1
|
Erkizan HV, Sukhadia S, Natarajan TG, Marino G, Notario V, Lichy JH, Wadleigh RG. Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma. Sci Rep 2021; 11:14814. [PMID: 34285259 PMCID: PMC8292420 DOI: 10.1038/s41598-021-94064-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Esophageal cancer has a strikingly low survival rate mainly due to the lack of diagnostic markers for early detection and effective therapies. In the U.S., 75% of individuals diagnosed with esophageal squamous cell carcinoma (ESCC) are of African descent. African American ESCC (AA ESCC) is particularly aggressive, and its biological underpinnings remain poorly understood. We sought to identify the genomic abnormalities by conducting whole exome sequencing of 10 pairs of matched AA esophageal squamous cell tumor and control tissues. Genomic analysis revealed diverse somatic mutations, copy number alterations (SCNAs), and potential cancer driver genes. Exome variants created two subgroups carrying either a high or low tumor mutation burden. Somatic mutational analysis based on the Catalog of Somatic Mutations in Cancer (COSMIC) detected SBS16 as the prominent signature in the high mutation rate group suggesting increased DNA damage. SBS26 was also detected, suggesting possible defects in mismatch repair and microsatellite instability. We found SCNAs in multiple chromosome segments, encoding MYC on 8q24.21, PIK3CA and SOX2 on 3q26, CCND1, SHANK2, CTTN on 11q13.3, and KRAS on 12p12. Amplifications of EGFRvIII and EGFRvIVa mutants were observed in two patients, representing a novel finding in ESCC that has potential clinical relevance. This present exome sequencing, which to our knowledge, represents the first comprehensive exome analysis exclusively in AA ESCC, and highlights novel mutated loci that might explain the aggressive nature of AA ESCC and lead to the development of diagnostic and prognostic markers as well as therapeutic targets.
Collapse
Affiliation(s)
- Hayriye Verda Erkizan
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington, DC, USA.
| | | | | | - Gustavo Marino
- Hepatology and Gastroenterology, Veterans Affairs Medical Center, Washington, DC, USA
| | - Vicente Notario
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Jack H Lichy
- Pathology and Laboratory Service, Veterans Affairs Medical Center, Washington, DC, USA
| | - Robert G Wadleigh
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington, DC, USA.,Hematology and Medical Oncology, Veterans Affairs Medical Center, Washington, DC, USA
| |
Collapse
|
2
|
Zhan X, He L, Song K, Cao S, Meng E, Wang Y. Case Report: Triple Primary Malignant Tumors of the Esophagus, Stomach, and Colon in a Patient With Genetic Analysis. Front Genet 2021; 12:676497. [PMID: 34306021 PMCID: PMC8299121 DOI: 10.3389/fgene.2021.676497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/15/2021] [Indexed: 01/03/2023] Open
Abstract
The incidence of multiple primary malignant tumors (MPMTs) has increased greatly with the progress of tumor diagnosis and therapy technology. However, triple primary cancer is still very rare, and its genetic change is not clear yet. This case report described a 70-year-old Chinese male patient with triple primary cancers of the esophagus, stomach and right-sided colon. Pathological examination confirmed that each malignant tumor developed independently. Next-generation sequencing (NGS) using a 599-gene panel revealed five TP53 mutations in three tumor tissues. These variations might contribute to development of the triple primary malignant tumors in the patient. The patient underwent laparoscopic feeding jejunostomy and postoperative radiotherapy for synchronous esophageal and gastric carcinomas. Then, he underwent laparoscopic-assisted resection of right-sided colonic cancer and lysis of abdominal adhesions. By the time of submitting this manuscript, the patient had been well and no sign of recurrence or metastasis had been observed. To the best of our knowledge, this case is the first one to clarify the genetic abnormalities of triple primary cancers of esophagus, stomach and colon in a Chinese patient. It may contribute to understanding the molecular pathogenesis of multiple primary digestive malignancies and providing valuable treatment strategies for the similar patients in the future.
