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Berkel C, Cacan E. Half of most frequently mutated genes in breast cancer are expressed differentially between premenopausal and postmenopausal breast cancer patients. Cancer Genet 2024; 286-287:11-17. [PMID: 38879914 DOI: 10.1016/j.cancergen.2024.06.001] [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: 08/24/2023] [Revised: 05/25/2024] [Accepted: 06/02/2024] [Indexed: 06/18/2024]
Abstract
Breast cancer has distinct causes and molecular characteristics at premenopausal and postmenopausal ages. The age-standardized incidence rate for postmenopausal breast cancer is more than 10 times higher than in premenopausal breast cancer. Here, we showed that the expression of 10 out of 20 most frequently mutated genes in breast cancer (namely, PIK3CA, CDH1, MUC16, PTEN, FAT3, FAT1, SPEN, ARID1A, LRP1B and RUNX1) is higher in premenopausal women with breast cancer than in postmenopausal women with breast cancer. The most significant differences in the expression in terms of menopause status were observed for RUNX1 and FAT1. Furthermore, we found that the majority of these 10 genes also show ER (estrogen receptor) or PR (progesterone receptor) status-dependent expression in both premenopausal and postmenopausal breast cancer patients. Unlike what we observed in the case of ER or PR status, the expression of most of these genes does not change depending on HER2 (human epidermal growth factor receptor 2) status in both premenopausal and postmenopausal breast cancer patients. Combined, our analysis suggests that menopause status might influence the expression of most frequently mutated genes in breast cancer, and that the most of these genes whose expression differ between pre- and post-menopausal women with breast cancer also show ER or PR status-dependent expression in women with breast cancer.
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Affiliation(s)
- Caglar Berkel
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, Türkiye.
| | - Ercan Cacan
- Department of Molecular Biology and Genetics, Tokat Gaziosmanpasa University, Tokat, Türkiye
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2
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Chen C, Li Y, Liu H, Liao M, Yang J, Liu J. FAT1 upregulation is correlated with an immunosuppressive tumor microenvironment and predicts unfavorable outcome of immune checkpoint therapy in non-small cell lung cancer. Heliyon 2024; 10:e28356. [PMID: 38560204 PMCID: PMC10979093 DOI: 10.1016/j.heliyon.2024.e28356] [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: 10/29/2023] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
Background Previous studies found that FAT1 was recurrently mutated and aberrantly expressed in multiple cancers, and the loss function of FAT1 promoted the formation of cancer-initiating cells in several cancers. However, in some types of cancer, FAT1 upregulation could lead to epithelial-mesenchymal transition (EMT). The role of FAT1 in cancer progression, which appears to be cancer-type-specific, is largely unknown. Methods QRT-PCR and immunochemistry were used to verify the expression of FAT1 in non-small cell lung cancer (NSCLC). QRT-PCR and Western blot were used to detect the influence of siFAT1 knockdown on the expression of potential targets of FAT1 in NSCLC cell lines. GEPIA, KM-plotter, CAMOIP, and ROC-Plotter were used to evaluate the association between FAT1 and clinical outcomes based on expression and clinical data from TCGA and immune checkpoint inhibitors (ICI) treated cohorts. Results We found that FAT1 upregulation was associated with the activation of TGF-β and EMT signaling pathways in NSCLC. Patients with a high FAT1 expression level tend to have a poor prognosis and hard to benefit from ICI therapy. Genes involved in TGF-β/EMT signaling pathways (SERPINE1, TGFB1/2, and POSTN) were downregulated upon knockdown of FAT1. Genomic and immunologic analysis showed that high cancer-associated fibroblast (CAF) abundance, decreased CD8+ T cells infiltration, and low TMB/TNB were correlated with the upregulation of FAT1, thus promoting an immunosuppressive tumor microenvironment (TME) which influence the effect of ICI-therapy. Conclusion Our findings revealed the pattern of FAT1 upregulation in the TME of patients with NSCLC, and demonstrated its utility as a biomarker for unfavorable clinical outcomes, thereby providing a potential therapeutic target for NSCLC treatment.
