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Kim Y, Kang JW, Kang J, Kwon EJ, Ha M, Kim YK, Lee H, Rhee JK, Kim YH. Novel deep learning-based survival prediction for oral cancer by analyzing tumor-infiltrating lymphocyte profiles through CIBERSORT. Oncoimmunology 2021; 10:1904573. [PMID: 33854823 PMCID: PMC8018482 DOI: 10.1080/2162402x.2021.1904573] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/22/2021] [Accepted: 03/13/2021] [Indexed: 01/13/2023] Open
Abstract
The tumor microenvironment (TME) within mucosal neoplastic tissue in oral cancer (ORCA) is greatly influenced by tumor-infiltrating lymphocytes (TILs). Here, a clustering method was performed using CIBERSORT profiles of ORCA data that were filtered from the publicly accessible data of patients with head and neck cancer in The Cancer Genome Atlas (TCGA) using hierarchical clustering where patients were regrouped into binary risk groups based on the clustering-measuring scores and survival patterns associated with individual groups. Based on this analysis, clinically reasonable differences were identified in 16 out of 22 TIL fractions between groups. A deep neural network classifier was trained using the TIL fraction patterns. This internally validated classifier was used on another individual ORCA dataset from the International Cancer Genome Consortium data portal, and patient survival patterns were precisely predicted. Seven common differentially expressed genes between the two risk groups were obtained. This new approach confirms the importance of TILs in the TME and provides a direction for the use of a novel deep-learning approach for cancer prognosis.
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Affiliation(s)
- Yeongjoo Kim
- Interdisplinary Program of Genomic Science, Pusan National University, Yangsan, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Ji Wan Kang
- Interdisplinary Program of Genomic Science, Pusan National University, Yangsan, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Junho Kang
- Interdisplinary Program of Genomic Science, Pusan National University, Yangsan, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Eun Jung Kwon
- Interdisplinary Program of Genomic Science, Pusan National University, Yangsan, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Mihyang Ha
- Interdisplinary Program of Genomic Science, Pusan National University, Yangsan, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Yoon Kyeong Kim
- Interdisplinary Program of Genomic Science, Pusan National University, Yangsan, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Hansong Lee
- Interdisplinary Program of Genomic Science, Pusan National University, Yangsan, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Je-Keun Rhee
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Yun Hak Kim
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
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Qadir F, Aziz MA, Sari CP, Ma H, Dai H, Wang X, Raithatha D, Da Silva LGL, Hussain M, Poorkasreiy SP, Hutchison IL, Waseem A, Teh MT. Transcriptome reprogramming by cancer exosomes: identification of novel molecular targets in matrix and immune modulation. Mol Cancer 2018; 17:97. [PMID: 30008265 PMCID: PMC6047127 DOI: 10.1186/s12943-018-0846-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/27/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Exosomes are extracellular vesicles released by almost all cell types, including cancer cells, into bodily fluids such as saliva, plasma, breast milk, semen, urine, cerebrospinal fluid, amniotic fluid, synovial fluid and sputum. Their key function being intercellular communication with both neighbouring as well as distant cells. Cancer exosomes have been shown to regulate organ-specific metastasis. However, little is known about the functional differences and molecular consequences of normal cells responding to exosomes derived from normal cells compared to those derived from cancer cells. METHODS Here, we characterised and compared the transcriptome profiles of primary human normal oral keratinocytes (HNOK) in response to exosomes isolated from either primary HNOK or head and neck squamous cell carcinoma (HNSCC) cell lines. RESULTS In recipient HNOK cells, we found that regardless of normal or cancer derived, exosomes altered molecular programmes involved in matrix modulation (MMP9), cytoskeletal remodelling (TUBB6, FEZ1, CCT6A), viral/dsRNA-induced interferon (OAS1, IFI6), anti-inflammatory (TSC22D3), deubiquitin (OTUD1), lipid metabolism and membrane trafficking (BBOX1, LRP11, RAB6A). Interestingly, cancer exosomes, but not normal exosomes, modulated expression of matrix remodelling (EFEMP1, DDK3, SPARC), cell cycle (EEF2K), membrane remodelling (LAMP2, SRPX), differentiation (SPRR2E), apoptosis (CTSC), transcription/translation (KLF6, PUS7). We have also identified CEP55 as a potential cancer exosomal marker. CONCLUSIONS In conclusion, both normal and cancer exosomes modulated unique gene expression pathways in normal recipient cells. Cancer cells may exploit exosomes to confer transcriptome reprogramming that leads to cancer-associated pathologies such as angiogenesis, immune evasion/modulation, cell fate alteration and metastasis. Molecular pathways and biomarkers identified in this study may be clinically exploitable for developing novel liquid-biopsy based diagnostics and immunotherapies.