Collapse
Affiliation(s)
- Xiaoli Zhan
- Department of General Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Lingzhe He
- Department of General Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Kai Song
- Department of Pathology, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Shuliang Cao
- ChosenMed Technology (Beijing) Co. Ltd., Beijing, China
| | - Erhong Meng
- ChosenMed Technology (Beijing) Co. Ltd., Beijing, China
| | - Yuedong Wang
- Department of General Surgery, The Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
3
|
PD_BiBIM: Biclustering-based biomarker identification in ESCC microarray data. J Biosci 2021. [DOI: 10.1007/s12038-021-00171-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
4
|
Zhang N, Shi J, Shi X, Chen W, Liu J. Mutational Characterization and Potential Prognostic Biomarkers of Chinese Patients with Esophageal Squamous Cell Carcinoma. Onco Targets Ther 2020; 13:12797-12809. [PMID: 33363385 PMCID: PMC7751839 DOI: 10.2147/ott.s275688] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
Purpose Esophageal squamous cell carcinoma (ESCC) is the most common type of esophageal cancer in China and the 5-year mortality rate is up to 70%. Studies on the ESCC genetic landscape are needed to further explore clinical therapeutic strategies. In this study, we evaluated the genetic landscape of ESCC to aid the search for clinical therapeutic strategies. Patients and Methods A total of 225 ESCC patients were enrolled in this study. Deep sequencing of 450 cancer genes was performed on formalin-fixed paraffin-embedded tumor biopsies and matched blood samples from patients. Tumor mutational burden (TMB) was calculated using an algorithm developed in-house. Results Our results showed that the most commonly mutated genes in ESCC were TP53 (96%), CCND1 (46%), FGF4 (44%), FGF19 (44%), FGF3 (44%), CDKN2A (31%), PIK3CA (26%), NOTCH1 (24%), KMT2D (18%), FAT1 (16%), and LRP1B (16%). We found that TMB correlated with patient drinking status. We identified mutations associated with sex, early ESCC, high TMB, and metastasis lymph nodes. KMT2D mutations associated with sex (P = 0.035), tumor stage (P = 0.016), high TMB (P = 0.0072), and overall survival of patients (P = 0.0026). SPEN mutations associated with high TMB (P = 0.0016) and metastasis-positive lymph nodes (P = 0.027). These results suggested that SPEN and KMT2D could be potential prognosis biomarkers for Chinese patients with ESCC. We also found that the number of positive lymph nodes was associated with disease-free survival. Clinical target gene analysis indicated that nearly half of Chinese ESCC patients might benefit from treatment with gene-specific target drugs. Conclusion Our study revealed the ESCC mutational landscape in 225 Chinese patients and uncovered the potential prognosis biomarker for Chinese patients with ESCC.
Collapse
Affiliation(s)
- Nan Zhang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| | - Junping Shi
- Department of Medicine, OrigiMed Co. Ltd, Shanghai, People's Republic of China
| | - Xiaoliang Shi
- Department of Medicine, OrigiMed Co. Ltd, Shanghai, People's Republic of China
| | - Wenting Chen
- Department of Medicine, OrigiMed Co. Ltd, Shanghai, People's Republic of China
| | - Junfeng Liu
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, People's Republic of China
| |
Collapse
|
5
|
Zhou M, Mao Y, Yu S, Li Y, Yin R, Zhang Q, Lu T, Sun R, Lin S, Qian Y, Xu Y, Fan H. LINC00673 Represses CDKN2C and Promotes the Proliferation of Esophageal Squamous Cell Carcinoma Cells by EZH2-Mediated H3K27 Trimethylation. Front Oncol 2020; 10:1546. [PMID: 33014799 PMCID: PMC7461945 DOI: 10.3389/fonc.2020.01546] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs), some of the most abundant epigenetic regulators, play an important role in esophageal squamous cell carcinoma (ESCC). In the current study, the functions and mechanisms of the lncRNA LINC00673 were investigated. The expression levels of LINC00673 and its potential target genes were assessed by quantitative real-time polymerase chain reaction (qPCR) in ESCC surgical specimens and ESCC cell lines. RNA fluorescence in situ hybridization (RNA FISH) was employed to detect the subcellular location and the levels of LINC00673 in ESCC samples from patients with different survival times. LINC00673 function in ESCC carcinogenesis was also evaluated in vivo and in vitro. Cell cycle synchronization was performed using serum withdrawal; the cell cycle was monitored by fluorescence analysis and cellular DNA was detected by flow cytometry. The molecular mechanisms underlying LINC00673 were explored via Western blotting, chromatin immunoprecipitation (ChIP), and ChIP-PCR. Up-regulated LINC00673 was associated with poor prognosis in ESCC patients and promoted the proliferation of ESCC cells both in vitro and in vivo. Compared to the control group, depletion of LINC00673 in ESCC cells arrested the cell cycle, at least, at the G1/S checkpoint. Knockdown of LINC00673 significantly enhanced posttranscriptional expression of CDKN2C, and histone 3 lysine 27 trimethylation (H3K27me3) was enriched at the promoter region of CDKN2C. After inhibiting EZH2, the CDKN2C expression levels were increased. The present findings are the first to reveal that LINC00673 represses CDKN2C expression and promotes ESCC cell proliferation by elevating EZH2-mediated H3K27me3 levels. These data suggest that LINC00673 regulates the cell cycle in ESCC and that it is a promising target for clinical therapy.