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Affiliation(s)
- Chao Chen
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China
| | - Yanling Li
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Haozhen Liu
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China
| | - Mengying Liao
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen, 518035, China
| | - Jianyi Yang
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China
| | - Jixian Liu
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China
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Wang Z, Zhang C, Guo J, Wang W, Si Q, Chen C, Luo Y, Duan Z. Exosomal miRNA-223-3p derived from tumor associated macrophages promotes pulmonary metastasis of breast cancer 4T1 cells. Transl Oncol 2023; 35:101715. [PMID: 37329828 PMCID: PMC10366638 DOI: 10.1016/j.tranon.2023.101715] [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: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023] Open
Abstract
Research about the effect of exosomes derived from tumor associated macrophages (TAM-exos) in the distant organ metastasis of breast cancer is limited. In this study, we found that TAM-exos could promote the migration of 4T1 cells. Through comparing the expression of microRNAs in 4T1 cells, TAM-exos, and exosomes from bone marrow derived macrophages (BMDM-exos) by sequencing, miR-223-3p and miR-379-5p were screened out as two noteworthy differentially expressed microRNAs. Furthermore, miR-223-3p was confirmed to be the reason for the improved migration and metastasis of 4T1 cells. The expression of miR-223-3p was also increased in 4T1 cells isolated from the lung of tumor-bearing mice. Cbx5, which has been reported to be closely related with metastasis of breast cancer, was identified to be the target of miR-223-3p. Based on the information of breast cancer patients from online databases, miR-223-3p had a negative correlation with the overall survival rate of breast cancer patients within a three-year follow-up, while Cbx5 showed an opposite relationship. Taken together, miR-223-3p in TAM-exos can be delivered into 4T1 cells and exosomal miR-223-3p promotes pulmonary metastasis of 4T1 cells by targeting Cbx5.
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Affiliation(s)
- Ziyuan Wang
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Chen Zhang
- Department of Immunology, Nankai University, Tianjin 300071, China
| | - Jian Guo
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Wei Wang
- BioMetas(Shanghai) Limited, 201203, China
| | - Qin Si
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Chong Chen
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China
| | - Yunping Luo
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China.
| | - Zhaojun Duan
- Department of Immunology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences; School of Basic Medicine, Peking Union Medical College, Beijing 100730, China.
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Bu J, Zhang Y, Wu S, Li H, Sun L, Liu Y, Zhu X, Qiao X, Ma Q, Liu C, Niu N, Xue J, Chen G, Yang Y, Liu C. KK-LC-1 as a therapeutic target to eliminate ALDH + stem cells in triple negative breast cancer. Nat Commun 2023; 14:2602. [PMID: 37147285 PMCID: PMC10163259 DOI: 10.1038/s41467-023-38097-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 04/14/2023] [Indexed: 05/07/2023] Open
Abstract
Failure to achieve complete elimination of triple negative breast cancer (TNBC) stem cells after adjuvant therapy is associated with poor outcomes. Aldehyde dehydrogenase 1 (ALDH1) is a marker of breast cancer stem cells (BCSCs), and its enzymatic activity regulates tumor stemness. Identifying upstream targets to control ALDH+ cells may facilitate TNBC tumor suppression. Here, we show that KK-LC-1 determines the stemness of TNBC ALDH+ cells via binding with FAT1 and subsequently promoting its ubiquitination and degradation. This compromises the Hippo pathway and leads to nuclear translocation of YAP1 and ALDH1A1 transcription. These findings identify the KK-LC-1-FAT1-Hippo-ALDH1A1 pathway in TNBC ALDH+ cells as a therapeutic target. To reverse the malignancy due to KK-LC-1 expression, we employ a computational approach and discover Z839878730 (Z8) as an small-molecule inhibitor which may disrupt KK-LC-1 and FAT1 binding. We demonstrate that Z8 suppresses TNBC tumor growth via a mechanism that reactivates the Hippo pathway and decreases TNBC ALDH+ cell stemness and viability.
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Affiliation(s)
- Jiawen Bu
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Yixiao Zhang
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Sijin Wu
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
- Shenzhen Jingtai Technology Co., Ltd. (XtalPi), International Biomedical Industrial Park (Phase II) 3F, 2 Hongliu Rd, Futian District, 16023, Shenzhen, China
| | - Haonan Li
- School of Bioengineering, Dalian University of Technology, 116023, Dalian, China
| | - Lisha Sun
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Yang Liu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 110016, Shenyang, China
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, 110016, Shenyang, China
| | - Xudong Zhu
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Xinbo Qiao
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Qingtian Ma
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Chao Liu
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Nan Niu
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Jinqi Xue
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Guanglei Chen
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China
| | - Yongliang Yang
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China.
