ncRNAs) and summarize the current reports on their use in oncology focused on medical strategies tailored to patients' needs.
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Affiliation(s)
- Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater oland Cancer Centre, Poznan, Poland
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater oland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater oland Cancer Centre, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater oland Cancer Centre, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Centre, Poznan, Poland
| | - Izabela Makałowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
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Linkowska K, Bogiel T, Lamperska K, Marszałek A, Starzyński J, Szylberg Ł, Szwed-Kowalska A, Pawłowska M, Grzybowski T. Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation. Sci Rep 2023; 13:6991. [PMID: 37117538 PMCID: PMC10144901 DOI: 10.1038/s41598-023-34220-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/26/2023] [Indexed: 04/30/2023] Open
Abstract
Although infection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) does not appear to be as serious a threat to public health as it was in 2020-2021, the increased transmissibility of multiple Omicron descendants may constitute a continuous challenge for health care systems, and reliable detection of new variants is still imperative. This study evaluates the performance of three SARS-CoV-2 diagnostic tests: Novel Coronavirus (2019-nCoV) Real Time Multiplex RT-PCR Kit (Liferiver); Vitassay qPCR SARS-CoV-2 (Vitaassay) and TaqPath COVID‑19 CE-IVD RT-PCR Kit (Thermo Fisher Scientific). The analytical sensitivity of the assays as well as their specificity were determined with the use of synthetic nucleic acid standards and clinical samples. All assays appeared to be 100% specific for SARS-CoV-2 RNA in general and the Omicron variant in particular. The LOD determined during this validation was 10 viral RNA copies/reaction for Liferiver and TaqPath and 100 viral RNA copies for Vitassay. We cannot exclude that the LOD for the Vitassay might be lower and close to the manufacturer's declared value of ≥ 20 genome copies/reaction, as we obtained 90% positive results for 10 viral RNA copies/reaction. Mean Ct values at the concentration of 10 viral RNA copies/reaction for the Liferiver, Vitassay and TaqPath kits (35, 37 and 33, respectively) were significantly lower than the cutoff values declared by the manufacturers (≤ 41, ≤ 40 and ≤ 37, respectively). We suggest reporting outcomes based on LOD and cutoff Ct values determined during internal validation rather than those declared by the assays' producers.
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Grants
- ZES.WL.2.2021 Faculty of Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz Poland
- ZES.WL.2.2021 Faculty of Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz Poland
- ZES.WL.2.2021 Faculty of Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz Poland
- ZES.WL.2.2021 Faculty of Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz Poland
- ZES.WL.2.2021 Faculty of Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz Poland
- ZES.WL.2.2021 Faculty of Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz Poland
- ZES.WL.2.2021 Faculty of Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz Poland
- ZES.WL.2.2021 Faculty of Medicine, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz Poland
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Affiliation(s)
- Katarzyna Linkowska
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Curie-Skłodowskiej Str. 9, 85-094, Bydgoszcz, Poland.
| | - Tomasz Bogiel
- Department of Microbiology, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland
| | | | - Andrzej Marszałek
- Department of Oncologic Pathology and Prophylaxis, Greater Poland Cancer Centre, Poznań University of Medical Sciences, Poznań, Poland
| | - Jarosław Starzyński
- Department of Tumor Pathology and Pathomorphology, Oncology Centre - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Centre - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Department of Perinatology, Gynaecology and Gynaecologic Oncology, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Aleksandra Szwed-Kowalska
- Department of Laboratory Diagnostics, The Tadeusz Browicz Provincial Hospital for Infectious Diseases and Observation, Bydgoszcz, Poland
| | - Małgorzata Pawłowska
- Department of Infectious Diseases and Hepathology, Collegium Medicum of the Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Collegium Medicum of the Nicolaus Copernicus University, Curie-Skłodowskiej Str. 9, 85-094, Bydgoszcz, Poland
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Kolenda T, Paszkowska A, Braska A, Kozłowska-Masłoń J, Guglas K, Poter P, Wojtczak P, Bliźniak R, Lamperska K, Teresiak A. Host gene and its guest: short story about relation of long-noncoding MIR31HG transcript and microRNA miR-31. Rep Pract Oncol Radiother 2023; 28:114-134. [PMID: 37122913 PMCID: PMC10132190 DOI: 10.5603/rpor.a2023.0006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/25/2023] [Indexed: 05/02/2023] Open
Abstract
Epigenetics is the changes in a cellular phenotype without changes in the genotype. This term is not limited only to the modification of chromatin and DNA but also relates to some RNAs, like non-coding RNAs (ncRNAs), both short and long RNAs (lncRNAs) acting as molecular modifiers. Mobile RNAs, as a free form or encapsulated in exosomes, can regulate neighboring cells or be placed in distant locations. It underlines the vast capacity of ncRNAs as epigenetic elements of transmission information and message of life. One of the amazing phenomena is long non-coding microRNA-host-genes (lnc-MIRHGs) whose processed transcripts function as lncRNAs and also as short RNAs named microRNAs (miRNAs). MIR31HG functions as a modulator of important biological and cellular processes including cell proliferation, apoptosis, cell cycle regulation, EMT process, metastasis, angiogenesis, hypoxia, senescence, and inflammation. However, in most cases, the role of MIR31HG is documented only by one study and there is a lack of exact description of molecular pathways implicated in these processes, and for some of them, such as response to irradiation, no studies have been done. In this review, MIR31HG, as an example of lnc-MIRHGs, was described in the context of its known function and its potential uses as a biomarker in oncology.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
| | - Anna Paszkowska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
- Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Alicja Braska
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
- Faculty of Biology, Institute of Human Biology and Evolution, Adam Mickiewicz University, Poznań, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Paulina Poter
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
- Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Center, Poznan, Poland
- Department of Pathology, Pomeranian Medical University, Szczecin, Poland
| | | | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Poznan, Poland
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Sobocińska J, Nowakowska J, Molenda S, Olechnowicz A, Guglas K, Kozłowska-Masłoń J, Kazimierczak U, Machnik M, Oleksiewicz U, Teresiak A, Lamperska K, Kolenda T. Zinc Finger Proteins in Head and Neck Squamous Cell Carcinomas: ZNF540 May Serve as a Biomarker. Curr Oncol 2022; 29:9896-9915. [PMID: 36547193 PMCID: PMC9776630 DOI: 10.3390/curroncol29120779] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the ten most common cancers. Most cancer cases originate from alcohol and tobacco consumption. However, studies have demonstrated that human papillomavirus (HPV) infection, particularly HPV-16, may also significantly influence disease progression. The KRAB-ZNF family of genes is involved in epigenetic suppression, and its involvement in carcinogenesis is the subject of extensive studies. The available literature data demonstrate that they may play different roles, both as tumor suppressors and oncogenes. In this study, six ZNF genes, ZFP28, ZNF132, ZNF418, ZNF426, ZNF540, and ZNF880, were tested using several in silico approaches based on the TCGA and GEO datasets. Our analyses indicate that the expression of the analyzed ZNFs was significantly downregulated in tumor tissues and depended on tumor localization. The expression levels of ZNFs differed between HPV-positive vs. HPV-negative patients depending on the clinical-pathological parameters. More specifically, the patients with higher levels of ZNF418 and ZNF540 showed better survival rates than those with a lower expression. In addition, the level of ZNF540 expression in HPV-positive (HPV(+)) patients was higher than in HPV-negative (HPV(-)) patients (p < 0.0001) and was associated with better overall survival (OS). In conclusion, we demonstrate that ZNF540 expression highly correlates with HPV infection, which renders ZNF540 a potential biomarker for HNSCC prognosis and treatment.
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Affiliation(s)
- Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Joanna Nowakowska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Molecular and Cell Biology Unit, Poznan University of Medical Sciences, 60-572 Poznan, Poland
| | - Sara Molenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Anna Olechnowicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Histology and Embryology, Poznan University of Medical Sciences, Święcickiego 6 Street, 60-781 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Zwirki and Wigury Street 61, 02-091 Warsaw, Poland
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland
| | - Urszula Kazimierczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Marta Machnik
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Urszula Oleksiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Correspondence: (K.L.); (T.K.)
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary 15, 61-866 Poznan, Poland
- Correspondence: (K.L.); (T.K.)
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Paszkowska A, Kolenda T, Guglas K, Kozłowska-Masłoń J, Podralska M, Teresiak A, Bliźniak R, Dzikiewicz-Krawczyk A, Lamperska K. C10orf55, CASC2, and SFTA1P lncRNAs Are Potential Biomarkers to Assess Radiation Therapy Response in Head and Neck Cancers. J Pers Med 2022; 12:jpm12101696. [PMID: 36294833 PMCID: PMC9605465 DOI: 10.3390/jpm12101696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 11/07/2022] Open
Abstract
Long non-coding RNAs have proven to be important molecules in carcinogenesis. Due to little knowledge about them, the molecular mechanisms of tumorigenesis are still being explored. The aim of this work was to study the effect of ionizing radiation on the expression of lncRNAs in head and neck squamous cell carcinoma (HNSCC) in patients responding and non-responding to radiotherapy. The experimental model was created using a group of patients with response (RG, n = 75) and no response (NRG, n = 75) to radiotherapy based on the cancer genome atlas (TCGA) data. Using the in silico model, statistically significant lncRNAs were defined and further validated on six HNSCC cell lines irradiated at three different doses. Based on the TCGA model, C10orf55, C3orf35, C5orf38, CASC2, MEG3, MYCNOS, SFTA1P, SNHG3, and TMEM105, with the altered expression between the RG and NRG were observed. Analysis of pathways and immune profile indicated that these lncRNAs were associated with changes in processes, such as epithelial-to-mesenchymal transition, regulation of spindle division, and the p53 pathway, and differences in immune cells score and lymphocyte infiltration signature score. However, only C10orf55, CASC2, and SFTA1P presented statistically altered expression after irradiation in the in vitro model. In conclusion, the expression of lncRNAs is affected by ionization radiation in HNSCC, and these lncRNAs are associated with pathways, which are important for radiation response and immune response. Potentially presented lncRNAs could be used as biomarkers for personalized radiotherapy in the future. However, these results need to be verified based on an in vitro experimental model to show a direct net of interactions.
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Affiliation(s)
- Anna Paszkowska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Correspondence: (T.K.); (K.L.)
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Zwirki and Wigury Street 61, 02-091 Warsaw, Poland
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznan, Poland
| | - Marta Podralska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479 Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
| | | | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Research and Implementation Unit, Greater Poland Cancer Center, Garbary Street 15, 61-866 Poznan, Poland
- Correspondence: (T.K.); (K.L.)
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Tomaszewska W, Kozłowska-Masłoń J, Baranowski D, Perkowska A, Szałkowska S, Kazimierczak U, Severino P, Lamperska K, Kolenda T. miR-154 Influences HNSCC Development and Progression through Regulation of the Epithelial-to-Mesenchymal Transition Process and Could Be Used as a Potential Biomarker. Biomedicines 2021; 9:biomedicines9121894. [PMID: 34944712 PMCID: PMC8698850 DOI: 10.3390/biomedicines9121894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs and their role in cancer have been extensively studied for the past decade. Here, we analyzed the biological role and diagnostic potential of miR-154-5p and miR-154-3p in head and neck squamous cell carcinoma (HNSCC). miRNA expression analyses were performed using The Cancer Genome Atlas (TCGA) data accessed from cBioPortal, UALCAN, Santa Cruz University, and Gene Expression Omnibus (GEO). The expression data were correlated with clinicopathological parameters. The functional enrichment was assessed with Gene Set Enrichment Analysis (GSEA). The immunological profiles were assessed using the ESTIMATE tool and RNAseq data from TCGA. All statistical analyses were performed with GraphPad Prism and Statistica. The study showed that both miR-154-5p and miR-154-3p were downregulated in the HNSCC samples and their expression levels correlated with tumor localization, overall survival, cancer stage, tumor grade, and HPV p16 status. GSEA indicated that individuals with the increased levels of miR-154 had upregulated AKT-MTOR, CYCLIN D1, KRAS, EIF4E, RB, ATM, and EMT gene sets. Finally, the elevated miR-154 expression correlated with better immune response. This study showed that miR-154 is highly involved in HNSCC pathogenesis, invasion, and immune response. The implementation of miR-154 as a biomarker may improve the effectiveness of HNSCC treatment.
