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Kumari P, Tarighi S, Fuchshuber E, Li L, Fernández-Duran I, Wang M, Ayoson J, Castelló-García JM, Gámez-García A, Espinosa-Alcantud M, Sreenivasan K, Guenther S, Olivella M, Savai R, Yue S, Vaquero A, Braun T, Ianni A. SIRT7 promotes lung cancer progression by destabilizing the tumor suppressor ARF. Proc Natl Acad Sci U S A 2024; 121:e2409269121. [PMID: 38870055 DOI: 10.1073/pnas.2409269121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024] Open
Abstract
Sirtuin 7 (SIRT7) is a member of the mammalian family of nicotinamide adenine dinucleotide (NAD+)-dependent histone/protein deacetylases, known as sirtuins. It acts as a potent oncogene in numerous malignancies, but the molecular mechanisms employed by SIRT7 to sustain lung cancer progression remain largely uncharacterized. We demonstrate that SIRT7 exerts oncogenic functions in lung cancer cells by destabilizing the tumor suppressor alternative reading frame (ARF). SIRT7 directly interacts with ARF and prevents binding of ARF to nucleophosmin, thereby promoting proteasomal-dependent degradation of ARF. We show that SIRT7-mediated degradation of ARF increases expression of protumorigenic genes and stimulates proliferation of non-small-cell lung cancer (NSCLC) cells both in vitro and in vivo in a mouse xenograft model. Bioinformatics analysis of transcriptome data from human lung adenocarcinomas revealed a correlation between SIRT7 expression and increased activity of genes normally repressed by ARF. We propose that disruption of SIRT7-ARF signaling stabilizes ARF and thus attenuates cancer cell proliferation, offering a strategy to mitigate NSCLC progression.
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Affiliation(s)
- Poonam Kumari
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Shahriar Tarighi
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Eva Fuchshuber
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Luhan Li
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Irene Fernández-Duran
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia 08916, Spain
| | - Meilin Wang
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Joshua Ayoson
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Jose Manuel Castelló-García
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia 08916, Spain
| | - Andrés Gámez-García
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia 08916, Spain
| | - Maria Espinosa-Alcantud
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia 08916, Spain
| | - Krishnamoorthy Sreenivasan
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Stefan Guenther
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Mireia Olivella
- Facultat de Ciències, Tecnologia I Enginyeries, Universitat de Vic-Universitat Central de Catalunya, Vic, Barcelona 08500, Spain
- Institut de Recerca i Innovació en Ciències de la Vida i de la Salut a la Catalunya Central, Vic, Barcelona 08500, Spain
| | - Rajkumar Savai
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
- Lung Microenvironmental Niche in Cancerogenesis, Institute for Lung Health, Justus Liebig University, Giessen D-35392, Germany
| | - Shijing Yue
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Alejandro Vaquero
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Alessandro Ianni
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
- Chromatin Biology Laboratory, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia 08916, Spain
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Bader JM, Deigendesch N, Misch M, Mann M, Koch A, Meissner F. Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status. Cell Rep Med 2022; 4:100877. [PMID: 36584682 PMCID: PMC9873829 DOI: 10.1016/j.xcrm.2022.100877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 07/15/2022] [Accepted: 12/07/2022] [Indexed: 12/30/2022]
Abstract
High-grade adult-type diffuse gliomas are malignant neuroepithelial tumors with poor survival rates in combined chemoradiotherapy. The current WHO classification is based on IDH1/2 mutational and 1p/19q codeletion status. Glioma proteome alterations remain undercharacterized despite their promise for a better molecular patient stratification and therapeutic target identification. Here, we use mass spectrometry to characterize 42 formalin-fixed, paraffin-embedded (FFPE) samples from IDH-wild-type (IDHwt) gliomas, IDH-mutant (IDHmut) gliomas with and without 1p/19q codeletion, and non-neoplastic controls. Based on more than 5,500 quantified proteins and 5,000 phosphosites, gliomas separate by IDH1/2 mutational status but not by 1p/19q status. Instead, IDHmut gliomas split into two proteomic subtypes with widespread perturbations, including aerobic/anaerobic energy metabolism. Validations with three independent glioma proteome datasets confirm these subgroups and link the IDHmut subtypes to the established proneural and classic/mesenchymal subtypes in IDHwt glioma. This demonstrates common phenotypic subtypes across the IDH status with potential therapeutic implications for patients with IDHmut gliomas.