- School of Bioengineering, Dalian University of Technology, 116023, Dalian, China.
| | - Caigang Liu
- Cancer Stem Cell and Translation Medicine Lab, Department of Oncology, Innovative Cancer Drug Research and Development Engineering Center of Liaoning Province, Shengjing Hospital of China Medical University, 110004, Shenyang, China.
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The diverse functions of FAT1 in cancer progression: good, bad, or ugly? J Exp Clin Cancer Res 2022; 41:248. [PMID: 35965328 PMCID: PMC9377080 DOI: 10.1186/s13046-022-02461-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
FAT atypical cadherin 1 (FAT1) is among the most frequently mutated genes in many types of cancer. Its highest mutation rate is found in head and neck squamous cell carcinoma (HNSCC), in which FAT1 is the second most frequently mutated gene. Thus, FAT1 has great potential to serve as a target or prognostic biomarker in cancer treatment. FAT1 encodes a member of the cadherin-like protein family. Under normal physiological conditions, FAT1 serves as a molecular "brake" on mitochondrial respiration and acts as a receptor for a signaling pathway regulating cell-cell contact interaction and planar cell polarity. In many cancers, loss of FAT1 function promotes epithelial-mesenchymal transition (EMT) and the formation of cancer initiation/stem-like cells. However, in some types of cancer, overexpression of FAT1 leads to EMT. The roles of FAT1 in cancer progression, which seems to be cancer-type specific, have not been clarified. To further study the function of FAT1 in cancers, this review summarizes recent relevant literature regarding this protein. In addition to phenotypic alterations due to FAT1 mutations, several signaling pathways and tumor immune systems known or proposed to be regulated by this protein are presented. The potential impact of detecting or targeting FAT1 mutations on cancer treatment is also prospectively discussed.
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Lan T, Ge Q, Zheng K, Huang L, Yan Y, Zheng L, Lu Y, Zheng D. FAT1 Upregulates in Oral Squamous Cell Carcinoma and Promotes Cell Proliferation via Cell Cycle and DNA Repair. Front Oncol 2022; 12:870055. [PMID: 35646625 PMCID: PMC9130556 DOI: 10.3389/fonc.2022.870055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022] Open
Abstract
Objective Previous studies have revealed that FAT atypical cadherin 1 (FAT1) plays a tumor-suppressive or oncogenic role in a context-dependent manner in various cancers. However, the functions of FAT1 are ambiguous in tumorigenesis owing to inconsistent research in oral squamous cell carcinoma (OSCC). The present study aimed at gaining an insight into the role of FAT1 in the tumor genesis and development. Methods The expression, mutant, and survival data analyses were done using data from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO), and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) database, verified with clinical samples via real-time polymerase chain reaction (qRT-PCR), Western blot (WB), and immunohistochemical (IHC) staining. OSCC cells transfected with siRNA were employed for in vitro assessment in cell proliferation, apoptosis, and migration ability in appropriate ways. The underlying mechanism was explored by RNA sequencing after FAT1 silencing. Results Overall, FAT1 significantly increased in OSCC with a poor prognosis outcome. The in vitro experiment showed the promoting effect of FAT1 in the proliferation and migration of OSCC cells. FAT1 can also inhibit both the early and late apoptosis of OSCC cells. RNA-sequencing analysis of FAT1 silencing revealed that the cell cycle, DNA replication, and some core genes (MCM2, MCM5, CCNE1 SPC24, MYBL2, KIF2C) may be the potential mechanism in OSCC. Conclusions FAT1 may act as an oncogene in OSCC with potential mechanism influencing the cell cycle and DNA repair.