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Affiliation(s)
- Weronika Tomaszewska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (D.B.); (A.P.); (S.S.); (U.K.)
- Correspondence: (W.T.); (T.K.)
| | - Joanna Kozłowska-Masłoń
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (J.K.-M.); (K.L.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Faculty of Biology, Institute of Human Biology and Evolution, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Dawid Baranowski
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (D.B.); (A.P.); (S.S.); (U.K.)
| | - Anna Perkowska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (D.B.); (A.P.); (S.S.); (U.K.)
| | - Sandra Szałkowska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (D.B.); (A.P.); (S.S.); (U.K.)
| | - Urszula Kazimierczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (D.B.); (A.P.); (S.S.); (U.K.)
| | - Patricia Severino
- Centro de Pesquisa Experimental, Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, Av. Albert Einstein, 627-Jardim Leonor, São Paulo 05652-900, SP, Brazil;
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (J.K.-M.); (K.L.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (J.K.-M.); (K.L.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland
- Correspondence: (W.T.); (T.K.)
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Stasiak M, Kolenda T, Kozłowska-Masłoń J, Sobocińska J, Poter P, Guglas K, Paszkowska A, Bliźniak R, Teresiak A, Kazimierczak U, Lamperska K. The World of Pseudogenes: New Diagnostic and Therapeutic Targets in Cancers or Still Mystery Molecules? Life (Basel) 2021; 11:life11121354. [PMID: 34947885 PMCID: PMC8705536 DOI: 10.3390/life11121354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Pseudogenes were once considered as “junk DNA”, due to loss of their functions as a result of the accumulation of mutations, such as frameshift and presence of premature stop-codons and relocation of genes to inactive heterochromatin regions of the genome. Pseudogenes are divided into two large groups, processed and unprocessed, according to their primary structure and origin. Only 10% of all pseudogenes are transcribed into RNAs and participate in the regulation of parental gene expression at both transcriptional and translational levels through senseRNA (sRNA) and antisense RNA (asRNA). In this review, about 150 pseudogenes in the different types of cancers were analyzed. Part of these pseudogenes seem to be useful in molecular diagnostics and can be detected in various types of biological material including tissue as well as biological fluids (liquid biopsy) using different detection methods. The number of pseudogenes, as well as their function in the human genome, is still unknown. However, thanks to the development of various technologies and bioinformatic tools, it was revealed so far that pseudogenes are involved in the development and progression of certain diseases, especially in cancer.
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Affiliation(s)
- Maciej Stasiak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Tomasz Kolenda
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Correspondence: or (T.K.); or (K.L.)
| | - Joanna Kozłowska-Masłoń
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Faculty of Biology, Institute of Human Biology and Evolution, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Joanna Sobocińska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Paulina Poter
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Greater Poland Cancer Center, Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Garbary 15, 61-866 Poznan, Poland
- Department of Pathology, Pomeranian Medical University, Rybacka 1, 70-204 Szczecin, Poland
| | - Kacper Guglas
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Zwirki and Wigury, 02-091 Warsaw, Poland
| | - Anna Paszkowska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Renata Bliźniak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Anna Teresiak
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
| | - Urszula Kazimierczak
- Department of Cancer Immunology, Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland;
| | - Katarzyna Lamperska
- Greater Poland Cancer Centre, Laboratory of Cancer Genetics, Garbary 15, 61-866 Poznan, Poland; (M.S.); (J.K.-M.); (J.S.); (K.G.); (A.P.); (R.B.); (A.T.)
- Greater Poland Cancer Centre, Research and Implementation Unit, Garbary 15, 61-866 Poznan, Poland;
- Correspondence: or (T.K.); or (K.L.)
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Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE. Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma. Microb Ecol 2021; 82:1030-1046. [PMID: 33155101 PMCID: PMC8551143 DOI: 10.1007/s00248-020-01596-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/01/2020] [Indexed: 05/14/2023]
Abstract
The human microbiome has been the focus of numerous research efforts to elucidate the pathogenesis of human diseases including cancer. Oral cancer mortality is high when compared with other cancers, as diagnosis often occurs during late stages. Its prevalence has increased in the USA over the past decade and accounts for over 40,000 new cancer patients each year. Additionally, oral cancer pathogenesis is not fully understood and is likely multifactorial. To unravel the relationships that are associated with the oral microbiome and their virulence factors, we used 16S rDNA and metagenomic sequencing to characterize the microbial composition and functional content in oral squamous cell carcinoma (OSCC) tumor tissue, non-tumor tissue, and saliva from 18 OSCC patients. Results indicate a higher number of bacteria belonging to the Fusobacteria, Bacteroidetes, and Firmicutes phyla associated with tumor tissue when compared with all other sample types. Additionally, saliva metaproteomics revealed a significant increase of Prevotella in five OSCC subjects, while Corynebacterium was mostly associated with ten healthy subjects. Lastly, we determined that there are adhesion and virulence factors associated with Streptococcus gordonii as well as from known oral pathogens belonging to the Fusobacterium genera found mostly in OSCC tissues. From these results, we propose that not only will the methods utilized in this study drastically improve OSCC diagnostics, but the organisms and specific virulence factors from the phyla detected in tumor tissue may be excellent biomarkers for characterizing disease progression.
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Affiliation(s)
- Manolito G Torralba
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| | - Gajender Aleti
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Weizhong Li
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Kelvin Jens Moncera
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yi-Han Lin
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yanbao Yu
- Department of Genomic Medicine, J. Craig Venter Institute, 9605 Medical Center Drive Suite 150, Rockville, MD, 20850, USA
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Central Florida Blvd, Orlando, FL, 32827, USA
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Garbary 15, 61-866, Poznan, Poland
| | - Pawel Golusinski
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Garbary 15, 61-866, Poznan, Poland
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Podgórna 50, 65-246, Zielona Góra, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, room 5025, 61-866, Poznan, Poland
| | - Anna Edlund
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Marcelo Freire
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Karen E Nelson
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
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Torralba MG, Aleti G, Li W, Moncera KJ, Lin YH, Yu Y, Masternak MM, Golusinski W, Golusinski P, Lamperska K, Edlund A, Freire M, Nelson KE. Correction to: Oral Microbial Species and Virulence Factors Associated with Oral Squamous Cell Carcinoma. Microb Ecol 2021; 82:1047. [PMID: 33219400 PMCID: PMC9172741 DOI: 10.1007/s00248-020-01641-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Manolito G Torralba
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.
| | - Gajender Aleti
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Weizhong Li
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Kelvin Jens Moncera
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yi-Han Lin
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Yanbao Yu
- Department of Genomic Medicine, J. Craig Venter Institute, 9605 Medical Center Drive Suite 150, Rockville, MD, 20850, USA
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd, Central Florida Blvd, Orlando, FL, 32827, USA
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15, 61-866, Poznań, Poland
| | - Pawel Golusinski
- Department of Head and Neck Surgery, The Greater Poland Cancer Centre, Poznan University of Medical Sciences, Garbary 15, 61-866, Poznań, Poland
- Department of Otolaryngology and Maxillofacial Surgery, University of Zielona Gora, Podgórna 50, 65-246, Zielona Góra, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, Room 5025, 61-866, Poznan, Poland
| | - Anna Edlund
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Marcelo Freire
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
| | - Karen E Nelson
- Department of Genomic Medicine, J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA
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Kozłowska J, Kolenda T, Poter P, Sobocińska J, Guglas K, Stasiak M, Bliźniak R, Teresiak A, Lamperska K. Long Intergenic Non-Coding RNAs in HNSCC: From "Junk DNA" to Important Prognostic Factor. Cancers (Basel) 2021; 13:2949. [PMID: 34204634 PMCID: PMC8231241 DOI: 10.3390/cancers13122949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/24/2022] Open
Abstract
Head and neck squamous cell carcinoma is one of the most common and fatal cancers worldwide. Even a multimodal approach consisting of standard chemo- and radiotherapy along with surgical resection is only effective in approximately 50% of the cases. The rest of the patients develop a relapse of the disease and acquire resistance to treatment. Especially this group of individuals needs novel, personalized, targeted therapy. The first step to discovering such solutions is to investigate the tumor microenvironment, thus understanding the role and mechanism of the function of coding and non-coding sequences of the human genome. In recent years, RNA molecules gained great interest when the complex character of their impact on our biology allowed them to come out of the shadows of the "junk DNA" label. Furthermore, long non-coding RNAs (lncRNA), specifically the intergenic subgroup (lincRNA), are one of the most aberrantly expressed in several malignancies, which makes them particularly promising future diagnostic biomarkers and therapeutic targets. This review contains characteristics of known and validated lincRNAs in HNSCC, such as XIST, MALAT, HOTAIR, HOTTIP, lincRNA-p21, LINC02487, LINC02195, LINC00668, LINC00519, LINC00511, LINC00460, LINC00312, and LINC00052, with a description of their prognostic abilities. Even though much work remains to be done, lincRNAs are important factors in cancer biology that will become valuable biomarkers of tumor stage, outcome prognosis, and contribution to personalized medicine.
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Affiliation(s)
- Joanna Kozłowska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Paulina Poter
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Oncologic Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Centere, Garbary 15, 61-866 Poznan, Poland
- Department of Pathology, Pomeranian Medical University, Rybacka 1, 70-204 Szczecin, Poland
| | - Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, ul. Zwirki 61 and ul. Wigury, 02-091 Warsaw, Poland
| | - Maciej Stasiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland; (T.K.); (J.S.); (K.G.); (M.S.); (R.B.); (A.T.)
- Research and Implementation Unit, Greater Poland Cancer Centre, Garbary 15, 61-866 Poznan, Poland;
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Kolenda T, Ryś M, Guglas K, Teresiak A, Bliźniak R, Mackiewicz J, Lamperska K. Quantification of long non-coding RNAs using qRT-PCR: comparison of different cDNA synthesis methods and RNA stability. Arch Med Sci 2021; 17:1006-1015. [PMID: 34336028 PMCID: PMC8314425 DOI: 10.5114/aoms.2019.82639] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/29/2018] [Indexed: 12/02/2022] Open
Abstract
INTRODUCTION Long non-coding RNAs (lncRNAs), a class of regulatory RNA molecules, are over 200 nucleotides long and could be used as a new potential biomarker, but their detection methods such as qRT-PCR are still not validated, and the influence of RNA degradation on lncRNA quantification is not clear. In this study, commercially available cDNA synthesis kits were tested and the influence of RNA degradation was compared. MATERIAL AND METHODS Total RNA from FaDu cells was isolated and high quality RNA and highly degraded RNA samples were used. Reverse transcription was performed using three different commercially available kits and quantifications were performed using lncRNA Primer Plate and SYBR Green I Master by LightCycler 96. qRT-PCR was performed using three different cDNA samples and results are presented as the mean Ct values. A p-value < 0.05 was considered to be significant. RESULTS Lower lncRNA Ct values (61/90; 67.78%) after qRT-PCR quantification were observed for cDNA synthesized using random hexamer primers preceded by polyA-tailing and adaptor-anchoring steps. It was observed that 9/90 (10.00%) lncRNAs were not detectable using different cDNA synthesis methods. For 75/90 (83%) lncRNAs, RNA degradation weakly influenced lncRNA Ct values and no differences were observed between high quality RNA and degraded samples. Seventy percent of examined lncRNAs showed significantly different Ct values depending on RNA degradation. CONCLUSIONS cDNA synthesis kits with random hexamer primers preceded by polyA-tailing and adaptor-anchoring steps allows enhancement of lncRNA quantification specificity and sensitivity. In most cases degradation of RNA samples does not affect lncRNA quantification because these molecules have good stability.
