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Karabulut B, Yukruk FA, Yenidunya S, Kandemir O, Kosemehmetoglu K. Differential cyclin-E1 expression in CIC-rearranged sarcoma. Ann Diagn Pathol 2024; 72:152320. [PMID: 38703529 DOI: 10.1016/j.anndiagpath.2024.152320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024]
Abstract
CIC-rearranged sarcoma (CRS) is a group of high-grade undifferentiated small round cell sarcomas examined as a separate entity in the current WHO classification; since it shows more aggressive clinical behavior and distinct morphological and molecular features compared to Ewing sarcoma (ES). As CCNE1 expression is associated with tumor growth in CIC::DUX4 sarcomas, we aimed to demonstrate the value of cyclin E1 expression in CRS. Cyclin E1 immunohistochemistry and break-apart FISH for EWSR1 and CIC gene rearrangements were performed on 3-mm tissue microarrays composed of 40 small round cell tumors. Five cases were classified as CRS, whereas 22 were ES and 13 were unclassified (EWSR1-/CIC-). Among all three diagnostic groups, we found cyclin E1 expression level to be higher in CRS (80 %) and unclassified groups (61.5 %) compared to ES (4.5 %, p < 0.001). In addition, high cyclin E1 expression levels were associated with higher mean age at diagnosis, presence of atypical histology and myxoid stroma, low CD99 expression, and presence of metastasis at diagnosis. The sensitivity and specificity of high cyclin E1 expression in detecting non-ES cases were 95.5 % and 66.7 %, respectively. However, the correlation between cyclin E1 expression level and survival was not statistically significant. This is the first study that shows cyclin E1 immunohistochemical expression in EWSR1-negative undifferentiated small cell sarcomas, particularly CRS.
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MESH Headings
- Humans
- Male
- Oncogene Proteins/metabolism
- Oncogene Proteins/genetics
- Female
- Adult
- Cyclin E/metabolism
- Cyclin E/genetics
- Middle Aged
- Gene Rearrangement
- Adolescent
- Biomarkers, Tumor/metabolism
- Biomarkers, Tumor/genetics
- Young Adult
- Child
- Repressor Proteins/metabolism
- Repressor Proteins/genetics
- Immunohistochemistry/methods
- Sarcoma, Ewing/metabolism
- Sarcoma, Ewing/pathology
- Sarcoma, Ewing/genetics
- Sarcoma/pathology
- Sarcoma/metabolism
- Sarcoma/genetics
- Sarcoma/diagnosis
- In Situ Hybridization, Fluorescence/methods
- Aged
- Child, Preschool
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- Sarcoma, Small Cell/metabolism
- Sarcoma, Small Cell/genetics
- Sarcoma, Small Cell/pathology
- Sarcoma, Small Cell/diagnosis
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Affiliation(s)
- Berna Karabulut
- Department of Pathology, Dr. Abdurrahman Yurtaslan Ankara Oncology Training and Research Hospital, Ankara 06200, Turkey.
| | - Fisun Ardic Yukruk
- Department of Pathology, Dr. Abdurrahman Yurtaslan Ankara Oncology Training and Research Hospital, Ankara 06200, Turkey
| | - Sibel Yenidunya
- Department of Pathology, Dr. Abdurrahman Yurtaslan Ankara Oncology Training and Research Hospital, Ankara 06200, Turkey
| | | | - Kemal Kosemehmetoglu
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara 06230, Turkey.
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Otto J, Verwaayen A, Penners C, Hundertmark J, Lin C, Kallen C, Paffen D, Otto T, Berger H, Tacke F, Weiskirchen R, Nevzorova YA, Bartneck M, Trautwein C, Sonntag R, Liedtke C. Expression of Cyclin E1 in hepatic stellate cells is critical for the induction and progression of liver fibrosis and hepatocellular carcinoma in mice. Cell Death Dis 2023; 14:549. [PMID: 37620309 PMCID: PMC10449804 DOI: 10.1038/s41419-023-06077-4] [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: 01/18/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most severe malignancies with increasing incidence and limited treatment options. Typically, HCC develops during a multistep process involving chronic liver inflammation and liver fibrosis. The latter is characterized by the accumulation of extracellular matrix produced by Hepatic Stellate Cells (HSCs). This process involves cell cycle re-entry and proliferation of normally quiescent HSCs in an ordered sequence that is highly regulated by cyclins and associated cyclin-dependent kinases (CDKs) such as the Cyclin E1 (CCNE1)/CDK2 kinase complex. In the present study, we examined the role of Cyclin E1 (Ccne1) and Cdk2 genes in HSCs for liver fibrogenesis and hepatocarcinogenesis. To this end, we generated conditional knockout mice lacking Ccne1 or Cdk2 specifically in HSCs (Ccne1∆HSC or Cdk2∆HSC). Ccne1∆HSC mice showed significantly reduced liver fibrosis formation and attenuated HSC activation in the carbon tetrachloride (CCl4) model. In a combined model of fibrosis-driven hepatocarcinogenesis, Ccne1∆HSC mice revealed decreased HSC activation even after long-term observation and substantially reduced tumor load in the liver when compared to wild-type controls. Importantly, the deletion of Cdk2 in HSCs also resulted in attenuated liver fibrosis after chronic CCl4 treatment. Single-cell RNA sequencing revealed that only a small fraction of HSCs expressed Ccne1/Cdk2 at a distinct time point after CCl4 treatment. In summary, we provide evidence that Ccne1 expression in a small population of HSCs is sufficient to trigger extensive liver fibrosis and hepatocarcinogenesis in a Cdk2-dependent manner. Thus, HSC-specific targeting of Ccne1 or Cdk2 in patients with liver fibrosis and high risk for HCC development could be therapeutically beneficial.