Collapse
Affiliation(s)
- Menghan Zhou
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, Nanjing, China.,School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Yuhang Mao
- School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Shenling Yu
- School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Yiping Li
- Department of Pathology and Pathophysiology, Medical School of Southeast University, Nanjing, China
| | - Rong Yin
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Qin Zhang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Tianyu Lu
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, Nanjing, China
| | - Rui Sun
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, Nanjing, China
| | - Shaofeng Lin
- Department of Pathology, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Yanyan Qian
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, Nanjing, China
| | - Ying Xu
- School of Life Sciences and Technology, Southeast University, Nanjing, China
| | - Hong Fan
- The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Department of Medical Genetics and Developmental Biology, Medical School of Southeast University, Nanjing, China
| |
Collapse
|
6
|
Li M, Zhao J, Li X, Chen Y, Feng C, Qian F, Liu Y, Zhang J, He J, Ai B, Ning Z, Liu W, Bai X, Han X, Wu Z, Xu X, Tang Z, Pan Q, Xu L, Li C, Wang Q, Li E. HiFreSP: A novel high-frequency sub-pathway mining approach to identify robust prognostic gene signatures. Brief Bioinform 2020; 21:1411-1424. [PMID: 31350847 DOI: 10.1093/bib/bbz078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/19/2019] [Accepted: 06/04/2019] [Indexed: 02/05/2023] Open
Abstract
With the increasing awareness of heterogeneity in cancers, better prediction of cancer prognosis is much needed for more personalized treatment. Recently, extensive efforts have been made to explore the variations in gene expression for better prognosis. However, the prognostic gene signatures predicted by most existing methods have little robustness among different datasets of the same cancer. To improve the robustness of the gene signatures, we propose a novel high-frequency sub-pathways mining approach (HiFreSP), integrating a randomization strategy with gene interaction pathways. We identified a six-gene signature (CCND1, CSF3R, E2F2, JUP, RARA and TCF7) in esophageal squamous cell carcinoma (ESCC) by HiFreSP. This signature displayed a strong ability to predict the clinical outcome of ESCC patients in two independent datasets (log-rank test, P = 0.0045 and 0.0087). To further show the predictive performance of HiFreSP, we applied it to two other cancers: pancreatic adenocarcinoma and breast cancer. The identified signatures show high predictive power in all testing datasets of the two cancers. Furthermore, compared with the two popular prognosis signature predicting methods, the least absolute shrinkage and selection operator penalized Cox proportional hazards model and the random survival forest, HiFreSP showed better predictive accuracy and generalization across all testing datasets of the above three cancers. Lastly, we applied HiFreSP to 8137 patients involving 20 cancer types in the TCGA database and found high-frequency prognosis-associated pathways in many cancers. Taken together, HiFreSP shows higher prognostic capability and greater robustness, and the identified signatures provide clinical guidance for cancer prognosis. HiFreSP is freely available via GitHub: https://github.com/chunquanlipathway/HiFreSP.