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Affiliation(s)
- Tomasz Kolenda
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Marcel Ryś
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Kacper Guglas
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poznan, Poland
- Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
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Sobocińska J, Kolenda T, Teresiak A, Badziąg-Leśniak N, Kopczyńska M, Guglas K, Przybyła A, Filas V, Bogajewska-Ryłko E, Lamperska K, Mackiewicz A. Diagnostics of Mutations in MMR/ EPCAM Genes and Their Role in the Treatment and Care of Patients with Lynch Syndrome. Diagnostics (Basel) 2020; 10:diagnostics10100786. [PMID: 33027913 PMCID: PMC7600989 DOI: 10.3390/diagnostics10100786] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), is a disorder caused by an autosomal dominant heterozygous germline mutation in one of the DNA mismatch repair (MMR) genes. Individuals with LS are at an increased risk of developing colorectal and extracolonic cancers, such as endometrial, small bowel, or ovarian. In this review, the mutations involved with LS and their diagnostic methods are described and compared, as are their current uses in clinical decision making. Nowadays, LS diagnosis is based on a review of family medical history, and when necessary, microsatellite instability (MSI) or/and immunohistochemistry (IHC) analyses should be performed. In the case of a lack of MMR protein expression (dMMR) or MSI-H (MSI-High) detection in tumor tissue, molecular genetic testing can be undertaken. More and more genetic testing for LS is based mainly on next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA), which provide better and quicker information about the molecular profile of patients as well as individuals at risk. Testing based on these two methods should be the standard and commonly used. The identification of individuals with mutations provides opportunities for the detection of cancer at an early stage as well as the introduction of proper, more effective treatment, which will result in increased patient survival and reduced costs of medical care.
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Affiliation(s)
- Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
- Correspondence:
| | - Tomasz Kolenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (A.T.); (K.G.); (K.L.)
| | - Natalia Badziąg-Leśniak
- Oncological Genetics Clinic, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland;
| | - Magda Kopczyńska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (A.T.); (K.G.); (K.L.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Anna Przybyła
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
| | - Violetta Filas
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (V.F.); (E.B.-R.)
- Department of Cancer Pathology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Elżbieta Bogajewska-Ryłko
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (V.F.); (E.B.-R.)
- Department of Cancer Pathology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland; (A.T.); (K.G.); (K.L.)
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (T.K.); (M.K.); (A.P.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
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14
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Łasińska I, Kolenda T, Guglas K, Kopczyńska M, Sobocińska J, Teresiak A, Strzelecki NO, Lamperska K, Mackiewicz A, Mackiewicz J. Liquid lncRNA Biopsy for the Evaluation of Locally Advanced and Metastatic Squamous Cell Carcinomas of the Head and Neck. J Pers Med 2020; 10:E131. [PMID: 32947877 PMCID: PMC7564176 DOI: 10.3390/jpm10030131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Long non-coding RNA (lncRNA) are RNA molecules that are more than 200 nucleotides long and have the ability to modify the activity of genes. They can be found in both healthy and cancer tissues, as well as in plasma, saliva and other bodily fluids. They can also be used as biomarkers of early detection, prognosis and chemotherapy resistance in several cancer types. Treatment of head and neck squamous cell carcinoma (HNSCC) patients with locally advanced disease is still difficult, and choice of treatment should be based on more precise and available biomarkers, such as those obtained from a liquid biopsy. For improvement of treatment efficacy, identification and clinical implementation of new biomarkers are of the utmost importance. Methods: Plasma samples drawn before (p1) and three cycles post (p2) (TPF: docetaxel, cisplatin, 5-fluorouracil/PF: cisplatin, 5-fluorouracil) chemotherapy from 53 HNSCC patients (17 with locally advanced and 36 with metastatic disease) and 14 healthy volunteers were studied. Expression levels of 90 lncRNA expression were analyzed using the qRT-PCR method, and the obtained results were compared between proper groups. Statistical analyses were carried out using Jupyter Notebooks (5.7.2), Python (ver. 3.6) and GraphPad Prism 8. Results: The study demonstrated the differences between the expressions of several lncRNA in cancer patients' and healthy volunteers' plasma, as well as between locally advanced and metastatic patients' groups. A correlation between the response to systemic therapy and lncRNA expression levels was observed. Patients with a (high/low) expression of Alpha 250 and Emx2os showed statistically significant differences in progression free survival (PFS), as well as for overall survival (OS) depending on the level of Alpha 250, snaR, SNHG1. The univariate and multivariate Cox regression model showed Alpha 250 as the best prognostic factor for HNSCC patients. Conclusions: Liquid biopsies based on lncRNAs are promising diagnostic tools that can be used to differentiate between those with cancer and healthy individuals. Additionally, they can also serve as biomarkers for chemotherapy resistance. An identified, circulating lncRNA Alpha 250 seems to prove the best prognostic biomarker, associated with extended PFS and OS, and should be validated in a larger cohort in the future.
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Affiliation(s)
- Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18 Grunwaldzka Street, 60-786 Poznan, Poland
- Specialist Nursing Laboratory, Faculty of Medicine and Health Science, University of Zielona Góra, Energetyków Street 2, 65-00 Zielona Gora, Poland
| | - Tomasz Kolenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (M.K.); (J.S.); (N.O.S.); (A.M.)
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, room 5025, 61-866 Poznan, Poland; (K.G.); (A.T.); (K.L.)
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, room 5025, 61-866 Poznan, Poland; (K.G.); (A.T.); (K.L.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Zwirki i Wigury Street, 02-091 Warszawa, Poland
| | - Magda Kopczyńska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (M.K.); (J.S.); (N.O.S.); (A.M.)
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, room 5025, 61-866 Poznan, Poland; (K.G.); (A.T.); (K.L.)
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (M.K.); (J.S.); (N.O.S.); (A.M.)
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, room 5025, 61-866 Poznan, Poland; (K.G.); (A.T.); (K.L.)
| | - Norbert Oksza Strzelecki
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (M.K.); (J.S.); (N.O.S.); (A.M.)
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, room 5025, 61-866 Poznan, Poland; (K.G.); (A.T.); (K.L.)
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland; (M.K.); (J.S.); (N.O.S.); (A.M.)
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18 Grunwaldzka Street, 60-786 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland
- Department of Oncology, Poznan University of Medical Sciences, 82-84 Szamarzewskiego, 60-569 Poznan, Poland
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15
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Malicki J, Martenka P, Dyzmann-Sroka A, Paczkowska K, Leporowska E, Suchorska W, Lamperska K, Pieńkowski P, Chicheł A, Mocydlarz-Adamcewicz M, Urbaniak D, Bajon T, Cybulski Z, Bąk B, Machtyl A, Adamska K, Kaźmierska J, Milecki P, Marszałek A. Impact of COVID-19 on the performance of a radiation oncology department at a major comprehensive cancer centre in Poland during the first ten weeks of the epidemic. Rep Pract Oncol Radiother 2020; 25:820-827. [PMID: 32837336 PMCID: PMC7429079 DOI: 10.1016/j.rpor.2020.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 12/21/2022] Open
Abstract
The outbreak of SARS-CoV-2 coronavirus rapidly altered radiotherapy service delivery around the world. AIM The main objective of this study was to assess the impact of precautionary measures implemented in response to the COVID-19 pandemic on the performance of a radiation oncology departments and on mitigation the risk of COVID-19 contagion between and among patients and staff. METHODS The study period was from March 15 until May 22, 2020. We evaluated total number of patients irradiated and those who initiated treatments, taking into account tumours localisations. We assessed the relationship of potential risk of contagion with patients' domiciles locations in regions with high number of COVID19 case. RESULTS AND CONCLUSIONS The number of patients treated with radiotherapy during the study period decreased due to precautionary measures. After five weeks, the number of radiotherapy treatments began to increase. Just over half of the radiotherapy patients (53.5%) treated at the GPCC reside in the city of Poznan or in one of the ten surrounding counties where COVID19 incidence was low and reached at the end of the study period cumulative number of cases n = 204. The precautionary measures were effective qRT-PCR tests were performed in 1545 individuals (patients and hospital staff) revealing four staff members and none patient with a positive PCR result. Immunoglobulin testing was performed in 1132 individuals (patients and hospital staff). A total of 63 individuals were positive for antibodies.
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Affiliation(s)
- J Malicki
- Electroradiology Department, Poznan University of Medical Sciences, Poznań, Poland
- Medical Physics Department, Greater Poland Cancer Centre, Poznań, Poland
| | - P Martenka
- IV Radiotherapy Department, Greater Poland Cancer Centre, Piła, Poland
| | - A Dyzmann-Sroka
- Epidemiology and Prophylactics Department, Greater Poland Cancer Centre, Poznań, Poland
| | - K Paczkowska
- Section for Coordination of Work of Interdisciplinary Teams, Greater Poland Cancer Centre, Poznań, Poland
| | - E Leporowska
- Department of Laboratory Diagnostics, Greater Poland Cancer Centre, Poznań, Poland
| | - W Suchorska
- Electroradiology Department, Poznan University of Medical Sciences, Poznań, Poland
- Radiobiology Lab, Greater Poland Cancer Centre, Poznań, Poland
| | - K Lamperska
- Department of Cancer Immunology, Greater Poland Cancer Centre, Poznań, Poland
| | - P Pieńkowski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznań, Poland
| | - A Chicheł
- Brachytherapy Department, Greater Poland Cancer Centre, Poznań, Poland
| | - M Mocydlarz-Adamcewicz
- Electroradiology Department, Poznan University of Medical Sciences, Poznań, Poland
- IT Department, Greater Poland Cancer Centre, Poznań, Poland
| | - D Urbaniak
- Epidemiological Inspector, Greater Poland Cancer Centre, Poznań, Poland
| | - T Bajon
- II Radiotherapy Department, Greater Poland Cancer Centre, Poznań, Poland
| | - Z Cybulski
- Department of Microbiology, Greater Poland Cancer Centre, Poznań, Poland
| | - B Bąk
- Electroradiology Department, Poznan University of Medical Sciences, Poznań, Poland
- II Radiotherapy Department, Greater Poland Cancer Centre, Poznań, Poland
| | - A Machtyl
- Radiotherapy Department, Greater Poland Cancer Centre, Poznań, Poland
| | - K Adamska
- Electroradiology Department, Poznan University of Medical Sciences, Poznań, Poland
- III Radiotherapy Department, Greater Poland Cancer Centre, Poznań, Poland
| | - J Kaźmierska
- Electroradiology Department, Poznan University of Medical Sciences, Poznań, Poland
- II Radiotherapy Department, Greater Poland Cancer Centre, Poznań, Poland
| | - P Milecki
- Electroradiology Department, Poznan University of Medical Sciences, Poznań, Poland
- Radiotherapy Department, Greater Poland Cancer Centre, Poznań, Poland
| | - A Marszałek
- Department of Tumor Pathology and Prophylaxis, Poznan University of Medical Sciences, Poznań Poland
- Department of Oncologic Pathology, Greater Poland Cancer Centre, Poznan, Poland
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16
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Kolenda T, Guglas K, Baranowski D, Sobocińska J, Kopczyńska M, Teresiak A, Bliźniak R, Lamperska K. cfRNAs as biomarkers in oncology - still experimental or applied tool for personalized medicine already? Rep Pract Oncol Radiother 2020; 25:783-792. [PMID: 32904167 PMCID: PMC7451588 DOI: 10.1016/j.rpor.2020.07.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/13/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
Currently, the challenges of contemporary oncology are focused mainly on the development of personalized medicine and precise treatment, which could be achieved through the use of molecular biomarkers. One of the biological molecules with great potential are circulating free RNAs (cfRNAs) which are present in various types of body fluids, such as blood, serum, plasma, and saliva. Also, different types of cfRNA particles can be distinguished depending on their length and function: microRNA (miRNA), PIWI-interacting RNA (piRNA), tRNA-derived RNA fragments (tRFs), circular RNA (circRNA), long non-coding RNA (lncRNA), and messenger RNA (mRNA). Moreover, cfRNAs occur in various forms: as a free molecule alone, in membrane vesicles, such as exosomes, or in complexes with proteins and lipids. One of the modern approaches for monitoring patient's condition is a "liquid biopsy" that provides a non-invasive and easily available source of circulating RNAs. Both the presence of specific cfRNA types as well as their concentration are dependent on many factors including cancer type or even reaction to treatment. Despite the possibility of using circulating free RNAs as biomarkers, there is still a lack of validated diagnostic panels, defined protocols for sampling, storing as well as detection methods. In this work we examine different types of cfRNAs, evaluate them as possible biomarkers, and analyze methods of their detection. We believe that further research on cfRNA and defining diagnostic panels could lead to better and faster cancer identification and improve treatment monitoring.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Dawid Baranowski
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Sobocińska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
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17
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Kolenda T, Guglas K, Kopczyńska M, Sobocińska J, Teresiak A, Bliźniak R, Lamperska K. Good or not good: Role of miR-18a in cancer biology. Rep Pract Oncol Radiother 2020; 25:808-819. [PMID: 32884453 DOI: 10.1016/j.rpor.2020.07.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 04/24/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023] Open
Abstract
miR-18a is a member of primary transcript called miR-17-92a (C13orf25 or MIR17HG) which also contains five other miRNAs: miR-17, miR-19a, miR-20a, miR-19b and miR-92a. This cluster as a whole shows specific characteristics, where miR-18a seems to be unique. In contrast to the other members, the expression of miR-18a is additionally controlled and probably functions as its own internal controller of the cluster. miR-18a regulates many genes involved in proliferation, cell cycle, apoptosis, response to different kinds of stress, autophagy and differentiation. The disturbances of miR-18a expression are observed in cancer as well as in different diseases or pathological states. The miR-17-92a cluster is commonly described as oncogenic and it is known as 'oncomiR-1', but this statement is a simplification because miR-18a can act both as an oncogene and a suppressor. In this review we summarize the current knowledge about miR-18a focusing on its regulation, role in cancer biology and utility as a potential biomarker.