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Affiliation(s)
- Fatima Qadir
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK
| | - Mohammad Arshad Aziz
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK
| | - Chrisdina Puspita Sari
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK
| | - Hong Ma
- Department of Oral & Maxillofacial Surgery, China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Hospital & School of Stomatology, Guizhou Medical University, Guizhou, China
| | - Haiyan Dai
- Department of Oral & Maxillofacial Surgery, China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Hospital & School of Stomatology, Guizhou Medical University, Guizhou, China
| | - Xun Wang
- Department of Oral & Maxillofacial Surgery, China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Hospital & School of Stomatology, Guizhou Medical University, Guizhou, China
| | - Dhiresh Raithatha
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK
| | - Lucas Girotto Lagreca Da Silva
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK
| | - Muhammad Hussain
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK
| | - Seyedeh P Poorkasreiy
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK
| | - Iain L Hutchison
- Department of Oral & Maxillofacial Surgery, Barts & The London NHS Trust, London, England, UK
| | - Ahmad Waseem
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK
| | - Muy-Teck Teh
- Centre for Oral Immunobiology & Regenerative Medicine, Institute of Dentistry, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, The Blizard Building, 4, Newark Street, E1 2AT, London, England, UK. .,Department of Oral & Maxillofacial Surgery, China-British Joint Molecular Head and Neck Cancer Research Laboratory, Affiliated Hospital & School of Stomatology, Guizhou Medical University, Guizhou, China. .,Cancer Research Institute, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China.
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Luo A, Yu X, Li G, Ma G, Chen H, Ding F, Li Y, Liu Z. Differentiation-associated genes regulated by c-Jun and decreased in the progression of esophageal squamous cell carcinoma. PLoS One 2014; 9:e96610. [PMID: 24796531 PMCID: PMC4010476 DOI: 10.1371/journal.pone.0096610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/10/2014] [Indexed: 12/20/2022] Open
Abstract
Transcription factor c-Jun plays a key role in controlling epithelium cell proliferation, apoptosis and differentiation. However, molecular mechanism and biological functions of c-Jun in squamous differentiation and the progression of esophageal squamous cell carcinoma (ESCC) remain elusive. In this study, we found that c-Jun bound directly to the promoter region, and activated the transcription of differentiation-associated genes including cystatin A, involucrin and SPRR3 in vivo. Ectopic expression of c-Jun enhanced SPRR3 transactivation in KYSE450 cells. Conversely, TAM67, a dominant negative mutant of c-Jun, inhibited SPRR3 transactivation. c-Jun increased expression of SPPR3 mainly via a PKC/JNK pathway in response to TPA in KYSE450 cells. Furthermore, c-Jun was remarkably reduced in esophageal cancer. Interestingly, cystatin A, involucrin and SPRR3 were significantly downregulated as well, and associated with differentiation grade. Expression of c-Jun was correlated with the expression of these genes in normal epithelium and ESCC. Importantly, the expression of these genes was remarkably decreased during the malignant transformation from normal epithelium to low-grade intraepithelial neoplasia (LGIN) or high-grade intraepithelial neoplasia (HGIN). The expression of cystatin A and involucrin was significantly reduced from LGIN to HGIN. These results suggest c-Jun was involved in the regulation of differentiation-associated genes in ESCC. These genes might serve as the potential markers in distinguishing normal epithelium from esophageal squamous intraepithelial neoplasia.