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Affiliation(s)
- Jakob Maximilian Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nikolaus Deigendesch
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Martin Misch
- Department of Neurosurgery, Charité, Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Arend Koch
- Department of Neuropathology, Charité, Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany.
| | - Felix Meissner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Department of Systems Immunology and Proteomics, Institute of Innate Immunity, University Hospital Bonn, 53127 Bonn, Germany.
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3
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Dual Oxidase 2 (DUOX2) as a Proteomic Biomarker for Predicting Treatment Response to Chemoradiation Therapy for Locally Advanced Rectal Cancer: Using High-Throughput Proteomic Analysis and Machine Learning Algorithm. Int J Mol Sci 2022; 23:ijms232112923. [DOI: 10.3390/ijms232112923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
High-throughput mass-spectrometry-based quantitative proteomic analysis was performed using formalin-fixed, paraffin-embedded (FFPE) biopsy samples obtained before treatment from 13 patients with locally advanced rectal cancer (LARC), who were treated with concurrent chemoradiation therapy (CCRT) followed by surgery. Patients were divided into complete responder (CR) and non-complete responder (nCR) groups. Immunohistochemical (IHC) staining of 79 independent FFPE tissue samples was performed to validate the predictive ability of proteomic biomarker candidates. A total of 3637 proteins were identified, and the expression of 498 proteins was confirmed at significantly different levels (differentially expressed proteins—DEPs) between two groups. In Gene Ontology enrichment analyses, DEPs enriched in biological processes in the CR group included proteins linked to cytoskeletal organization, immune response processes, and vesicle-associated protein transport processes, whereas DEPs in the nCR group were associated with biosynthesis, transcription, and translation processes. Dual oxidase 2 (DUOX2) was selected as the most predictive biomarker in machine learning algorithm analysis. Further IHC validation ultimately confirmed DUOX2 as a potential biomarker for predicting the response of nCR to CCRT. In conclusion, this study suggests that the treatment response to RT may be affected by the pre-treatment tumor microenvironment. DUOX2 is a potential biomarker for the early prediction of nCR after CCRT.
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Ji L, Wang Z, Ji Y, Wang H, Guo M, Zhang L, Wang P, Xiao H. Proteomics and phosphoproteomics analysis of tissues for the reoccurrence prediction of colorectal cancer. Expert Rev Proteomics 2022; 19:263-277. [PMID: 36308708 DOI: 10.1080/14789450.2022.2142566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Many stage II/III colorectal cancer (CRC) patients may relapse after routine treatments. Aberrant phosphorylation can regulate pathophysiological processes of tumors, and finding characteristic protein phosphorylation is an efficient approach for the prediction of CRC relapse. RESEARCH DESIGN AND METHODS We compared the tissue proteome and phosphoproteome of stage II/III CRC patients between the relapsed group (n = 5) and the non-relapsed group (n = 5). Phosphopeptides were enriched with Ti4+-IMAC material. We utilized label-free quantification-based proteomics to screen differentially expressed proteins and phosphopeptides between the two groups. Gene Ontology (GO) analysis and Ingenuity Pathway Analysis (IPA) were used for bioinformatics analysis. RESULTS The immune response of the relapsed group (Z-score -2.229) was relatively poorer than that of the non-relapsed group (Z-score 1.982), while viability of tumor was more activated (Z-score 2.895) in the relapsed group, which might cause increased relapse risk. The phosphorylation degrees of three phosphosites (phosphosite 1362 of TP53BP1, phosphosite 809 of VCL and phosphosite 438 of STK10) might be reliable prognostic biomarkers. CONCLUSIONS Some promising proteins and phosphopeptides were discovered to predict the relapse risk in postoperative follow-ups.