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Key Words
- 5-FU, 5-fluorouracyl
- ACVR2A, activin A receptor type 2A
- AKT, AKT serine/threonine kinase
- AR, androgen receptor
- ATG7, autophagy related 7
- ATM, ATM serine/threonine kinase
- BAX, BCL2 associated Xapoptosis regulator
- BCL2, BCL2 apoptosis regulator
- BCL2L10, BCL2 like 10
- BDNF, brain derived neurotrophic factor
- BLCA, bladder urothelial carcinoma
- BRCA, breast cancer
- Biomarker
- Bp, base pair
- C-myc (MYCBP), MYC binding protein
- CASC2, cancer susceptibility 2
- CD133 (PROM1), prominin 1
- CDC42, cell division cycle 42
- CDKN1, Bcyclin dependent kinase inhibitor 1B
- COAD, colon adenocarcinoma
- Cancer
- Circulating miRNA
- DDR, DNA damage repair
- E2F family (E2F1, E2F2, E2F3), E2F transcription factors
- EBV, Epstein-Barr virus
- EMT, epithelial-to-mesenchymal transition
- ER, estrogen receptor
- ERBB (EGFR), epidermal growth factor receptor
- ESCA, esophageal carcinoma
- FENDRR, FOXF1 adjacent non-coding developmental regulatory RNA
- FER1L4, fer-1 like family member 4 (pseudogene)
- GAS5, growth arrest–specific 5
- HIF-1α (HIF1A), hypoxia inducible factor 1 subunit alpha
- HNRNPA1, heterogeneous nuclear ribonucleoprotein A1
- HNSC, head and neck squamous cell carcinoma
- HRR, homologous recombination-based DNA repair
- IFN-γ (IFNG), interferon gamma
- IGF1, insulin like growth factor 1
- IL6, interleukin 6
- IPMK, inositol phosphate multikinase
- KIRC, clear cell kidney carcinoma
- KIRP, kidney renal papillary cell carcinoma
- KRAS, KRAS proto-oncogene, GTPase
- LIHC, liver hepatocellular carcinoma
- LMP1, latent membrane protein 1
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- Liquid biopsy
- MAPK, mitogen-activated protein kinase
- MCM7, minichromosome maintenance complex component 7
- MET, mesenchymal-to-epithelial transition
- MTOR, mechanistic target of rapamycin kinase
- N-myc (MYCN), MYCN proto-oncogene, bHLH transcription factor
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOTCH2, notch receptor 2
- Oncogene
- PAAD, pancreatic adenocarcinoma
- PERK (EIF2AK3), eukaryotic translation initiation factor 2 alpha kinase 3
- PI3K (PIK3CA), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha
- PIAS3, protein inhibitor of activated STAT 3
- PRAD, prostate adenocarcinoma
- RISC, RNA-induced silencing complex
- SMAD2, SMAD family member 2
- SMG1, SMG1 nonsense mediated mRNA decay associated PI3K related kinase
- SNHG1, small nucleolar RNA host gene 1
- SOCS5, suppressor of cytokine signaling 5
- STAD, stomach adenocarcinoma
- STAT3, signal transducer and activator of transcription 3
- STK4, serine/threonine kinase 4
- Suppressor
- TCGA
- TCGA, The Cancer Genome Atlas
- TGF-β (TGFB1), transforming growth factor beta 1
- TGFBR2, transforming growth factor beta receptor 2
- THCA, papillary thyroid carcinoma
- TNM, Classification of Malignant Tumors: T - tumor / N - lymph nodes / M – metastasis
- TP53, tumor protein p53
- TP53TG1, TP53 target 1
- TRIAP1, p53-regulating inhibitor of apoptosis gene
- TSC1, TSC complex subunit 1
- UCA1, urothelial cancer associated 1
- UCEC, uterine corpus endometrial carcinoma
- UTR, untranslated region
- WDFY3-AS2, WDFY3 antisense RNA 2
- WEE1, WEE1 G2 checkpoint kinase
- WNT family, Wingless-type MMTV integration site family/Wnt family ligands
- ZEB1/ZEB2, zinc finger E-box binding homeobox 1 and 2
- ceRNA, competitive endogenous RNA
- cncRNA, protein coding and non-coding RNA
- lncRNA, long-non coding RNA
- miR-17-92a
- miR-18a
- miRNA
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
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18
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Guglas K, Kołodziejczak I, Kolenda T, Kopczyńska M, Teresiak A, Sobocińska J, Bliźniak R, Lamperska K. YRNAs and YRNA-Derived Fragments as New Players in Cancer Research and Their Potential Role in Diagnostics. Int J Mol Sci 2020; 21:ijms21165682. [PMID: 32784396 PMCID: PMC7460810 DOI: 10.3390/ijms21165682] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/02/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
YRNAs are a type of short, noncoding RNAs. A total of four different transcripts can be distinguished, which are YRNA1, YRNA3, YRNA4 and YRNA5. All YRNAs are relatively small, made up of about 100 nucleotides each. YRNAs are characterized by a stem-loop structure and each part of that structure carries a different function. YRNAs are transcribed in the nucleus by RNA polymerase III. Then, the YRNA molecule is bound to the polyuridine tail of the La protein responsible for both its nuclear retention and protection from degradation. They also bind to the Ro60 protein, making the molecule more stable. In turn, YRNA-derived small RNAs (YsRNAs) are a class of YRNAs produced in apoptotic cells as a result of YRNA degradation. This process is performed by caspase-3-dependent pathways that form two groups of YsRNAs, with lengths of either approximately 24 or 31 nucleotides. From all four YRNA transcripts, 75 well-described pseudogenes are generated as a result of the mutation. However, available data indicates the formation of up to 1000 pseudogenes. YRNAs and YRNA-derived small RNAs may play a role in carcinogenesis due to their altered expression in cancers and influence on cell proliferation and inflammation. Nevertheless, our knowledge is still limited, and more research is required. The main aim of this review is to describe the current state of knowledge about YRNAs, their function and contribution to carcinogenesis, as well as their potential role in cancer diagnostics. To confirm the promising potential of YRNAs and YRNA-derived fragments as biomarkers, their significant role in several tumor types was taken into consideration.
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Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Iga Kołodziejczak
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
- International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
| | - Joanna Sobocińska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznań, Poland
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19
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Guglas K, Kolenda T, Stasiak M, Kopczyńska M, Teresiak A, Ibbs M, Bliźniak R, Lamperska K. YRNAs: New Insights and Potential Novel Approach in Head and Neck Squamous Cell Carcinoma. Cells 2020; 9:cells9051281. [PMID: 32455790 PMCID: PMC7290662 DOI: 10.3390/cells9051281] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/28/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022] Open
Abstract
YRNAs are a class of non-coding RNAs that are components of the Ro60 ribonucleoprotein particle and are essential for initiation of DNA replication. Ro60 ribonucleoprotein particle is a target of autoimmune antibodies in patients suffering from systemic lupus erythematosus and Sjögren’s syndrome. Deregulation of YRNAs has been confirmed in many cancer types, but not in head and neck squamous cell carcinoma (HNSCC). The main aim of this study was to determine the biological role of YRNAs in HNSCC, the expression of YRNAs, and their usefulness as potential HNSCC biomarkers. Using quantitative reverse transcriptase (qRT)-PCR, the expression of YRNAs was measured in HNSCC cell lines, 20 matched cancer tissues, and 70 FFPETs (Formaline-Fixed Paraffin-Embedded Tissue) from HNSCC patients. Using TCGA (The Cancer Genome Atlas) data, an analysis of the expression levels of selected genes, and clinical-pathological parameters was performed. The expression of low and high YRNA1 expressed groups were analysed using gene set enrichment analysis (GSEA). YRNA1 and YRNA5 are significantly downregulated in HNSCC cell lines. YRNA1 was found to be significantly downregulated in patients’ tumour sample. YRNAs were significantly upregulated in T4 stage. YRNA1 showed the highest sensitivity, allowing to distinguish healthy from cancer tissue. An analysis of TCGA data revealed that expression of YRNA1 was significantly altered in the human papilloma virus (HPV) infection status. Patients with medium or high expression of YRNA1 showed better survival outcomes. It was noted that genes correlated with YRNA1 were associated with various processes occurring during cancerogenesis. The GSEA analysis showed high expression enrichment in eight vital processes for cancer development. YRNA1 influence patients’ survival and could be used as an HNSCC biomarker. YRNA1 seems to be a good potential biomarker for HNSCC, however, more studies must be performed and these observations should be verified using an in vitro model.
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Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland, ul. Garbary 15, 61-866 Poznan, Poland; (T.K.); (M.K.); (A.T.); (R.B.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, ul. Zwirki 61 and ul. Wigury, 02-091 Warsaw, Poland
- Correspondence: (K.G.); (K.L.)
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland, ul. Garbary 15, 61-866 Poznan, Poland; (T.K.); (M.K.); (A.T.); (R.B.)
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, ul. Rokietnicka 8, 60-101 Poznan, Poland
| | - Maciej Stasiak
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, ul. Rokietnicka 8, 60-101 Poznan, Poland;
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland, ul. Garbary 15, 61-866 Poznan, Poland; (T.K.); (M.K.); (A.T.); (R.B.)
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, ul. Rokietnicka 8, 60-101 Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland, ul. Garbary 15, 61-866 Poznan, Poland; (T.K.); (M.K.); (A.T.); (R.B.)
| | - Matthew Ibbs
- Department of Tumour Pathology, Greater Poland Cancer Centre, Poznan, Poland, ul. Garbary 15, 61-866 Poznan, Poland;
- Chair and Department of Tumour Pathology and Prophylaxis, Poznan University of Medical Sciences, ul. Garbary 15, 61-866 Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland, ul. Garbary 15, 61-866 Poznan, Poland; (T.K.); (M.K.); (A.T.); (R.B.)