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Affiliation(s)
- Ting Lan
- Fujian Key Laboratory of Oral Diseases, Fujian Biological Materials Engineering and Technology Center of Stomatology, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Qi Ge
- Fujian Key Laboratory of Oral Diseases, Fujian Biological Materials Engineering and Technology Center of Stomatology, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Ke Zheng
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Li Huang
- Department of Dentistry, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Yuxiang Yan
- Fujian Key Laboratory of Oral Diseases, Fujian Biological Materials Engineering and Technology Center of Stomatology, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Lixin Zheng
- School of Mathematics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Youguang Lu
- Fujian Key Laboratory of Oral Diseases, Fujian Biological Materials Engineering and Technology Center of Stomatology, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China.,Department of Preventive Dentistry, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
| | - Dali Zheng
- Fujian Key Laboratory of Oral Diseases, Fujian Biological Materials Engineering and Technology Center of Stomatology, School and Hospital of Stomatology, Fujian Medical University, Fuzhou, China
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Peng Z, Gong Y, Liang X. Role of FAT1 in health and disease. Oncol Lett 2021; 21:398. [PMID: 33777221 PMCID: PMC7988705 DOI: 10.3892/ol.2021.12659] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/25/2021] [Indexed: 01/15/2023] Open
Abstract
FAT atypical cadherin 1 (FAT1), which encodes a protocadherin, is one of the most frequently mutated genes in human cancer. Over the past 20 years, the role of FAT1 in tissue growth and in the development of diseases has been extensively studied. There is definitive evidence that FAT1 serves a substantial role in the maintenance of organs and development, and its expression appears to be tissue-specific. FAT1 activates a variety of signaling pathways through protein-protein interactions, including the Wnt/β-catenin, Hippo and MAPK/ERK signaling pathways, which affect cell proliferation, migration and invasion. Abnormal FAT1 expression may lead to the development of tumors and may affect prognosis. Therefore, FAT1 may have potential in tumor therapy. The structural and functional changes mediated by FAT1, its tissue distribution and changes in FAT1 expression in human diseases are described in the present review, which provides further insight for understanding the role of FAT1 in development and disease.
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Affiliation(s)
- Zizhen Peng
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang School of Medicine, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Yanyu Gong
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang School of Medicine, University of South China, Hengyang, Hunan 421001, P.R. China
| | - Xiaoqiu Liang
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang School of Medicine, University of South China, Hengyang, Hunan 421001, P.R. China
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Chromosomal and molecular pathway alterations in the neuroendocrine carcinoma and adenocarcinoma components of gastric mixed neuroendocrine-nonneuroendocrine neoplasm. Mod Pathol 2020; 33:2602-2613. [PMID: 32461621 DOI: 10.1038/s41379-020-0579-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 12/18/2022]
Abstract
Gastric mixed adenoneuroendocrine carcinoma (MANEC) is a clinically aggressive subtype of mixed neuroendocrine-nonneuroendocrine neoplasm (MiNEN) with unclear clonal origin. In this study, we analyzed high-resolution copy number (CN) profiling data using the OncoScan CNV Assay in the neuroendocrine carcinoma (NEC) and adenocarcinoma components of eight MANECs. Some common CNVs, including the gain of CCNE1 (19q12) and the loss of FAT1 (4q35.2), were frequently detected in both components; these CNVs were verified by FISH, qPCR and immunohistochemistry staining assays in samples with sufficient material. The identification of common CNVs in both components supports the likelihood of single clonal origin of morphologically heterogeneous tumor cells and suggests several novel genetic events potentially involved in the development of gastric MANEC. We also detected and validated some CNVs and alterations specific for the NEC component, such as MAPK1 loss and MAPK signaling pathway alterations, which could contribute to the neuroendocrine differentiation of gastric MANEC. In addition, we found that the NEC component presented more CNVs and greater CN loss than the adenocarcinoma component (P = 0.007 and P = 0.004, respectively); the NEC components from different cases were not clustered in the hierarchical clustering analysis, indicating the marked genetic heterogenicity of the NEC component in gastric MANEC. In summary, this study describes the cytogenetic characteristics of each component of gastric MANEC, providing some clues for further studies on the development and progression of gastric MANEC as well as providing some potential therapeutic targets.