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Affiliation(s)
- Liyun Ji
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Yin Ji
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co Ltd 210042, Nanjing, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Miao Guo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
| | - Peng Wang
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Pharmaceutical Co Ltd 210042, Nanjing, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University 200240, Shanghai, China
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5
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Fragkiadaki P, Renieri E, Kalliantasi K, Kouvidi E, Apalaki E, Vakonaki E, Mamoulakis C, Spandidos DA, Tsatsakis A. Τelomerase inhibitors and activators in aging and cancer: A systematic review. Mol Med Rep 2022; 25:158. [PMID: 35266017 PMCID: PMC8941523 DOI: 10.3892/mmr.2022.12674] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/25/2022] [Indexed: 01/09/2023] Open
Abstract
The main aim of the present systematic review was to summarize the most frequently used telomerase regulators with an impact on aging and cancer that are referred to in in vitro and in vivo studies. For this purpose, a systematic review of the available literature on telomerase regulators referred to in articles from PubMed and Scopus libraries published from 2002 to 2021 and in accordance with PRISMA 2020 criteria, was conducted. Articles were included if they met the following criteria: They referred to telomerase modulators in aging and in cancer and were in vitro and/or in vivo studies, while studies that did not provide sufficient data or studies not written in English were excluded. In the present systematic review, 54 publications were included, of which 29 were full-text published studies, 11 were full-text reviews, 10 structure-based design studies and 4 abstracts are reported in this review. Telomerase regulators were then categorized as synthetic direct telomerase inhibitors, synthetic indirect telomerase inhibitors, synthetic telomerase activators, natural direct telomerase activators, natural telomerase inhibitors and natural indirect telomerase activators, according to their origin and their activity. On the whole, as demonstrated herein, telomerase regulators appear to be promising treatment agents in various age-related diseases. However, further in vivo and in vitro studies need to be performed in order to clarify the potentiality of telomerase as a therapeutic target.
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Affiliation(s)
- Persefoni Fragkiadaki
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece.,Spin‑Off Toxplus S.A., Heraklion 71601, Greece
| | - Elisavet Renieri
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Katerina Kalliantasi
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Elisavet Kouvidi
- Genesis Genoma Lab, Genetic Diagnosis, Clinical Genetics and Research, Athens 15232, Greece
| | - Evita Apalaki
- Department of Immunology, Genetics and Pathology (IGP), Uppsala University, 75105 Uppsala, Sweden
| | - Elena Vakonaki
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece.,Spin‑Off Toxplus S.A., Heraklion 71601, Greece
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Aristidis Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece.,Spin‑Off Toxplus S.A., Heraklion 71601, Greece
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Talotta R, Bahrami S, Laska MJ. Sequence complementarity between human noncoding RNAs and SARS-CoV-2 genes: What are the implications for human health? Biochim Biophys Acta Mol Basis Dis 2022; 1868:166291. [PMID: 34662705 PMCID: PMC8518135 DOI: 10.1016/j.bbadis.2021.166291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/17/2021] [Accepted: 10/09/2021] [Indexed: 12/12/2022]
Abstract
Objectives To investigate in silico the presence of nucleotide sequence complementarity between the RNA genome of Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) and human non-coding (nc)RNA genes. Methods The FASTA sequence (NC_045512.2) of each of the 11 SARS-CoV-2 isolate Wuhan-Hu-1 genes was retrieved from NCBI.nlm.nih.gov/gene and the Ensembl.org library interrogated for any base-pair match with human ncRNA genes. SARS-CoV-2 gene-matched human ncRNAs were screened for functional activity using bioinformatic analysis. Finally, associations between identified ncRNAs and human diseases were searched in GWAS databases. Results A total of 252 matches were found between the nucleotide sequence of SARS-CoV-2 genes and human ncRNAs. With the exception of two small nuclear RNAs, all of them were long non-coding (lnc)RNAs expressed mainly in testis and central nervous system under physiological conditions. The percentage of alignment ranged from 91.30% to 100% with a mean nucleotide alignment length of 17.5 ± 2.4. Thirty-three (13.09%) of them contained predicted R-loop forming sequences, but none of these intersected the complementary sequences of SARS-CoV-2. However, in 31 cases matches fell on ncRNA regulatory sites, whose adjacent coding genes are mostly involved in cancer, immunological and neurological pathways. Similarly, several polymorphic variants of detected non-coding genes have been associated with neuropsychiatric and proliferative disorders. Conclusion This pivotal in silico study shows that SARS-CoV-2 genes have Watson-Crick nucleotide complementarity to human ncRNA sequences, potentially disrupting ncRNA epigenetic control of target genes. It remains to be elucidated whether this could result in the development of human disease in the long term.