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland, ul. Garbary 15, 61-866 Poznan, Poland; (T.K.); (M.K.); (A.T.); (R.B.)
- Correspondence: (K.G.); (K.L.)
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20
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Kolenda T, Rutkowski P, Michalak M, Kozak K, Guglas K, Ryś M, Galus Ł, Woźniak S, Ługowska I, Gos A, Teresiak A, Mackiewicz A, Lamperska K, Mackiewicz J. Plasma lncRNA expression profile as a prognostic tool in BRAF-mutant metastatic melanoma patients treated with BRAF inhibitor. Oncotarget 2019; 10:3879-3893. [PMID: 31231466 PMCID: PMC6570476 DOI: 10.18632/oncotarget.26989] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/13/2019] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNA) are dysregulated in many cancer types. Abnormal baseline levels of these lncRNAs display diagnostic and prognostic potential in cancer patients. The aim of this study was to evaluate the prognostic value of plasma lncRNAs in BRAF-mutant advanced melanoma patients treated with a BRAF inhibitor. Total RNA was isolated from plasma samples collected from 58 advanced BRAF-mutant melanoma patients and 15 healthy donors. The expression levels of 90 lncRNAs were estimated using the LncProfiler qPCR Array Kit (SBI) and LightCycler 96 (Roche). LncRNA expression levels correlated with responses to the BRAF inhibitor (vemurafenib) treatment. The patients were stratified into three groups based on their lncRNA levels with various lncRNA expressions (low, medium, and high). A Cox proportional hazards regression model was used to determine the lncRNAs that were significantly associated with both progression-free and overall survivals (PFS and OS, respectively) in patients receiving vemurafenib. The expression level of 12 lncRNAs was down-regulated, while five lncRNAs were up-regulated in melanoma patients compared to healthy donors. Kaplan-Meier analysis showed that upregulation or downregulation of 11 and 16 different lncRNAs were associated with longer median PFS and OS, respectively. Further analysis demonstrated that the baseline lncRNAs for IGF2AS, anti-Peg11, MEG3, Zeb2NAT are independent prognostic factors in BRAF-mutant advanced melanoma patients treated with vemurafenib. Evaluation of plasma lncRNAs expression level for advanced melanoma diagnosis and prognosis evaluation appears to be a safe and valuable method; however, this method requires further validation in larger cohorts and randomized trials.
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Affiliation(s)
- Tomasz Kolenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Michał Michalak
- Department of Computer Science and Statistics, University of Medical Sciences, Poznan, Poland
| | - Katarzyna Kozak
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Kacper Guglas
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Marcel Ryś
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Łukasz Galus
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poznan, Poland.,Department of Chemotherapy, Greater Poland Cancer Centre, Poznan, Poland
| | - Sebastian Woźniak
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poznan, Poland
| | - Iwona Ługowska
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland.,Early Phase Clinical Trials Unit, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Aleksandra Gos
- Department of Translational Oncology, Maria Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
| | | | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poznan, Poland.,Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland.,Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, Poznan, Poland
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21
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Kolenda T, Guglas K, Kopczyńska M, Teresiak A, Bliźniak R, Mackiewicz A, Lamperska K, Mackiewicz J. Oncogenic Role of ZFAS1 lncRNA in Head and Neck Squamous Cell Carcinomas. Cells 2019; 8:cells8040366. [PMID: 31010087 PMCID: PMC6523746 DOI: 10.3390/cells8040366] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/15/2022] Open
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with high mortality. The identification of specific HNSCC biomarkers will increase treatment efficacy and limit the toxicity of current therapeutic strategies. Long non-coding RNAs (lncRNAs) are promising biomarkers. Accordingly, here we investigate the biological role of ZFAS1 and its potential as a biomarker in HNSCC. Methods: The expression level of ZFAS1 in HNSCC cell lines was analyzed using qRT-PCR. Based on the HNSCC TCGA data, the ZFAS1 expression profile, clinicopathological features, and expression of correlated genes were analyzed in patient tissue samples. The selected genes were classified according to their biological function using the PANTHER tool. The interaction between lncRNA:miRNA and miRNA:mRNA was tested using available online tools. All statistical analyses were accomplished using GraphPad Prism 5. Results: The expression of ZFAS1 was up-regulated in the metastatic FaDu cell line relative to the less aggressive SCC-25 and SCC-040 and dysplastic DOK cell lines. The TCGA data indicated an up-regulation of ZFAS1 in HNSCCs compared to normal tissue samples. The ZFAS1 levels typically differed depending on the cancer stage and T-stage. Patients with a lower expression of ZFAS1 presented a slightly longer disease-free survival and overall survival. The analysis of genes associated with ZFAS1, as well its targets, indicate that they are linked with crucial cellular processes. In the group of patients with low expression of ZFAS1, we detected the up-regulation of suppressors and down-regulation of genes associated with epithelial-to-mesenchymal transition (EMT) process, metastases, and cancer-initiating cells. Moreover, the negative correlation between ZFAS1 and its host gene, ZNFX1, was observed. The analysis of interactions indicated that ZFAS1 has a binding sequence for miR-150-5p. The expression of ZFAS1 and miR-150-5p is negatively correlated in HNSCC patients. miR-150-5p can regulate the 3′UTR of EIF4E mRNA. In the group of patients with high expression of ZFAS1 and low expression of miR-150-5p, we detected an up-regulation of EIF4E. Conclusions: In HNSCC, ZFAS1 displays oncogenic properties, regulates important processes associated with EMT, cancer-initiating cells, and metastases, and might affect patients’ clinical outcomes. ZFAS1 likely regulates the cell phenotype through miR-150-5p and its downstream targets. Following further validation, ZFAS1 might prove a new and valuable biomarker.
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Affiliation(s)
- Tomasz Kolenda
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland.
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, Room 5025, 61-866 Poznan, Poland.
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, Room 5025, 61-866 Poznan, Poland.
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 61 Zwirki i Wigury Street, 02-091 Warszawa, Poland.
| | - Magda Kopczyńska
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland.
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, Room 5025, 61-866 Poznan, Poland.
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, Room 5025, 61-866 Poznan, Poland.
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, Room 5025, 61-866 Poznan, Poland.
| | - Andrzej Mackiewicz
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland.
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland.
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary Street, Room 5025, 61-866 Poznan, Poland.
| | - Jacek Mackiewicz
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 15 Garbary Street, 61-866 Poznan, Poland.
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, 16/18 Grunwaldzka Street, 60-786 Poznan, Poland.
- Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznan, Poland.
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22
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Kolenda T, Guglas K, Teresiak A, Bliźniak R, Lamperska K. Low let-7d and high miR-205 expression levels positively influence HNSCC patient outcome. J Biomed Sci 2019; 26:17. [PMID: 30755200 PMCID: PMC6373017 DOI: 10.1186/s12929-019-0511-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/04/2019] [Indexed: 12/26/2022] Open
Abstract
Introduction Head and neck squamous carcinoma (HNSCC) is one of the most invasive types of cancer with high mortality. A previous study has indicated that low levels of let-7d and miR-205 in HNSCC patients are correlated with poor survival. Let-7d and miR-205 are tumor suppressors and regulators of epithelial-to-mesenchymal transition (EMT). However, it is unclear if let-7d and miR-205 together influence cancer cells. Aim To determine if let-7d and miR-205 expression levels influence HNSCC patient outcome. Methods The TCGA expression data for let-7d, miR-205 and their targets as well as clinical data were downloaded from cBioPortal and starBase v2.0 for 307 patients. The expression levels of let-7d and miR-205 were verified according to clinicopathological parameters. The let-7d and miR-205 high- and low-expression groups as well as disease-free survival (DFS), overall survival (OS) and expression levels of genes related to EMT, cancer stem cells, metastasis, cell cycle, drug response and irradiation response were investigated. Results Let-7d and miR-205 were frequently upregulated in HNSCC compared to normal samples, and ROC analysis showed high discrimination ability for let-7d and miR-205 (area 0.7369 and 0.7739, respectively; p < 0.0001). Differences between expression levels of let-7d or miR-205 and grade, angiolymphatic invasion, perineural invasion and alcohol consumption were indicated. No differences were observed in N-stage, tumor localization, gender or patient age. Patients with lower let-7d levels and higher miR-205 levels had significantly better OS (p = 0.0325) than patients with higher let-7d levels and lower miR-205 levels. In the low let-7d level and high miR-205 level group, a lower percentage of more advanced cancers was observed. The analysis of genes related to EMT, cancer stem cells, metastasis, cell cycle, drug response and irradiation response revealed a distinct phenotype of analyzed groups. Conclusions The present findings indicated that let-7d down-regulation and miR-205 overexpression create a unique cell phenotype with different behavior compared to cells with upregulated let-7d and down-regulated miR-205. Thus, let-7d and miR-205 are good candidates for new HNSCC biomarkers.
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Affiliation(s)
- Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, room 5025, 61-866, Poznan, Poland. .,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland. .,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland.
| | - Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, room 5025, 61-866, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, room 5025, 61-866, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, room 5025, 61-866, Poznan, Poland
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 15th Garbary Street, room 5025, 61-866, Poznan, Poland.
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23
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Guglas K, Kolenda T, Teresiak A, Kopczyńska M, Łasińska I, Mackiewicz J, Mackiewicz A, Lamperska K. lncRNA Expression after Irradiation and Chemoexposure of HNSCC Cell Lines. Noncoding RNA 2018; 4:ncrna4040033. [PMID: 30441874 PMCID: PMC6315432 DOI: 10.3390/ncrna4040033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cause of cancer mortality in the world. To improve the quality of diagnostics and patients' treatment, new and effective biomarkers are needed. Recent studies have shown that the expression level of different types of long non-coding RNAs (lncRNAs) is dysregulated in HNSCC and correlates with many biological processes. In this study, the response of lncRNAs in HNSCC cell lines after exposure to irradiation and cytotoxic drugs was examined. The SCC-040, SCC-25, FaDu, and Cal27 cell lines were treated with different radiation doses as well as exposed to cisplatin and doxorubicin. The expression changes of lncRNAs after exposure to these agents were checked by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Target prediction was performed using available online tools and classified into specific biological processes and cellular pathways. The results indicated that the irradiation, as well as chemoexposure, causes changes in lncRNA expression and the effect depends on the cell line, type of agents as well as their dose. After irradiation using the dose of 5 Gy significant dysregulation of 4 lncRNAs, 10 Gy-5 lncRNAs, and 20 Gy-3 lncRNAs, respectively, were observed in all cell lines. Only lncRNAs Zfhx2as was down-regulated in all cell lines independently of the dose used. After cisplatin exposure, 14 lncRNAs showed lower and only two higher expressions. Doxorubicin resulted in lower expressions of eight and increased four of lncRNAs. Common effects of cytotoxic drugs were observed in the case of antiPEG11, BACE1AS, PCGEM1, and ST7OT. Analysis of the predicted targets for dysregulated lncRNAs indicated that they are involved in important biological processes, regulating cellular pathways connected with direct response to irradiation or chemoexposure, cellular phenotype, cancer initiating cells, and angiogenesis. Both irradiation and chemoexposure caused specific changes in lncRNAs expression. However, the common effect is potentially important for cellular response to the stress and survival. Further study will show if lncRNAs are useful tools in patients' treatment monitoring.
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Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznan, Poland.
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warszawa, Poland.
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznan, Poland.
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznan, Poland.
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warszawa, Poland.
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznan, Poland.
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznan, Poland.
| | - Magda Kopczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznan, Poland.
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznan, Poland.
| | - Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, University of Medical Sciences, 60-355 Poznan, Poland.
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, University of Medical Sciences, 60-355 Poznan, Poland.
- Department of Biology and Environmental Studies, University of Medical Sciences, 61-701 Poznan, Poland.
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland.
| | - Andrzej Mackiewicz
- Chair of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznan, Poland.
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland.
| | - Katarzyna Lamperska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, 61-866 Poznan, Poland.