Collapse
Affiliation(s)
- Meng Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Jianmei Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Xuecang Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Yang Chen
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Fengcui Qian
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Yuejuan Liu
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Jianzhong He
- Institute of Oncologic Pathology, Shantou University Medical College
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Ziyu Ning
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Wei Liu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Xuefeng Bai
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Xiaole Han
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Zhiyong Wu
- Departments of Oncology Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University
| | - Xiue Xu
- Institute of Oncologic Pathology, Shantou University Medical College
| | - Zhidong Tang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Liyan Xu
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Qiuyu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Enmin Li
- Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| |
Collapse
|
7
|
Li D, Wang X, Lu S, Wang P, Wang X, Yin W, Zhu W, Li S. Integrated analysis revealing genome-wide chromosomal copy number variation in supraglottic laryngeal squamous cell carcinoma. Oncol Lett 2020; 20:1201-1212. [PMID: 32724360 PMCID: PMC7377034 DOI: 10.3892/ol.2020.11653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/27/2020] [Indexed: 01/22/2023] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a genetically complex tumor type and one of the leading causes of cancer-associated disability and mortality. Genetic instability, such as chromosomal instability, is associated with the tumorigenesis of LSCC. Copy number variations (CNVs) have been demonstrated to contribute to the genetic diversity of tumor pathogenesis. Comparative genomic hybridization (CGH) has emerged as a high-throughput genomic technology that facilitates the aggregation of high-resolution data of cancer-associated genomic imbalances. In the present study, a total of 38 primary supraglottic LSCC cases were analyzed by high-resolution array-based CGH (aCGH) to improve the understanding of the genetic alterations in LSCC. Additionally, integration with bioinformatic analysis of microarray expression profiling data from the Gene Expression Omnibus (GEO) database provided a fundamental method for the identification of putative target genes. Genomic CNVs were detected in all cases. The size of net genomic imbalances per case ranged between a loss of 682.3 Mb (~24% of the genome) and a gain of 1,958.6 Mb (~69% of the genome). Recurrent gains included 2pter-q22.1, 3q26.1-qter, 5pter-p12, 7p22.3p14.1, 8p12p11.22, 8q24.13q24.3, 11q13.2q13.4, 12pter-p12.2, 18pter-p11.31 and 20p13p12.1, whereas recurrent losses included 3pter-p21.32, 4q28.1-q35.2, 5q13.2-qter, 9pter-p21.3 and monosomy 13. Gains of 3q26.1-qter were associated with tumor stage, poor differentiation and smoking history. Additionally, through integration with bioinformatic analysis of data from the GEO database, putative target oncogenes, including sex-determining region Y-box 2, eukaryotic translation initiation factor 4 gamma 1, fragile X-related gene 1, disheveled segment polarity protein 3, defective n cullin neddylation 1 domain containing 1, insulin like growth factor 2 mRNA binding protein 2 and CCDC26 long non-coding RNA, and tumor suppressor genes, such as CUB and sushi multiple domains 1, cyclin dependent kinase inhibitor 2A, protocadherin 20, serine peptidase inhibitor Kazal type 5 and Nei like DNA glycosylase 3, were identified in supraglottic LSCC. Supraglottic LSCC is a genetically complex tumor type and aCGH was demonstrated to be effective in the determination of molecular profiles with higher resolution. The present results enable the identification of putative target oncogenes and tumor suppressor gene mapping in supraglottic LSCC.
Collapse
Affiliation(s)
- Dongjie Li
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xianfu Wang
- Department of Pediatrics, Genetics Laboratory, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Shunfei Lu
- Department of Clinical Medicine, Lishui College of Medicine, Lishui, Zhejiang 323000, P.R. China
| | - Ping Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xin Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wanzhong Yin
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wei Zhu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shibo Li
- Department of Pediatrics, Genetics Laboratory, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| |
Collapse
|
8
|
Matsuoka T, Yashiro M. Precision medicine for gastrointestinal cancer: Recent progress and future perspective. World J Gastrointest Oncol 2020; 12:1-20. [PMID: 31966910 PMCID: PMC6960076 DOI: 10.4251/wjgo.v12.i1.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 10/12/2019] [Accepted: 11/04/2019] [Indexed: 02/05/2023] Open
Abstract
Gastrointestinal (GI) cancer has a high tumor incidence and mortality rate worldwide. Despite significant improvements in radiotherapy, chemotherapy, and targeted therapy for GI cancer over the last decade, GI cancer is characterized by high recurrence rates and a dismal prognosis. There is an urgent need for new diagnostic and therapeutic approaches. Recent technological advances and the accumulation of clinical data are moving toward the use of precision medicine in GI cancer. Here we review the application and status of precision medicine in GI cancer. Analyses of liquid biopsy specimens provide comprehensive real-time data of the tumor-associated changes in an individual GI cancer patient with malignancy. With the introduction of gene panels including next-generation sequencing, it has become possible to identify a variety of mutations and genetic biomarkers in GI cancer. Although the genomic aberration of GI cancer is apparently less actionable compared to other solid tumors, novel informative analyses derived from comprehensive gene profiling may lead to the discovery of precise molecular targeted drugs. These progressions will make it feasible to incorporate clinical, genome-based, and phenotype-based diagnostic and therapeutic approaches and apply them to individual GI cancer patients for precision medicine.
