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Zhang J, Zou L, Tan F, Wang H, Wen Z, Wang H, Li L. Screening of co-expressed genes in hypopharyngeal carcinoma with esophageal carcinoma based on RNA sequencing and Clinical Research. Sci Rep 2024; 14:13796. [PMID: 38877096 PMCID: PMC11178892 DOI: 10.1038/s41598-024-64162-w] [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: 12/20/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
To explore the hub comorbidity genes and potential pathogenic mechanisms of hypopharyngeal carcinoma with esophageal carcinoma, and evaluate their diagnostic value for hypopharyngeal carcinoma with co-morbid esophageal carcinoma. We performed gene sequencing on tumor tissues from 6 patients with hypopharyngeal squamous cell carcinoma with esophageal squamous cell carcinoma (hereafter referred to as "group A") and 6 patients with pure hypopharyngeal squamous cell carcinoma (hereafter referred to as "group B"). We analyzed the mechanism of hub genes in the development and progression of hypopharyngeal squamous cell carcinoma with esophageal squamous cell carcinoma through bioinformatics, and constructed an ROC curve and Nomogram prediction model to analyze the value of hub genes in clinical diagnosis and treatment. 44,876 genes were sequenced in 6 patients with group A and 6 patients with group B. Among them, 76 genes showed significant statistical differences between the group A and the group B.47 genes were expressed lower in the group A than in the group B, and 29 genes were expressed higher. The top five hub genes were GABRG2, CACNA1A, CNTNAP2, NOS1, and SCN4B. GABRG2, CNTNAP2, and SCN4B in the hub genes have high diagnostic value in determining whether hypopharyngeal carcinoma patients have combined esophageal carcinoma (AUC: 0.944, 0.944, 0.972). These genes could possibly be used as potential molecular markers for assessing the risk of co-morbidity of hypopharyngeal carcinoma combined with esophageal carcinoma.
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Affiliation(s)
- Jianing Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China
| | - Liangyu Zou
- Department of Otorhinolaryngology Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China
| | - Fuxian Tan
- Department of Otorhinolaryngology Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China
| | - Hongmin Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China
| | - Zhenlei Wen
- Department of Otorhinolaryngology Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China
| | - Hongmei Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China
| | - Lianhe Li
- Department of Otorhinolaryngology Head and Neck Surgery, Central Hospital of Chaoyang, Liaoning, 122000, China.
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Kleo K, Jovanovic VM, Arndold A, Lehmann A, Lammert H, Berg E, Harloff H, Treese C, Hummel M, Daum S. Response prediction in patients with gastric and esophagogastric adenocarcinoma under neoadjuvant chemotherapy using targeted gene expression analysis and next-generation sequencing in pre-therapeutic biopsies. J Cancer Res Clin Oncol 2023; 149:1049-1061. [PMID: 35246724 PMCID: PMC9984352 DOI: 10.1007/s00432-022-03944-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/02/2022] [Indexed: 10/18/2022]
Abstract
OBJECTIVES Perioperative chemo-(radio-) therapy is the accepted standard in European patients with locally advanced adenocarcinoma of the esophagogastric junction or stomach (AEG/AS). However, 30-85% of patients do not respond to this treatment. The aim of our study was the identification of predictive biomarkers in pre-therapeutic endoscopic tumor biopsies from patients with histopathologic response (Becker-1) versus non-response (Becker-2/3) to preoperative chemotherapy. METHODS Formalin-fixed paraffin-embedded biopsies from 36 Caucasian patients (Becker-1 n = 11, Becker-2 n = 7, Becker-3 n = 18) with AEG/AS, taken prior to neoadjuvant chemotherapy were selected. For RNA expression analysis, we employed the NanoString nCounter System. To identify genomic alterations like single nucleotide variants (SNV), copy number variation (CNV) and fusion events, we used Illumina TST170 gene panel. For HER2 and FGFR2 protein expression, immunostaining was performed. Furthermore, we analyzed the microsatellite instability (MSI) and Epstein-Barr virus (EBV) infection status by EBER in situ hybridization. RESULTS Heat map and principal component analyses showed no clustering by means of gene expression according to regression grade. Concerning two recently proposed predictive markers, our data showed equal distribution for MSI (Becker-1: 2; Becker-2: 1; Becker-3: 3; out of 29 tested) and EBV infection was rare (1/32). We could not reveal discriminating target genes concerning SNV, but found a higher mutational burden in non-responders versus responders and fusion (in 6/14) and CNV events (in 5/14) exclusively in Becker-3. CONCLUSIONS Although we could not identify discriminating target genes, our data suggest that molecular alterations are in general more prevalent in patients with AEG/AS belonging to the non-responding Becker group 3.