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Affiliation(s)
- Rossella Talotta
- Department of Clinical and Experimental Medicine, Rheumatology Unit, AOU "Gaetano Martino", University of Messina, Messina, Italy.
| | - Shervin Bahrami
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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Zou W, Wang Z, Zhang X, Xu S, Wang F, Li L, Deng Z, Wang J, Pan K, Ge X, Li C, Liu R, Hu M. PIWIL4 and SUPT5H combine to predict prognosis and immune landscape in intrahepatic cholangiocarcinoma. Cancer Cell Int 2021; 21:657. [PMID: 34876138 PMCID: PMC8649993 DOI: 10.1186/s12935-021-02310-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/01/2021] [Indexed: 01/03/2023] Open
Abstract
Background Intrahepatic cholangiocarcinoma (ICC) is a fatal primary liver cancer, and its long-term survival rate remains poor. RNA-binding proteins (RBPs) play an important role in critical cellular processes, failure of any one or more processes can lead to the development of multiple cancers. This study aimed to explore pivotal biomarkers and corresponding mechanisms to predict the prognosis of patients with ICC. Methods The transcriptomic and clinical information of patients were collected from The Cancer Genome Atlas and Gene Expression Omnibus databases. Bioinformatic methods were used to identify survival-related and differentially-expressed biomarkers. Quantitative real-time PCR (qRT-PCR) and immunohistochemistry were used to detect the expression levels of key biomarkers in independent real-world cohorts. Subsequently, a prognostic signature was constructed that effectively distinguished patients in the high- and low-risk groups. Independent prognosis analysis was used to verify the signature’s independent predictive capabilities, and two nomograms were developed to predict survival. Results PIWIL4 and SUPT5H were identified and considered as pivotal biomarkers, and the same expression trends of upregulation in ICC were also validated via qRT-PCR and immunohistochemistry in the separate real-world sample cohorts. The prognostic signature showed good predictive capabilities according to the area under the curve. The correlation of the biomarkers with the tumour microenvironment suggested that the high riskScore was positively related to the enrichment of resting natural killer cells and activated memory CD4 + T cells. Conclusion In the present study, we demonstrated that PIWIL4 and SUPT5H could be used as novel prognostic biomarkers to develop a prognostic signature. This study provides potential biomarkers of prognostic value for patients with intrahepatic cholangiocarcinoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02310-2.
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Affiliation(s)
- Wenbo Zou
- Medical School of Chinese PLA, Beijing, China.,Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zizheng Wang
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Xiuping Zhang
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Shuai Xu
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China.,School of Medicine, Nankai University, Tianjin, China
| | - Fei Wang
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Lincheng Li
- Medical School of Chinese PLA, Beijing, China.,Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zhaoda Deng
- Medical School of Chinese PLA, Beijing, China.,Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Jing Wang
- Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Ke Pan
- Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Xinlan Ge
- Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Chonghui Li
- Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepetobiliary Surgery, PLA, Beijing, China
| | - Rong Liu
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China.
| | - Minggen Hu
- Faculty of Hepato-Pancreato-Biliary Surgery, The First Medical Center of Chinese People's Liberation Army (PLA) General Hospital, No.28 Fuxing Road, Haidian District, Beijing, 100853, China.
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Nikolouzakis TK, Vakonaki E, Stivaktakis PD, Alegakis A, Berdiaki A, Razos N, Souglakos J, Tsatsakis A, Tsiaoussis J. Novel Prognostic Biomarkers in Metastatic and Locally Advanced Colorectal Cancer: Micronuclei Frequency and Telomerase Activity in Peripheral Blood Lymphocytes. Front Oncol 2021; 11:683605. [PMID: 34262868 PMCID: PMC8274420 DOI: 10.3389/fonc.2021.683605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023] Open
Abstract
PURPOSE Due to the current practice on colorectal cancer (CRC) management, chemoresistance is most often recognized at the end of the treatment. Therefore, effective and easy-to-use prognostic biomarkers are needed. EXPERIMENTAL DESIGN We evaluated the prognostic significance of two novel CRC biomarkers: a) micronuclei frequency (MNf) in 55 metastatic CRC (mCRC) and 21 locally advanced rectal cancer (laRC) patients using cytokinesis block micronucleus assay (CBMN assay) and b) telomerase activity (TA) in 23 mCRC and five laRC patients using TRAP-ELISA. Both biomarkers were evaluated in peripheral blood lymphocytes (PBLs) before, at the middle, and at the end of the therapy (approximately 0, 3, and 6 months) for mCRC patients before, at the end of the therapy, and after surgery for laRC patients. RESULTS Overall, MNf demonstrated significant prognostic value since a decrease of MNf less than 29% between middle and initial MNf measurements can discriminate between progressive and stable/responsive disease with sensitivity of 36% and specificity of 87.0% while being able to identify responsive disease with sensitivity of 72.7% and specificity of 59.3%. On the other hand, TA presented a significant trend of increase (p = 0.07) in patients with progressive disease at the middle measurement. CONCLUSIONS The findings of this study suggest that the MN frequency may serve as a promising prognostic biomarker for the monitoring of the treatment response of patients with CRC, while TA should be evaluated in a larger group of patients to further validate its significance.