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24
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Kapałczyńska M, Kolenda T, Przybyła W, Zajączkowska M, Teresiak A, Filas V, Ibbs M, Bliźniak R, Łuczewski Ł, Lamperska K. 2D and 3D cell cultures - a comparison of different types of cancer cell cultures. Arch Med Sci 2018; 14:910-919. [PMID: 30002710 PMCID: PMC6040128 DOI: 10.5114/aoms.2016.63743] [Citation(s) in RCA: 403] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/27/2016] [Indexed: 02/07/2023] Open
Abstract
Cell culture is a widely used in vitro tool for improving our understanding of cell biology, tissue morphology, and mechanisms of diseases, drug action, protein production and the development of tissue engineering. Most research regarding cancer biology is based on experiments using two-dimensional (2D) cell cultures in vitro. However, 2D cultures have many limitations, such as the disturbance of interactions between the cellular and extracellular environments, changes in cell morphology, polarity, and method of division. These disadvantages led to the creation of models which are more closely able to mimic conditions in vivo. One such method is three-dimensional culture (3D). Optimisation of the culture conditions may allow for a better understanding of cancer biology and facilitate the study of biomarkers and targeting therapies. In this review, we compare 2D and 3D cultures in vitro as well as different versions of 3D cultures.
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Affiliation(s)
- Marta Kapałczyńska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Tomasz Kolenda
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, University of Warsaw, Warsaw, Poland
| | - Weronika Przybyła
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Maria Zajączkowska
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Violetta Filas
- Department of Tumour Pathology, Greater Poland Cancer Centre, Poznan, Poland
| | - Matthew Ibbs
- Department of Tumour Pathology, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Łukasz Łuczewski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
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25
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Guglas K, Bogaczyńska M, Kolenda T, Ryś M, Teresiak A, Bliźniak R, Łasińska I, Mackiewicz J, Lamperska K. lncRNA in HNSCC: challenges and potential. Contemp Oncol (Pozn) 2017; 21:259-266. [PMID: 29416430 PMCID: PMC5798417 DOI: 10.5114/wo.2017.72382] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 10/27/2017] [Indexed: 01/17/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cause of cancer mortality in the world. Some progress has been made in the therapy of HNSCC, however treatment remains unsatisfactory. Recent studies have shown that different types of long non-coding RNAs (lncRNAs) are dysregulated in HNSCC and correlate with tumor progression, lymph node metastasis, clinical stage and poor prognosis. lncRNAs are a class of functional RNA molecules that can not be translated into proteins but can modulate the activity of transcription factors or regulate changes in chromatin structure. The lncRNAs might have potential of biomarker in HNSCC diagnosis, prognosis, prediction and targeted treatment. In this review we describe the potential role of lncRNAs as new biomarkers and discuss their features including source of origin, extraction methods, stability, detection methods and data normalization and potential function as biomarkers in HNSCC.
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Affiliation(s)
- Kacper Guglas
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta Bogaczyńska
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- HAN University of Applied Sciences, Nijmegen, Netherlands
| | - Tomasz Kolenda
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Marcel Ryś
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Teresiak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
| | - Renata Bliźniak
- Laboratory of Cancer Genetic, Greater Poland Cancer Centre, Poznan, Poland
| | - Izabela Łasińska
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poland
| | - Jacek Mackiewicz
- Department of Medical and Experimental Oncology, Heliodor Swiecicki Clinical Hospital, Poznan University of Medical Sciences, Poland
- Department of Biology and Environmental Sciences, Poznan University of Medical Sciences, Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland
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26
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Zhi X, Lamperska K, Golusinski P, Schork NJ, Luczewski L, Kolenda T, Golusinski W, Masternak MM. Gene expression analysis of head and neck squamous cell carcinoma survival and recurrence. Oncotarget 2016; 6:547-55. [PMID: 25575813 PMCID: PMC4381614 DOI: 10.18632/oncotarget.2772] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/15/2014] [Indexed: 11/25/2022] Open
Abstract
The squamous cell carcinomas represent about 90 % of all head and neck cancers, ranking the sixth most common human cancer. Approximately 450,000 of new cases of head and neck squamous cell carcinoma (HNSCC) are diagnosed every year. Unfortunately, because of diagnosis at the advanced stages and early metastasis to the lymph nodes, the HNSCC is associated with very high death rate. Identification of signature biomarkers and molecularly targeted therapies could provide more effective and specific cancer treatment, prevent recurrence, and increase survival rate. We used paired tumor and adjacent normal tissue samples to screen with RT² Profiler™ PCR Array Human Cancer PathwayFinderTM . Total of 20 up-regulated genes and two down-regulated genes were screened out. Out of 22 genes, 12 genes were subsequently validated to be significantly altered in the HNSCC; the samples were from all 41 patients. Five year survival and recurrence selected genes that could represent the biomarkers of survival and recurrence of the disease. We believe that comprehensive understanding of the unique genetic characteristics of HNSCC could provide novel diagnostic biomarkers and meet the requirement for molecular-targeted therapy for the HNSCC.
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Affiliation(s)
- Xu Zhi
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing, China. College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA
| | - Katarzyna Lamperska
- Deptartment of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Paweł Golusinski
- Department of Enviromental Biology, Poznan University of Medical Sciences, Poznan, Poland. Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Lukasz Luczewski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | - Tomasz Kolenda
- Deptartment of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland. Postgraduate School of Molecular Medicine, Medical University of Warsaw, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | - Michal M Masternak
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, USA. Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
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27
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Martinez BV, Dhahbi JM, Lopez YON, Lamperska K, Golusinski P, Luczewski L, Kolenda T, Atamna H, Spindler SR, Golusinski W, Masternak MM. Circulating small non-coding RNA signature in head and neck squamous cell carcinoma. Oncotarget 2015; 6:19246-63. [PMID: 26057471 PMCID: PMC4662488 DOI: 10.18632/oncotarget.4266] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [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: 03/18/2015] [Accepted: 05/13/2015] [Indexed: 12/23/2022] Open
Abstract
The Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common human cancer, causing 350,000 individuals die worldwide each year. The overall prognosis in HNSCC patients has not significantly changed for the last decade. Complete understanding of the molecular mechanisms in HNSCC carcinogenesis could allow an earlier diagnosis and the use of more specific and effective therapies. In the present study we used deep sequencing to characterize small non-coding RNAs (sncRNAs) in serum from HNSCC patients and healthy donors. We identified, for the first time, a multi-marker signature of 3 major classes of circulating sncRNAs in HNSCC, revealing the presence of circulating novel and known miRNAs, and tRNA- and YRNA-derived small RNAs that were significantly deregulated in the sera of HNSCC patients compared to healthy controls. By implementing a triple-filtering approach we identified a subset of highly biologically relevant miRNA-mRNA interactions and we demonstrated that the same genes/pathways affected by somatic mutations in cancer are affected by changes in the abundance of miRNAs. Therefore, one important conclusion from our work is that during cancer development, there seems to be a convergence of oncogenic processes driven by somatic mutations and/or miRNA regulation affecting key cellular pathways.
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Affiliation(s)
- Berta Victoria Martinez
- University of Central Florida, Burnett School of Biomedical Sciences, College of Medicine Orlando, FL, USA
| | - Joseph M. Dhahbi
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Yury O. Nunez Lopez
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL, USA
| | - Katarzyna Lamperska
- Deptartment of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
| | - Paweł Golusinski
- Department of Biology and Environmental Studies, Poznan University of Medical Sciences, Poznan, Poland
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | - Lukasz Luczewski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | - Tomasz Kolenda
- Deptartment of Cancer Genetics, Greater Poland Cancer Centre, Poznan, Poland
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Hani Atamna
- Department of Medical Education, California Northstate University, Elk Grove, CA, USA
| | - Stephen R. Spindler
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
| | - Michal M. Masternak
- University of Central Florida, Burnett School of Biomedical Sciences, College of Medicine Orlando, FL, USA
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poznan, Poland
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Golusinski P, Zhi X, Lamperska K, Luczewski L, Schork N, Golusinski W, Masternak M. 15 Genetic biomarkers in head and neck squamous cell carcinoma. Oral Oncol 2015. [DOI: 10.1016/j.oraloncology.2015.02.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Kycler W, Korski K, Loziński C, Teresiak-Mańczak A, Przybyła A, Mackiewicz A, Cybulski Z, Lamperska K. The anti-cancer actions of O6-methylguanine-DNA-methyltransferase in relation to colon polyps. Pharmacol Rep 2014; 66:1060-4. [PMID: 25443735 DOI: 10.1016/j.pharep.2014.06.019] [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: 09/01/2013] [Revised: 05/05/2014] [Accepted: 06/25/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Genetic variability in DNA repair genes may contribute to differences in DNA repair capacity and susceptibility to colon polyps and cancer. In this study, we examined the role of MGMT polymorphisms in colon polyps formation. METHODS PCR-SSCP analysis was performed included 254 patients with colon polyps and 330 controls. RESULTS The homozygous F84F genotype was significantly more prevalent in study group than in controls. The polymorphic allele 84F was more frequent appeared in group of older patients and in group of smoking patients. On the other hand, there were no association between 84F and gender, size of polyps, cancer family history. CONCLUSIONS We concluded that high frequency of 84F allele in the group of patients may suggest the role of the MGMT variant in colon polyps etiology.
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Affiliation(s)
- Witold Kycler
- Department of Oncological Surgery II, Greater Poland Cancer Centre, Poznań, Poland.
| | - Konstanty Korski
- Department of Pathology, Greater Poland Cancer Centre, Poznań, Poland
| | - Cezary Loziński
- Department of Oncological Surgery II, Greater Poland Cancer Centre, Poznań, Poland
| | | | | | - Andrzej Mackiewicz
- University of Medical Sciences, Poznań, Poland; Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznań, Poland
| | - Zefiryn Cybulski
- Microbiology Laboratory, Greater Poland Cancer Centre, Poznań, Poland
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Masternak M, Zhi X, Lamperska K, Golusinski P, Luczewski L, Schork N, Golusinski W. Genetic Biomarkers in Head and Neck Squamous Cell Carcinoma. Otolaryngol Head Neck Surg 2014. [DOI: 10.1177/0194599814541629a94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Objectives: Head and neck squamous cell carcinoma (HNSCC) is known as one of the 6 most common human cancers mainly caused by consumption of tobacco and alcohol. There is also a genetic factor; however, the genetic markers are not yet established. Our objectives were to (1) validate the genetic signature of molecular targets expressed by tumors in HNSCC and (2) determine potential biomarkers for earlier detection, potential therapies, and prediction of patients’ survival. Methods: The HNSCC patients were recruited to the study in the Greater Poland Cancer Centre in 2010. Oral cancer and normal epithelium tissue taken at a minimum of 2 cm distal from the tumors’ margins from 41 patients were used for analysis by Cancer Pathway Finder array and followed with real-time polymerase chain reaction. Results: Analysis indicated up-regulation of 11 genes including KRT14, ACLY, MCM2, SKP2, STMN1, CDC20, SNAI2, MKI67, SLC2A1, BCL2L11, and IGFBP3 ( P < .05), suggesting altered regulation of cell cycle, cell senescence, metabolism, apoptosis, and hypoxia. Interestingly, 3-year patient follow-up survival analysis indicated that skp2, cdh2, vegfc, and bcl2l11 genes expression was significantly associated with survival of the patients. Conclusions: Our data indicate that there is significant activation of several cellular pathways in tumor tissue that should be further investigated. Importantly, observed significant association between the expression of skp2, cdh2, vegfc, and bcl2l11 and survival indicate that the larger the difference between the expression in tumor and normal tissue of these genes, the shorter the survival time of the patient.