Collapse
Affiliation(s)
- Tasuku Matsuoka
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Gastroenterological Surgery, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
- Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, Osaka 5458585, Japan
| |
Collapse
|
9
|
Wang J, Chen X, Tian Y, Zhu G, Qin Y, Chen X, Pi L, Wei M, Liu G, Li Z, Chen C, Lv Y, Cai G. Six-gene signature for predicting survival in patients with head and neck squamous cell carcinoma. Aging (Albany NY) 2020; 12:767-783. [PMID: 31927533 PMCID: PMC6977678 DOI: 10.18632/aging.102655] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/24/2019] [Indexed: 12/21/2022]
Abstract
The prognosis of head and neck squamous cell carcinoma (HNSCC) patients remains poor. High-throughput sequencing data have laid a solid foundation for identifying genes related to cancer prognosis, but a gene marker is needed to predict clinical outcomes in HNSCC. In our study, we downloaded RNA Seq, single nucleotide polymorphism, copy number variation, and clinical follow-up data from TCGA. The samples were randomly divided into training and test. In the training set, we screened genes and used random forests for feature selection. Gene-related prognostic models were established and validated in a test set and GEO verification set. Six genes (PEX11A, NLRP2, SERPINE1, UPK, CTTN, D2HGDH) were ultimately obtained through random forest feature selection. Cox regression analysis confirmed the 6-gene signature is an independent prognostic factor in HNSCC patients. This signature effectively stratified samples in the training, test, and external verification sets (P < 0.01). The 5-year survival AUC in the training and verification sets was greater than 0.74. Thus, we have constructed a 6-gene signature as a new prognostic marker for predicting survival of HNSCC patients.
Collapse
Affiliation(s)
- Juncheng Wang
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Xun Chen
- Department of Oral and Maxillofacial Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou 362000, People's Republic of China
| | - Yuxi Tian
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008 People's Republic of China
| | - Gangcai Zhu
- Department of Otolaryngology, Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Yuexiang Qin
- Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Xuan Chen
- Department of Stomatology, Changzheng Hospital, Second Military Medcial University, Shanghai 200003, People's Republic of China
| | - Leiming Pi
- Department of Otolaryngology, Head and Neck Surgery, HeYuan People's Hospital, Jinan University, He Yuan,517000, People's Republic of China
| | - Ming Wei
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Guancheng Liu
- Department of Otolaryngology, Head and Neck Surgery, Affiliated Hospital of Guilin University, Guilin 541000, People's Republic of China
| | - Zhexuan Li
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Changhan Chen
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yunxia Lv
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, People's Republic of China
| | - Gengming Cai
- Department of Otolaryngology, Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou 362000, People's Republic of China
| |
Collapse
|
10
|
Tai AS, Peng CH, Peng SC, Hsieh WP. Decomposing the subclonal structure of tumors with two-way mixture models on copy number aberrations. PLoS One 2018; 13:e0206579. [PMID: 30540749 PMCID: PMC6291075 DOI: 10.1371/journal.pone.0206579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 10/16/2018] [Indexed: 12/02/2022] Open
Abstract
Multistage tumorigenesis is a dynamic process characterized by the accumulation of mutations. Thus, a tumor mass is composed of genetically divergent cell subclones. With the advancement of next-generation sequencing (NGS), mathematical models have been recently developed to decompose tumor subclonal architecture from a collective genome sequencing data. Most of the methods focused on single-nucleotide variants (SNVs). However, somatic copy number aberrations (CNAs) also play critical roles in carcinogenesis. Therefore, further modeling subclonal CNAs composition would hold the promise to improve the analysis of tumor heterogeneity and cancer evolution. To address this issue, we developed a two-way mixture Poisson model, named CloneDeMix for the deconvolution of read-depth information. It can infer the subclonal copy number, mutational cellular prevalence (MCP), subclone composition, and the order in which mutations occurred in the evolutionary hierarchy. The performance of CloneDeMix was systematically assessed in simulations. As a result, the accuracy of CNA inference was nearly 93% and the MCP was also accurately restored. Furthermore, we also demonstrated its applicability using head and neck cancer samples from TCGA. Our results inform about the extent of subclonal CNA diversity, and a group of candidate genes that probably initiate lymph node metastasis during tumor evolution was also discovered. Most importantly, these driver genes are located at 11q13.3 which is highly susceptible to copy number change in head and neck cancer genomes. This study successfully estimates subclonal CNAs and exhibit the evolutionary relationships of mutation events. By doing so, we can track tumor heterogeneity and identify crucial mutations during evolution process. Hence, it facilitates not only understanding the cancer development but finding potential therapeutic targets. Briefly, this framework has implications for improved modeling of tumor evolution and the importance of inclusion of subclonal CNAs.