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Affiliation(s)
- Karsten Kleo
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Vladimir M Jovanovic
- Institute of Informatics, Bioinformatics Solution Center, Freie Universität (FU), Takustr. 9, 14195, Berlin, Germany
| | - Alexander Arndold
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Annika Lehmann
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Hedwig Lammert
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Erika Berg
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Hannah Harloff
- Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany
| | - Christoph Treese
- Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany
- Experimental and Clinical Research Center, Charité University Medicine, Berlin and Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Chariteplatz 1, 10117, Berlin, Germany
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Chariteplatz 1, 10117, Berlin, Germany
| | - Severin Daum
- Medical Department, Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Hindenburgdamm 30, 12200, Berlin, Germany.
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
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Niyaz M, Ainiwaer J, Abudureheman A, Zhang L, Sheyhidin I, Turhong A, Cai R, Hou Z, Awut E. Association between TP53 gene deletion and protein expression in esophageal squamous cell carcinoma and its prognostic significance. Oncol Lett 2020; 20:1855-1865. [PMID: 32724429 PMCID: PMC7377104 DOI: 10.3892/ol.2020.11709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/20/2020] [Indexed: 12/24/2022] Open
Abstract
The aim of the present study was to investigate the association between tumor protein 53 (TP53) gene deletion and protein expression and clinical features in esophageal squamous cell carcinoma (ESCC), and to evaluate the predictive value of these two characteristics in the prognosis of ESCC. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) were performed to detect the expression of p53 protein and gene deletion in ESCC tissue samples from different ethnic groups in Xinjiang, in order to analyze their association with clinicopathological characteristics and patient prognosis, as well as the sensitivity and specificity of the two methods. In addition, the results were further validated by tissue microarray from a different region. The positive rate of p53 protein expression was 54.5% (201/369) in the multi-ethnic group, and was significantly different between sex (P=0.026) and between tumor differentiation groups (P=0.032). FISH demonstrated that the TP53 gene deletion rate was 31.8% (68/214), which was significantly different between different tumor differentiation (P=0.002), lymph node metastasis (P=0.005) and vascular invasion (P<0.001) groups. The survival rate of patients with TP53 gene deletion was significantly lower than those without TP53 gene deletion (P<0.05). The positive rate of p53 protein expression in the tissue microarray was 58.1% (68/117), which was significantly different between the depth of invasion groups (P=0.011). The TP53 gene deletion rate was 47.9% (56/117), which significantly differed according to lymph node metastasis (P=0.003) and TNM stage (P=0.01). In addition, the total concordance rates of the two methods were 60.3 and 64.1%, respectively. There were also significant differences in the positive rate of TP53 gene deletion and protein expression in different stages of ESCC (P<0.05), which increased gradually with the progression of ESCC. The deletion of the TP53 gene in esophageal cancer was associated with poor prognosis and may be an important biomarker for evaluating the prognosis of patients with ESCC. The combination of FISH and IHC methods could significantly improve the detection rate of TP53 gene abnormalities and the accuracy of prognostic assessment of ESCC.
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Affiliation(s)
- Madiniyet Niyaz
- Clinical Medicine Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Julaiti Ainiwaer
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Abulajiang Abudureheman
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Liwei Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Ilyar Sheyhidin
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Abduheny Turhong
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Ren Cai
- Clinical Medicine Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Zhichao Hou
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
| | - Edris Awut
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, P.R. China
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