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Zhi X, Lamperska K, Golusinski P, Schork NJ, Luczewski L, Golusinski W, Masternak MM. Expression levels of insulin-like growth factors 1 and 2 in head and neck squamous cell carcinoma. Growth Horm IGF Res 2014; 24:137-141. [PMID: 24802266 PMCID: PMC4083007 DOI: 10.1016/j.ghir.2014.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 11/16/2022]
Abstract
Insulin-like growth factors (IGF) 1 and 2 are known as potential mitogens for normal and neoplastic cells. IGF2 is a main fetal growth factor while IGF1 is activated through growth hormone action during postnatal growth and development. However, there is strong evidence that activation of IGF2 by its E2F transcription factor 3 (E2F3) is present in different types of cancer. Also high levels of IGF1 strongly correlate with cancer development due to anti-apoptotic properties and enhancement of cancer cell differentiation, which can be attenuated by IGFBP3. Head and neck cancer is known as one of the six most common human cancers. The main risk factor for head and neck cancer is consumption of tobacco and alcohol as well as viral infection and bacterial infection by stimulation of chronic local inflammation. There is also a genetic basis for this form of cancer; however, the genetic markers are not yet established. In this study we investigated the levels of the expression of IGF2, IGF1, E2F3 and IGFBP3 in human cancers and healthy tissues surrounding the tumor obtained from each of 41 patients. Our study indicated that there is no alteration of the levels of expression of IGF2, E2F3 and IGF1 in head and neck squamous cell carcinoma (HNSCC) cases studied in selected experimental population, but there was evidence for upregulation of pro-apoptotic IGFBP3 in cancer when comparing to healthy tissue. These important findings indicate that insulin-growth factors are not directly associated with HNSCC showing some variability between patients and location of tumor. However, elevated level of IGFBP3 suggests possible regulatory role of IGF signal by its binding protein in this type of tumor.
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Affiliation(s)
- Xu Zhi
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA; Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
| | - Katarzyna Lamperska
- Deptartment of Cancer Genetics, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Paweł Golusinski
- Dept. of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences, Poland
| | - Nicholas J Schork
- Human Biology, The J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Lukasz Luczewski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences,15 Garbary St., 61-866 Poznan, Poland
| | - Wojciech Golusinski
- Department of Head and Neck Surgery, Greater Poland Cancer Centre, Poznan University of Medical Sciences,15 Garbary St., 61-866 Poznan, Poland.
| | - Michal M Masternak
- College of Medicine, Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA.
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Stojcev Z, Banasiewicz T, Kaszuba M, Sikorski A, Szczepkowski M, Bobkiewicz A, Paszkowski J, Krokowicz Ł, Biczysko M, Szmeja J, Jurkowska M, Majewski P, Mackiewicz A, Lamperska K, Drews M, Wojciechowicz J. Development of a new, simple and cost-effective diagnostic tool for genetic screening of hereditary colorectal cancer--the DNA microarray assay. Acta Biochim Pol 2013. [DOI: 10.18388/abp.2013_1971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Detection of mutations in families with a hereditary predisposition to colon cancer gives an opportunity to precisely define the high-risk group. 36 patients operated on for colon cancer, with familiar prevalence of this malignancy, were investigated using the DNA microarrays method with the potential detection of 170 mutations in MLH1, MSH2, MSH6, CHEK2, and NOD2 genes. In microarrays analysis of DNA in 9 patients (25% of the investigated group), 6 different mutations were found. The effectiveness of genetic screening using the microarray method is comparable to the effectiveness of other, much more expensive and time-consuming methods.
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Stojcev Z, Banasiewicz T, Kaszuba M, Sikorski A, Szczepkowski M, Bobkiewicz A, Paszkowski J, Krokowicz Ł, Biczysko M, Szmeja J, Jurkowska M, Majewski P, Mackiewicz A, Lamperska K, Drews M, Wojciechowicz J. Development of a new, simple and cost-effective diagnostic tool for genetic screening of hereditary colorectal cancer--the DNA microarray assay. Acta Biochim Pol 2013; 60:195-198. [PMID: 23741719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 04/14/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
Detection of mutations in families with a hereditary predisposition to colon cancer gives an opportunity to precisely define the high-risk group. 36 patients operated on for colon cancer, with familiar prevalence of this malignancy, were investigated using the DNA microarrays method with the potential detection of 170 mutations in MLH1, MSH2, MSH6, CHEK2, and NOD2 genes. In microarrays analysis of DNA in 9 patients (25% of the investigated group), 6 different mutations were found. The effectiveness of genetic screening using the microarray method is comparable to the effectiveness of other, much more expensive and time-consuming methods.
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Affiliation(s)
- Zoran Stojcev
- Regional Specialistic Hospital, Słupsk, Department of General, Vascular and Oncologic, Surgery, Słupsk, Poland
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Kycler W, Szarzyńska B, Loziński C, Korski K, Lamperska K. Analysis of O6-methylguanine-DNA methyltransferase methylation status in sporadic colon polyps. Rep Pract Oncol Radiother 2012; 17:13-8. [PMID: 24376999 DOI: 10.1016/j.rpor.2011.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 10/13/2011] [Accepted: 11/10/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND/AIM The aim of our study was to check how MGMT methylation status together with known factors influenced the risk of colon cancer development. MATERIALS AND METHODS We examined patients with colon polyps. Information concerning gender, age, lifestyle, diet, anthropometry and medical information, including cancer and family history of cancer, was analyzed. Polymorphism variety of MGMT gene was investigated in another study. Genetic analysis for MGMT methylation assessment was performed for polyp tissue samples from 143 patients. RESULTS Positive methylation MGMT status was found in 55 patients. There was no correlation between gender and MGMT methylation status (p = 0.43). We did not find correlation between patients younger and older than 60 (p = 0.87). There was no correlation between smoking and MGMT methylation status (p = 0.36). We did not find correlation between BMI and MGMT methylation status (p = 0.86). We did not find correlation between MGMT methylation status and colon cancer in familial history (p = 0.45). CONCLUSION Our study showed no correlations between methylation status of MGMT polymorphisms and clinical features like age, gender, polyp localization, smoking status, or obesity. It has been shown previously that MGMT methylation status may show nonspecific methylation in colon polyps. Gene methylation status in adenoma tissues has also been associated by other authors with the adenoma's size, histology, and degree of atypia. In our study, we evaluated the gene methylation status in colon polyps and found no association with adenoma characteristics. The present study showed no correlation for MGMT methylation in polyps in different regions of colon.
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Affiliation(s)
- Witold Kycler
- Department of Oncological Surgery II, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | | | - Cezary Loziński
- Department of Oncological Surgery II, Greater Poland Cancer Centre, 15 Garbary St., 61-866 Poznan, Poland
| | - Konstanty Korski
- Department of Pathology, Greater Poland Cancer Centre, Poznan, Poland
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Golusinski P, Lamperska K, Pazdrowski J, Golusinski W. [Analysis of mutations within the TP53 gene in patients with squamous cell carcinoma of the head and neck]. Otolaryngol Pol 2011; 65:114-21. [PMID: 21735667 DOI: 10.1016/s0030-6657(11)70640-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Head and neck cancer is the sixth most common type of cancer. Tobacco and alcohol consumption are implicated in 75% of all SCCHN and have a multiplicative combined effect. It is considered to be the main risk factor for the cancer development. The identification of a number of these genetic alterations, for example mutations in the p53 tumour suppressor gene, paved the way for their use as molecular markers. Mutations in the TP53 gene frequently occur in many cancers and are present in 50-60% of head and neck cancers, p53 plays a sentinel role in the pathways that prevent development of cancer by inducing apoptosis, DNA repair and cell cycle arrest in response to different types of cellular stress The aim of the study, was the assessment of the TP53 mutations prevalence in the head and neck cancer patients and it's relation with the clinical data and course of the disease. The material comprised of peripheral blood and tumour tissue obtained from 50 HNSCC patients with a primary tumour in the oral cavity, oropharynx or larynx, who were scheduled for surgical treatment. The mutations in TP53, were detected with use of PCR-SSCP technique. In total 8 patients (16%), showed TP53 mutation in primary tumour. The significant correlation between tobacco and alcohol consumption and the mutation incidence has been observed. The site of the tumour and histopathological grading were also related to the prevalence of mutations, however without reaching the level of statistical significance. There was no correlation between mutations and the T and N stage of the disease.
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Affiliation(s)
- Paweł Golusinski
- Oddział Chirurgii Głowy i Szyi i Onkologii Laryngologicznej, Wielkopolskie Centrum Onkologii, Poznań.
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Wysocki PJ, Korski K, Lamperska K, Zaluski J, Mackiewicz A. Primary resistance to docetaxel-based chemotherapy in metastatic breast cancer patients correlates with a high frequency of BRCA1 mutations. Med Sci Monit 2008; 14:SC7-SC10. [PMID: 18591931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Docetaxel is a member of the taxoid anticancer agents routinely used in the treatment of high-risk or metastatic breast cancer. A recent study demonstrated that a low response rate to taxane-based neoadjuvant chemotherapy is associated with BRCA1 mutations. Therefore the frequency of BRCA1 mutations in a population of metastatic docetaxel-refractory patients was analyzed. MATERIAL/METHODS Nineteen treatment-refractory patients were selected from a group of 175 metastatic breast cancer patients treated with docetaxel-based therapy. DNA isolated from blood or from paraffin-embedded tissue samples was screened for three founder mutations common (>80%) in the Polish population. Additionally, the frequency of BRCA1 mutations was compared with the particular phenotype of breast cancer cells. RESULTS BRCA1 mutations were found in 5 of the 19 of patients (26.3%), all 5 being of the 7 patients with triple-negative breast cancer (71%, p<0.002). CONCLUSIONS This study indicates that the administration of taxanes, especially docetaxel, to metastatic BRCA1 breast cancer patients requires consideration. Moreover, BRCA1 testing in triple-negative breast cancer patients resistant to docetaxel-based treatment may help to identify families with germinal mutations without a history of hereditary breast cancer.
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Affiliation(s)
- Piotr J Wysocki
- Department of Cancer Immunology, University of Medical Sciences, Poznań, Poland.
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Wysocki PJ, Korski K, Lamperska K, Zaluski J, Mackiewicz A. Primary resistance to docetaxel-based chemotherapy in metastatic breast cancer patients correlates with a high frequency of BRCA1 mutations. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.1079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Jassem E, Ramlau R, Dziadziuszko R, Szymanowska A, Jakóbkiewicz J, Lamperska K, Kobierska G, Skokowski J, Dyszkiewicz W, Mackiewicz A, Żylicz M, Jassem J. Mutacje genów p53 i p1616 w niedrobnokomórkowym raku płuca. Pneumonol Alergol Pol 2008. [DOI: 10.5603/arm.28262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Lubiński J, Górski B, Huzarski T, Byrski T, Gronwald J, Serrano-Fernández P, Domagała W, Chosia M, Uciński M, Grzybowska E, Lange D, Maka B, Mackiewicz A, Karczewska A, Breborowicz J, Lamperska K, Stawicka M, Gozdecka-Grodecka S, Bebenek M, Sorokin D, Wojnar A, Haus O, Sir J, Mierzwa T, Niepsuj S, Gugała K, Góźdź S, Sygut J, Kozak-Klonowska B, Musiatowicz B, Posmyk M, Kordek R, Morawiec M, Zambrano O, Waśko B, Fudali L, Skret J, Surdyka D, Urbański K, Mituś J, Ryś J, Szwiec M, Rozmiarek A, Dziuba I, Wandzel P, Wiśniowski R, Szczylik C, Kozak A, Kozłowski W, Narod SA. BRCA1-positive breast cancers in young women from Poland. Breast Cancer Res Treat 2006; 99:71-6. [PMID: 16541315 DOI: 10.1007/s10549-006-9182-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 01/29/2006] [Indexed: 11/27/2022]
Abstract
We identified 4316 unselected incident cases of early-onset breast cancers (<51 ears of age at diagnosis) in 18 Polish hospitals between 1996 and 2003. We were able to obtain a blood sample for DNA analysis from 3472 of these (80.4%). All cases were tested for the presence of three founder mutations in BRCA1. The proportion of cases with a BRCA1 mutation was 5.7%. The hereditary proportions were higher than this for women with breast cancer diagnosed before age 40 (9%), for women with cancer of medullary or atypical medullary histology (28%), for those with bilateral cancer (29%) or with a family history of breast or ovarian cancer (13%). It is reasonable to offer genetic testing to women with early-onset breast cancer in Poland.