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Affiliation(s)
- Julia Otto
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Anna Verwaayen
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Christian Penners
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Jana Hundertmark
- Charité - Universitätsmedizin Berlin, Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Cheng Lin
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Carina Kallen
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Daniela Paffen
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Tobias Otto
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Hilmar Berger
- Charité - Universitätsmedizin Berlin, Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Frank Tacke
- Charité - Universitätsmedizin Berlin, Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), University Hospital RWTH Aachen, Aachen, Germany
| | - Yulia A Nevzorova
- Department of Immunology, Ophthalmology and ENT, Complutense University School of Medicine, Madrid, Spain
| | - Matthias Bartneck
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
- DWI - Leibniz Institute for Interactive Materials, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Aachen, Germany
| | - Christian Trautwein
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Roland Sonntag
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Christian Liedtke
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.
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Khandia R, Pandey MK, Zaki MEA, Al-Hussain SA, Baklanov I, Gurjar P. Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities. Front Mol Neurosci 2023; 16:1200523. [PMID: 37383425 PMCID: PMC10293642 DOI: 10.3389/fnmol.2023.1200523] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Neurodegeneration and cancer present in comorbidities with inverse effects due to the expression of genes and pathways acting in opposition. Identifying and studying the genes simultaneously up or downregulated during morbidities helps curb both ailments together. Methods This study examines four genes. Three of these (Amyloid Beta Precursor Protein (APP), Cyclin D1 (CCND1), and Cyclin E2 (CCNE2) are upregulated, and one protein phosphatase 2 phosphatase activator (PTPA) is simultaneously downregulated in both disorders. We investigated molecular patterns, codon usage, codon usage bias, nucleotide bias in the third codon position, preferred codons, preferred codon pairs, rare codons, and codon context. Results Parity analysis revealed that T is preferred over A, and G is preferred over C in the third codon position, suggesting composition plays no role in nucleotide bias in both the upregulated and downregulated gene sets and that mutational forces are stronger in upregulated gene sets than in downregulated ones. Transcript length influenced the overall %A composition and codon bias, and the codon AGG exerted the strongest influence on codon usage in both the upregulated and downregulated gene sets. Codons ending in G/C were preferred for 16 amino acids, and glutamic acid-, aspartic acid-, leucine-, valine-, and phenylalanine-initiated codon pairs were preferred in all genes. Codons CTA (Leu), GTA (Val), CAA (Gln), and CGT (Arg) were underrepresented in all examined genes. Discussion Using advanced gene editing tools such as CRISPR/Cas or any other gene augmentation technique, these recoded genes may be introduced into the human body to optimize gene expression levels to augment neurodegeneration and cancer therapeutic regimens simultaneously.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal, Madhya Pradesh, India
| | - Megha Katare Pandey
- Translational Medicine Center, All India Institute of Medical Sciences, Bhopal, India
| | - Magdi E. A. Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Sami A. Al-Hussain
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Igor Baklanov
- Department of Philosophy, North Caucasus Federal University, Stavropol, Russia
| | - Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
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Abdelrazek AS, Ghoniem K, Ahmed ME, Joshi V, Mahmoud AM, Saeed N, Khater N, Elsharkawy MS, Gamal A, Kwon E, Kendi AT. Prostate Cancer: Advances in Genetic Testing and Clinical Implications. URO 2023. [DOI: 10.3390/uro3020012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The demand for genetic testing (GT) for prostate cancer (PCa) is expanding, but there is limited knowledge about the genetic counseling (GC) needs of men. A strong-to-moderate inherited genetic predisposition causes approximately 5–20% of prostate cancer (PCa). In men with prostate cancer, germline testing may benefit the patient by informing treatment options, and if a mutation is noticed, it may also guide screening for other cancers and have family implications for cascade genetic testing (testing of close relatives for the same germline mutation). Relatives with the same germline mutations may be eligible for early cancer detection strategies and preventive measures. Cascade family testing can be favorable for family members, but it is currently unutilized, and strategies to overcome obstacles like knowledge deficiency, family communication, lack of access to genetic services, and testing expenses are needed. In this review, we will look at the genetic factors that have been linked to prostate cancer, as well as the role of genetic counseling and testing in the early detection of advanced prostate cancer.