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Affiliation(s)
- Aiping Luo
- State Key Lab of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinfeng Yu
- Department of Pharmacology, School of Chemical Biology & Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Guichang Li
- Department of Media and Biology Control, Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Gang Ma
- State Key Lab of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Hongyan Chen
- State Key Lab of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Fang Ding
- State Key Lab of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yi Li
- State Key Lab of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihua Liu
- State Key Lab of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing, China
- * E-mail:
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Luo A, Chen H, Ding F, Zhang Y, Wang M, Xiao Z, Liu Z. Small proline-rich repeat protein 3 enhances the sensitivity of esophageal cancer cells in response to DNA damage-induced apoptosis. Mol Oncol 2013; 7:955-67. [PMID: 23820115 DOI: 10.1016/j.molonc.2013.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 05/28/2013] [Accepted: 05/28/2013] [Indexed: 12/12/2022] Open
Abstract
Small proline-rich repeat protein 3 (SPRR3) has been linked with the altered chemoradiosensitivity, however the underlying molecular mechanisms remain elusive. Here, we report that ectopic overexpression of SPRR3 enhanced the sensitivity of cells in response to DNA damage-induced apoptosis via loss of mitochondrial membrane potential (MMP), and increasing activation of caspase 3 in human esophageal cancer cell lines. Conversely, siRNA knockdown of SPRR3 reduced apoptosis. We found that SPRR3 was localized in mitochondria and interacted with Bcl-2 in vivo, thus facilitating Bax mitochondrial translocation and the subsequent release of cytochrome c, and thereby enhancing cell sensitivity to DNA damage stimuli. In clinical samples, expression of SPRR3 was associated with the pathologic response (P = 0.007 in radiotherapy group, P = 0.035 in preoperative radiotherapy group) and good survival of patients with locally advanced esophageal squamous cell carcinoma (ESCC, P = 0.008). Taken together, our results implicate that SPRR3 might serve as a radiation-sensitive predictor of ESCC.
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Affiliation(s)
- Aiping Luo
- State Key Lab of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing 100021, PR China
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Shen J, Person MD, Zhu J, Abbruzzese JL, Li D. Protein expression profiles in pancreatic adenocarcinoma compared with normal pancreatic tissue and tissue affected by pancreatitis as detected by two-dimensional gel electrophoresis and mass spectrometry. Cancer Res 2005; 64:9018-26. [PMID: 15604267 DOI: 10.1158/0008-5472.can-04-3262] [Citation(s) in RCA: 262] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pancreatic cancer is a rapidly fatal disease, and there is an urgent need for early detection markers and novel therapeutic targets. The current study has used a proteomic approach of two-dimensional (2D) gel electrophoresis and mass spectrometry (MS) to identify differentially expressed proteins in six cases of pancreatic adenocarcinoma, two normal adjacent tissues, seven cases of pancreatitis, and six normal pancreatic tissues. Protein extracts of individual sample and pooled samples of each type of tissues were separated on 2D gels using two different pH ranges. Differentially expressed protein spots were in-gel digested and identified by MS. Forty proteins were identified, of which five [i.e., alpha-amylase; copper zinc superoxide dismutase; protein disulfide isomerase, pancreatic; tropomyosin 2 (TM2); and galectin-1] had been associated previously with pancreatic disease in gene expression studies. The identified proteins include antioxidant enzymes, chaperones and/or chaperone-like proteins, calcium-binding proteins, proteases, signal transduction proteins, and extracellular matrix proteins. Among these proteins, annexin A4, cyclophilin A, cathepsin D, galectin-1, 14-3-3zeta, alpha-enolase, peroxiredoxin I, TM2, and S100A8 were specifically overexpressed in tumors compared with normal and pancreatitis tissues. Differential expression of some of the identified proteins was further confirmed by Western blot analyses and/or immunohistochemical analysis. These results show the value of a proteomic approach in identifying potential markers for early diagnosis and therapeutic manipulation. The newly identified proteins in pancreatic tumors may eventually serve as diagnostic markers or therapeutic targets.
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Affiliation(s)
- Jianjun Shen
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M. D. Anderson Cancer Center, Smithville, Texas, USA
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