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Affiliation(s)
| | - Elena Vakonaki
- Laboratory of Toxicology, Medical School, University of Crete, Heraklion, Greece
| | | | - Athanasios Alegakis
- Laboratory of Toxicology, Medical School, University of Crete, Heraklion, Greece
| | - Aikaterini Berdiaki
- Laboratory of Histology-Embryology, Medical School, The University of Crete, Heraklion, Greece
| | - Nikolaos Razos
- Department of Anatomy, Medical School, University of Crete, Heraklion, Greece
| | - John Souglakos
- Department of Medical Oncology, University General Hospital of Heraklion, and Laboratory of Translational Oncology, Medical School, University of Crete, Heraklion, Greece
| | - Aristidis Tsatsakis
- Department of Forensic Sciences and Toxicology, Medical School, University of Crete, Heraklion, Greece
| | - John Tsiaoussis
- Department of Anatomy, Medical School, University of Crete, Heraklion, Greece
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9
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Jiang Q, Xue D, Shi F, Qiu J. Prognostic significance of an autophagy-related long non-coding RNA signature in patients with oral and oropharyngeal squamous cell carcinoma. Oncol Lett 2020; 21:29. [PMID: 33240435 PMCID: PMC7681235 DOI: 10.3892/ol.2020.12290] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Traditional clinicopathological indices are insufficient in predicting the prognosis of patients diagnosed with oral and oropharyngeal squamous cell carcinoma (OSCC/OPSCC). Notably, autophagy and long non-coding RNAs (lncRNAs) regulate the development and progression of various types of cancer. The present study aimed to assess the association between autophagy-related lncRNAs and the prognosis of patients diagnosed with OSCC/OPSCC. Gene sequencing and clinicopathological data of patients with OSCC/OPSCC were downloaded from The Cancer Genome Atlas database, while gene set functional classification was downloaded from the Gene Set Enrichment Analysis database. Out of the 413 transcriptome data samples and 402 clinicopathological data samples retrieved, a total of nine autophagy-related lncRNAs, including PTCSC2, AC099850.3, LINC01963, RTCA-AS1, AP002884.1, UBAC2-AS1, AL512274.1, MIR600HG and AL354733.3, were screened. This was geared towards establishing a signature through gene co-expression network, univariate and Least Absolute Shrinkage and Selection Operator Cox regression analyses. Based on this signature, the patients were subdivided into a high-risk group and a low-risk group. Kaplan-Meier survival analysis revealed that the overall survival of the high-risk group was significantly lower than that of the low-risk group. Furthermore, principal components analysis demonstrated that the patients diagnosed with OSCC/OPSCC could be distinguished into low-survival and high-survival groups according to the signature. Univariate and multivariate Cox regression analyses of clinicopathological data and the signature revealed that the signature could potentially be used as an independent prognostic factor for OSCC/OPSCC. In addition, reverse transcription-quantitative PCR analysis of clinical samples demonstrated the validity of the signature. In summary, the present study revealed that the signature based on autophagy-related lncRNAs potentially acts as an independent prognostic indicator for patients with OSCC/OPSCC. Furthermore, it promotes research on targeted diagnosis and treatment of patients diagnosed with OSCC/OPSCC.