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Ullah MA, Farzana M, Islam MS, Moni R, Zohora US, Rahman MS. Identification of the prognostic and therapeutic values of cyclin E1 (CCNE1) gene expression in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma: A database mining approach. Heliyon 2022; 8:e10367. [PMID: 36091953 PMCID: PMC9459432 DOI: 10.1016/j.heliyon.2022.e10367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/18/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
Cyclin E1 (CCNE1) is a protein-coding gene that belongs to the Cyclin family of genes which controls the G1/S phase transition of the cell cycle. Previously, its abnormal expression pattern has been examined and found to be correlated with ovarian and breast cancer progression. Herein, we exploited a bioinformatics and database mining strategy to unveil the therapeutic and prognostic significance of CCNE1 gene expression in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC). CCNE1 gene was reported to be highly expressed in LUAD and LUSC tissues. Its promoter and coding sequences were reported to be aberrantly methylated in LUAD and LUSC tissues than in normal tissues. Moreover, around 12 somatic mutations (frequency: 0.7%) were recorded in the CCNE1 coding region from different studies involving LUAD and LUSC patients' whole genome sequences. The CCNE1 gene expression was also correlated with LUAD and LUSC patients’ overall and disease-specific survival. Immune infiltration analysis revealed the association between CCNE1 gene expression and the abundance of numerous immune cells (i.e., T cells and B Cells) infiltration in LUAD and LUSC patients. Two previously known genes involved in oncogenic processes i.e., CDC45 and PDCD5 were identified as the most highly co-expressed genes of CCNE1 in LUAD and LUSC tissues. Altogether, the CCNE1 gene and its transcriptional and translational products may serve as a prognostic or therapeutic target in the diagnosis and treatment of LUAD and LUSC patients. The scientific findings of this study should assist in translating CCNE1 into clinical practice for lung cancer diagnosis and treatment. CCNE1 gene is highly expressed in LUAD and LUSC tissues CCNE1 gene is differentially methylated in LUAD and LUSC tissues CCNE1 overexpression is associated with the poor overall survival of LUAD and LUSC patients
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Affiliation(s)
- Md. Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Maisha Farzana
- Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Md. Shariful Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Ripa Moni
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Umme Salma Zohora
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Mohammad Shahedur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
- Wazed Miah Science Research Center, Jahangirnagar University, Dhaka, Bangladesh
- Corresponding author.
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Yang J, Chen Z, Gong Z, Li Q, Ding H, Cui Y, Tang L, Li S, Wan L, Li Y, Ju S, Ding C, Zhao J. Immune Landscape and Classification in Lung Adenocarcinoma Based on a Novel Cell Cycle Checkpoints Related Signature for Predicting Prognosis and Therapeutic Response. Front Genet 2022; 13:908104. [PMID: 35646074 PMCID: PMC9130860 DOI: 10.3389/fgene.2022.908104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/26/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is one of the most common malignancies with the highest mortality globally, and it has a poor prognosis. Cell cycle checkpoints play a central role in the entire system of monitoring cell cycle processes, by regulating the signalling pathway of the cell cycle. Cell cycle checkpoints related genes (CCCRGs) have potential utility in predicting survival, and response to immunotherapies and chemotherapies. To examine this, based on CCCRGs, we identified two lung adenocarcinoma subtypes, called cluster1 and cluster2, by consensus clustering. Enrichment analysis revealed significant discrepancies between the two subtypes in gene sets associated with cell cycle activation and tumor progression. In addition, based on Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression, we have developed and validated a cell cycle checkpoints-related risk signature to predict prognosis, tumour immune microenvironment: (TIME), immunotherapy and chemotherapy responses for lung adenocarcinoma patients. Results from calibration plot, decision curve analysis (DCA), and time-dependent receiver operating characteristic curve (ROC) revealed that combining age, gender, pathological stages, and risk score in lung adenocarcinoma patients allowed for a more accurate and predictive nomogram. The area under curve for lung adenocarcinoma patients with 1-, 3-, 5-, and 10-year overall survival was: 0.74, 0.73, 0.75, and 0.81, respectively. Taken together, our proposed 4-CCCRG signature can serve as a clinically useful indicator to help predict patients outcomes, and could provide important guidance for immunotherapies and chemotherapies decision for lung adenocarcinoma patients.
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Affiliation(s)
- Jian Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhike Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zetian Gong
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qifan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hao Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lijuan Tang
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, China
| | - Shiqin Li
- Department of Urinary Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Li Wan
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou, China
| | - Yu Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Sheng Ju
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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