Collapse
Affiliation(s)
- An-Shun Tai
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | - Chien-Hua Peng
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
- * E-mail: (WPH); (CHP)
| | - Shih-Chi Peng
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | - Wen-Ping Hsieh
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
- * E-mail: (WPH); (CHP)
| |
Collapse
|
11
|
Cortactin as a potential predictor of second esophageal neoplasia in hypopharyngeal carcinoma. Auris Nasus Larynx 2018; 46:260-266. [PMID: 30107961 DOI: 10.1016/j.anl.2018.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 06/22/2018] [Accepted: 08/01/2018] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Hypopharyngeal carcinoma has a very poor prognosis. The high incidence of second esophageal neoplasia is one of the major causes. To establish an efficient follow-up scheme for increasing the diagnostic yield and reducing the adverse impact of second esophageal neoplasia on survival, the purpose of this study was to explore a biomarker to predict second esophageal neoplasia. METHODS In this retrospective cohort study, consecutive tissue specimens from those patients who underwent tumor resection between September 2007 and October 2015 were collected. Gene amplification was performed by real-time PCR. The expression of cortactin was evaluated by immunohistochemistry. The predictive risk factors of developing second esophageal neoplasia and prognostic factors related to survival were analyzed. RESULTS A total of 187 patients were included with a mean follow-up of 48months (12-118months). Second esophageal tumors were found in 53 (28.3%), including 41 (21.9%) esophageal squamous cell carcinoma and 12 severe dysplasia. The results of multivariate analyses revealed that age (OR 2.81, 95% CI 1.16-6.78), cortactin overexpression (OR 2.49, 95% CI 1.17-5.33), and stage IV versus I (OR 6.49, 95% CI 1.68-25.18) were independent predictors of second esophageal neoplasia, and second esophageal neoplasia (HR 1.78, 95% CI 1.05-3.01) was an independent predictor of overall survival. CONCLUSION This is the first report to identify a potential biomarker for predicting second esophageal neoplasia in patients with hypopharyngeal carcinoma. In those patients with cortactin overexpression and younger age (≤60years old), close surveillance for second esophageal neoplasia is required. In addition, the real effect of cortactin overexpression on development of primary esophageal carcinoma is required to be validated in a large cohort study.
Collapse
|
12
|
Abstract
Actin remodeling plays an essential role in diverse cellular processes such as cell motility, vesicle trafficking or cytokinesis. The scaffold protein and actin nucleation promoting factor Cortactin is present in virtually all actin-based structures, participating in the formation of branched actin networks. It has been involved in the control of endocytosis, and vesicle trafficking, axon guidance and organization, as well as adhesion, migration and invasion. To migrate and invade through three-dimensional environments, cells have developed specialized actin-based structures called invadosomes, a generic term to designate invadopodia and podosomes. Cortactin has emerged as a critical regulator of invadosome formation, function and disassembly. Underscoring this role, Cortactin is frequently overexpressed in several types of invasive cancers. Herein we will review the roles played by Cortactin in these specific invasive structures.
Collapse
Affiliation(s)
- Pauline Jeannot
- CRCT INSERM UMR1037, Université Toulouse III Paul Sabatier , CNRS ERL5294, Toulouse, France.,Cell Signalling Group, Cancer Research UK Manchester Institute, The University of Manchester , Manchester M20 4BX, UK
| | - Arnaud Besson
- CRCT INSERM UMR1037, Université Toulouse III Paul Sabatier , CNRS ERL5294, Toulouse, France.,LBCMCP , Centre de Biologie Intégrative, Université de Toulouse , CNRS, UPS, Toulouse Cedex, France
| |
Collapse
|