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Affiliation(s)
- Qingkun Jiang
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Danfeng Xue
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Fanzhe Shi
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jiaxuan Qiu
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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Chow EYC, Zhang J, Qin H, Chan TF. Characterization of Hepatocellular Carcinoma Cell Lines Using a Fractionation-Then-Sequencing Approach Reveals Nuclear-Enriched HCC-Associated lncRNAs. Front Genet 2019; 10:1081. [PMID: 31781161 PMCID: PMC6857473 DOI: 10.3389/fgene.2019.01081] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Advances in sequencing technologies have greatly improved our understanding of long noncoding RNA (lncRNA). These transcripts with lengths of >200 nucleotides may play significant regulatory roles in various biological processes. Importantly, the dysregulation of better characterized lncRNAs has been associated with multiple types of cancers, including hepatocellular carcinoma (HCC). There are many studies on altered lncRNA expression levels, very few, however, have focused on their subcellular localizations, from which accumulating evidences have indicated their close relationships to lncRNA functions. A transcriptome-wide investigation of the subcellular distributions of lncRNAs might thus provide new insights into their roles and functions in cancers. Results: In this study, we subjected eight patient-derived HCC cell lines to subcellular fractionation and independently sequenced RNAs from the nuclear and cytoplasmic compartments. With the integration of tumor and tumor-adjacent RNA-seq datasets of liver hepatocellular carcinoma (LIHC) from The Cancer Genome Atlas (TCGA), de novo transcriptome assembly and differential expression analysis were conducted successively and identified 26 nuclear-enriched HCC-associated lncRNAs shared between the HCC samples and the TCGA datasets, including the reported cancer driver PXN-AS1. The majority of nuclear-enriched HCC-associated lncRNAs were associated with the survival outcomes of HCC patients, exhibited characteristics similar to those of many experimentally supported HCC prognostic lncRNAs, and were co-expressed with protein-coding genes that have been linked to disease progression in various cancer types. Conclusion: We adopted a fractionation-then-sequencing approach on multiple patient-derived HCC samples and identified nuclear-enriched, HCC-associated lncRNAs that could serve as important targets for HCC diagnosis and therapeutic development. This approach could be widely applicable to other studies into the disease etiologies of lncRNA.
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Affiliation(s)
| | - Jizhou Zhang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hao Qin
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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11
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Martin G, Selcuklu SD, Schouest K, Nembaware V, McKeown PC, Seoighe C, Spillane C. Allele-specific splicing effects on DKKL1 and ZNF419 transcripts in HeLa cells. Gene 2017; 598:107-112. [PMID: 27826023 DOI: 10.1016/j.gene.2016.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/16/2016] [Accepted: 11/03/2016] [Indexed: 10/20/2022]
Abstract
Allele-specific splicing is the production of different RNA isoforms from different alleles of a gene. Altered splicing patterns such as exon skipping can have a dramatic effect on the final protein product yet have traditionally proven difficult to predict. We investigated the splicing effects of a set of nine single nucleotide polymorphisms (SNPs) which are predicted to have a direct impact on mRNA splicing, each in a different gene. Predictions were based on SNP location relative to splice junctions and intronic/exonic splicing elements, combined with an analysis of splice isoform expression data from public sources. Of the nine genes tested, six SNPs led to direct impacts on mRNA splicing as determined by the splicing reporter minigene assay and RT-PCR in human HeLa cells, of which four were allele-specific effects. These included previously unreported alternative splicing patterns in the genes ZNF419 and DKKL1. Notably, the SNP in ZNF419, a transcription factor, leads to the deletion of a DNA-binding domain from the protein and is associated with an expression QTL, while the SNP in DKKL1 leads to shortened transcripts predicted to produce a truncated protein. We conclude that the impact of SNP mutations on mRNA splicing, and its biological relevance, can be predicted by integrating SNP position with available data on relative isoform abundance in human cell lines.
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Affiliation(s)
- Grace Martin
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - S Duygu Selcuklu
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Katherine Schouest
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Victoria Nembaware
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Private Bag, Rondebosch, 7700 Cape Town, South Africa
| | - Peter C McKeown
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - Charles Spillane
- Genetics & Biotechnology Lab, School of Natural Sciences, College of Science, National University of Ireland, Galway, Ireland.
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12
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Transcription Regulation of the Human Telomerase Reverse Transcriptase (hTERT) Gene. Genes (Basel) 2016; 7:genes7080050. [PMID: 27548225 PMCID: PMC4999838 DOI: 10.3390/genes7080050] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/23/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022] Open
Abstract
Embryonic stem cells and induced pluripotent stem cells have the ability to maintain their telomere length via expression of an enzymatic complex called telomerase. Similarly, more than 85%–90% of cancer cells are found to upregulate the expression of telomerase, conferring them with the potential to proliferate indefinitely. Telomerase Reverse Transcriptase (TERT), the catalytic subunit of telomerase holoenzyme, is the rate-limiting factor in reconstituting telomerase activity in vivo. To date, the expression and function of the human Telomerase Reverse Transcriptase (hTERT) gene are known to be regulated at various molecular levels (including genetic, mRNA, protein and subcellular localization) by a number of diverse factors. Among these means of regulation, transcription modulation is the most important, as evident in its tight regulation in cancer cell survival as well as pluripotent stem cell maintenance and differentiation. Here, we discuss how hTERT gene transcription is regulated, mainly focusing on the contribution of trans-acting factors such as transcription factors and epigenetic modifiers, as well as genetic alterations in hTERT proximal promoter.
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