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Affiliation(s)
- J Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, ul. Połabska 4, 70-115 Szczecin, Poland.
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Menkiszak J, Gronwald J, Górski B, Jakubowska A, Huzarski T, Byrski T, Foszczyńska-Kłoda M, Haus O, Janiszewska H, Perkowska M, Brozek I, Grzybowska E, Zientek H, Góźdź S, Kozak-Klonowska B, Urbański K, Miturski R, Kowalczyk J, Pluzańska A, Niepsuj S, Koc J, Szwiec M, Drosik K, Mackiewicz A, Lamperska K, Strózyk E, Godlewski D, Stawicka M, Waśko B, Bebenek M, Rozmiarek A, Rzepka-Górska I, Narod SA, Lubiński J. Hereditary ovarian cancer in Poland. Int J Cancer 2003; 106:942-5. [PMID: 12918074 DOI: 10.1002/ijc.11338] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
There is increasing evidence that hereditary factors play a greater role in ovarian cancer than in any of the other common cancers of adulthood. This is attributable, to a large extent, to a high frequency of mutations in the BRCA1 or BRCA2 genes. In Poland, 3 common founder mutations in BRCA1 account for the majority of families with identified BRCA mutations. Our study was conducted in order to estimate the prevalence of any of 3 founder BRCA1 mutations (5382insC, C61G and 4153delA) in 364 unselected women with ovarian cancer, and among 177 women with ovarian cancer and a family history of breast or ovarian cancer. A mutation was identified in 49 out of 364 unselected women with ovarian cancer (13.5%) and in 58 of 177 women with familial ovarian cancer (32.8%). The majority of women with ovarian cancer and a BRCA1 mutation have no family history of breast or ovarian cancer. The high frequency of BRCA1 mutations in Polish women with ovarian cancer supports the recommendation that all Polish women with ovarian cancer should be offered testing for genetic susceptibility, and that counseling services be made available to them and to their relatives. It is important that mutation surveys be conducted in other countries prior to the introduction of national genetic screening programs.
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Affiliation(s)
- Janusz Menkiszak
- Department of Surgical Gynecology and Gynecological Oncology of Adults and Adolescents, Pomeranian Medical University, Szczecin, Poland.
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Lamperska K, Mackiewicz K, Kaczmarek A, Kwiatkowska E, Starzycka M, Romanowska B, Heizman J, Stachura J, Mackiewicz A. Expression of p16 in sporadic primary uveal melanoma. Acta Biochim Pol 2003; 49:377-85. [PMID: 12362979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Expression of p16 protein, intragenic mutations of CDKN2A and hypermethylation of CDKN2A promoter region in 41 sporadic primary uveal melanomas were studied. There were 2 cases of spindle cell B histological type, 11 of A + B and 28 of mixed type. All melanomas infiltrated sclera but in 28 cases infiltration was superficial while in 13 profound. In 7 cases the tumor infiltrated the optic nerve. Expression of p16 was studied by immunohistochemistry and recorded by assessment of the proportion of positive tumor cells and staining intensity. Results were expressed as staining index (IRS). Intragenic mutations were studied by PCR-SSCP followed by sequencing, while hypermethylation of the promoter region by CpG methylation assay. In 15% of cases less than 10% of melanoma cells were p16 positive, in 70% of cases less than 50% of cells, while in 7% more than 80% of cells stained for p16 (mean IRS for all cases was 4.87 +/- 2.43). In B type the IRS was 8.5 +/- 0.7, in A + B type 6.0 +/- 2.1 and in the mixed type 4.17 +/- 2.43 (differences statistically significant). In melanomas profoundly infiltrating sclera mean IRS was 4.16, while in those infiltrating optic nerve 3.71 (statistically not significant). Analysis of the intragenic mutations revealed in two patients a GAC/GAT substitution in codon 84--a silent mutation. No hypermethylation of the CpG island of the p16 promoter region was found. In conclusion, we found that the degree of p16 expression is related to the histological type of tumor but not to the histological indicators of tumor invasiveness and that intragenic mutations and promoter hypermethylation are not major mechanisms of p16 inactivation in sporadic uveal melanoma.
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Affiliation(s)
- Katarzyna Lamperska
- Department of Cancer Immunology, University School of Medical Sciences and GreatPoland Cancer Center, Poznań
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Lamperska K, Karezewska A, Kwiatkowska E, Mackiewicz A. Analysis of mutations in the p16/CDKN2A gene in sporadic and familial melanoma in the Polish population. Acta Biochim Pol 2003; 49:369-76. [PMID: 12362978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Mutations in CDKN2A have been found in sporadic cutaneous malignant (CMM), in familial CMM and in other syndromes associated with melanoma. In this study DNA was obtained from 207 individuals and five cell lines. There were 157 CMM patients and 50 healthy members of melanoma patients families. The CMM group included patients with one or two melanoma cases in the family, families with dysplastic nevus syndrom (DNS) and patients with a spectrum of other types of cancers in the family. PCR-SSCP analysis and sequencing identified: six substitutions in codon 58 CGA/TGA (Arg/Stop), 16 substitutions GAC/GAT in codon 84 (Asp/Asp), six substitutions CGA/TGA in codon 148 (Arg/Thr), 14 substitutions G/C in 3'UTR and 4 double changes (two in codon 84 and 3'UTR; two in codon 148 and 3'UTR). The mutation identified in codon 58 was found in tissue only. Other substitutions were polymorphisms found in DNA from tissue and blood samples. Most of them were identified in sporadic CMM (six in codon 148 Ala/Thr, 12 in codon 84 Asp/Asp and six in 3'UTR). The frequency of the polymorphisms was also high in DNS and CMM/DNS families (four in codon 84 Asp/Asp and six in 3'UTR). No mutations or polymorphisms were found in CMM patients with one or two melanoma cases and CMM patients, with other cancers in family history. The analysis of the CDKN2A gene mutations in the Polish population demonstrated: (i) no germline mutations; (ii) a relatively high number of genetic changes in sporadic melanoma; (iii) a high number of polymorphisms in DNS and CMM/DNS families.
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Affiliation(s)
- Katarzyna Lamperska
- Department of Cancer Immunology, K Marcinkowski University of Medical Sciences, GreatPoland Cancer Center, Poznań
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Lamperska K, Przybyła A, Bliźniak R, Dams-Kozłowska H, Wojciechowska – Łącka A, Steffen J, Mackiewicz A. 31. Analiza mutacji w genie NBS1 u chorych na czerniaka. Rep Pract Oncol Radiother 2003. [DOI: 10.1016/s1507-1367(03)70515-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Jassem E, Ramlau R, Dziadziuszko R, Szymanowska A, Jakóbkiewicz J, Lamperska K, Kobierska G, Skokowski J, Dyszkiewicz W, Mackiewicz A, Zylicz M, Jassem J. [P53 and P16 gene mutations in non-small cell lung cancer]. Pneumonol Alergol Pol 2002; 70:64-70. [PMID: 12148179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
The aim of this study was to assess prospectively the occurrence of p53 and p16 mutations (considered separately and together) in NSCLC in terms of their clinical and prognostic relevance. Study group included 87 patients who underwent pulmonary resection for cure. p53 and p16 mutations were found in 22 (25%) and 14 (16%) cases, respectively. In eight patients (9%) both mutations were present, and the tendency for their common occurrence was significant (p = 0.02). There was no relation between mutation and clinical characteristics. Median survival in the entire group was 17 months and the 3-year survival probability--41%. There was no correlation between the occurrence of any mutation (considered separately or together) and survival. These results indicate that p53 and p16 gene mutations tend to occur together in NSCLC, however these alterations seem not to have noteworthy clinical and prognostic significance.
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Affiliation(s)
- Ewa Jassem
- Klinika Chorób Płuc i Gruźlicy, AM w Gdańsku
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Lamperska K, Mackiewicz K, Kaczmarek A, Kwiatkowska E, Starzycka M, Romanowska B, Heizman J, Stachura J, Mackiewicz A. Expression of p16 in sporadic primary uveal melanoma. Acta Biochim Pol 2002. [DOI: 10.18388/abp.2002_3796] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Expression of p16 protein, intragenic mutations of CDKN2A and hypermethylation of CDKN2A promoter region in 41 sporadic primary uveal melanomas were studied. There were 2 cases of spindle cell B histological type, 11 of A + B and 28 of mixed type. All melanomas infiltrated sclera but in 28 cases infiltration was superficial while in 13 profound. In 7 cases the tumor infiltrated the optic nerve. Expression of p16 was studied by immunohistochemistry and recorded by assessment of the proportion of positive tumor cells and staining intensity. Results were expressed as staining index (IRS). Intragenic mutations were studied by PCR-SSCP followed by sequencing, while hypermethylation of the promoter region by CpG methylation assay. In 15% of cases less than 10% of melanoma cells were p16 positive, in 70% of cases less than 50% of cells, while in 7% more than 80% of cells stained for p16 (mean IRS for all cases was 4.87 +/- 2.43). In B type the IRS was 8.5 +/- 0.7, in A + B type 6.0 +/- 2.1 and in the mixed type 4.17 +/- 2.43 (differences statistically significant). In melanomas profoundly infiltrating sclera mean IRS was 4.16, while in those infiltrating optic nerve 3.71 (statistically not significant). Analysis of the intragenic mutations revealed in two patients a GAC/GAT substitution in codon 84--a silent mutation. No hypermethylation of the CpG island of the p16 promoter region was found. In conclusion, we found that the degree of p16 expression is related to the histological type of tumor but not to the histological indicators of tumor invasiveness and that intragenic mutations and promoter hypermethylation are not major mechanisms of p16 inactivation in sporadic uveal melanoma.
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Lamperska K, Karezewska A, Kwiatkowska E, Mackiewicz A. Analysis of mutations in the p16/CDKN2A gene in sporadic and familial melanoma in the Polish population. Acta Biochim Pol 2002. [DOI: 10.18388/abp.2002_3795] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mutations in CDKN2A have been found in sporadic cutaneous malignant (CMM), in familial CMM and in other syndromes associated with melanoma. In this study DNA was obtained from 207 individuals and five cell lines. There were 157 CMM patients and 50 healthy members of melanoma patients families. The CMM group included patients with one or two melanoma cases in the family, families with dysplastic nevus syndrom (DNS) and patients with a spectrum of other types of cancers in the family. PCR-SSCP analysis and sequencing identified: six substitutions in codon 58 CGA/TGA (Arg/Stop), 16 substitutions GAC/GAT in codon 84 (Asp/Asp), six substitutions CGA/TGA in codon 148 (Arg/Thr), 14 substitutions G/C in 3'UTR and 4 double changes (two in codon 84 and 3'UTR; two in codon 148 and 3'UTR). The mutation identified in codon 58 was found in tissue only. Other substitutions were polymorphisms found in DNA from tissue and blood samples. Most of them were identified in sporadic CMM (six in codon 148 Ala/Thr, 12 in codon 84 Asp/Asp and six in 3'UTR). The frequency of the polymorphisms was also high in DNS and CMM/DNS families (four in codon 84 Asp/Asp and six in 3'UTR). No mutations or polymorphisms were found in CMM patients with one or two melanoma cases and CMM patients, with other cancers in family history. The analysis of the CDKN2A gene mutations in the Polish population demonstrated: (i) no germline mutations; (ii) a relatively high number of genetic changes in sporadic melanoma; (iii) a high number of polymorphisms in DNS and CMM/DNS families.
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Lamperska K, Murawa P, Teresiak M, Wasiewicz J, Mackiewicz A. 31 Mutacje genu p16 u chorych na czerniaka złośliwego. Rep Pract Oncol Radiother 1998. [DOI: 10.1016/s1507-1367(98)70205-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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