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Li S, Lai M, Zhen J, Deng G, Li H, Cheng L, Liu X, Li J, Zhou J, Hu Q, Ye M, Wen L, Zhou C, Zhou Z, Shan C, Hong W, Xiao X, Wang H, Yang Y, Ai R, Cai L. Bone metastases in an adult patient with diffuse midline glioma: a case report. Neurooncol Adv 2020; 3:vdaa156. [PMID: 33543143 PMCID: PMC7846091 DOI: 10.1093/noajnl/vdaa156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shaoqun Li
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Mingyao Lai
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Junjie Zhen
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Guanhua Deng
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Hainan Li
- Department of Pathology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Lina Cheng
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Xuchen Liu
- Department of Orthopedics, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Juan Li
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Jiangfen Zhou
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Qingjun Hu
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Minting Ye
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Lei Wen
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Cheng Zhou
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Zhaoming Zhou
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Changguo Shan
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Weiping Hong
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Xiao Xiao
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Hui Wang
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Yanying Yang
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Ruyu Ai
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China
| | - Linbo Cai
- Department of Neuro-Oncology, Guangdong Sanjiu Brain Hospital, Guangzhou, China.,Department of Medical Imaging, Guangdong Sanjiu Brain Hospital, Guangzhou, China
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Mitrea C, Bollig-Fischer A, Voichiţa C, Donato M, Romero R, Drăghici S. Detecting qualitative changes in biological systems. Sci Rep 2020; 10:8146. [PMID: 32424123 PMCID: PMC7235093 DOI: 10.1038/s41598-020-62578-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/04/2020] [Indexed: 01/09/2023] Open
Abstract
Currently, most diseases are diagnosed only after significant disease-associated transformations have taken place. Here, we propose an approach able to identify when systemic qualitative changes in biological systems happen, thus opening the possibility for therapeutic interventions before the occurrence of symptoms. The proposed method exploits knowledge from biological networks and longitudinal data using a system impact analysis. The method is validated on eight biological phenomena, three synthetic datasets and five real datasets, for seven organisms. Most importantly, the method accurately detected the transition from the control stage (benign) to the early stage of hepatocellular carcinoma on an eight-stage disease dataset.
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Affiliation(s)
- Cristina Mitrea
- Wayne State University, Department of Computer Science, Detroit, 48202, USA
- Wayne State University, Department of Oncology, Detroit, 48201, USA
| | - Aliccia Bollig-Fischer
- Wayne State University, Department of Oncology, Detroit, 48201, USA
- Karmanos Cancer Institute, Detroit, 48201, USA
| | - Călin Voichiţa
- Wayne State University, Department of Computer Science, Detroit, 48202, USA
| | - Michele Donato
- Stanford University, Institute for Immunity, Transplantation and Infection, Stanford, 94305, USA
| | - Roberto Romero
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NICHD/NIH/DHHS, Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Detroit, 48201, USA
- University of Michigan, Department of Obstetrics and Gynecology, Ann Arbor, 48109, USA
- Michigan State University, Department of Epidemiology and Biostatistics, East Lansing, 48824, USA
- Wayne State University, Center for Molecular Medicine and Genetics, Detroit, 48201, USA
| | - Sorin Drăghici
- Wayne State University, Department of Computer Science, Detroit, 48202, USA.
- Wayne State University, Department of Obstetrics and Gynecology, Detroit, 48201, USA.
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11
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Lin LH, Chang KW, Cheng HW, Liu CJ. SMAD4 Somatic Mutations in Head and Neck Carcinoma Are Associated With Tumor Progression. Front Oncol 2019; 9:1379. [PMID: 31867281 PMCID: PMC6909744 DOI: 10.3389/fonc.2019.01379] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
As the incidence and the mortality rate of head and neck squamous cell carcinoma (HNSCC) is increasing worldwide, gaining knowledge about the genomic changes which happen in the carcinogenesis of HNSCC is essential for the diagnosis and therapy of the disease. SMAD4 (DPC4) is a tumor suppressor gene. It is located at chromosome 18q21.1 and a member of the SMAD family. Which mediates the TGF-β signaling pathway, thereby controlling the growth of epithelial cells. In the study presented here, we analyzed tumor samples by multiplex PCR-based next-generation sequencing (NGS) and found deleterious mutations of SMAD4 in 4.1% of the tumors. Knock-down experiments of endogenous and exogenous SMAD4 expression demonstrated that SMAD4 is involved in the migration and invasion of HNSCC cells. Functional analysis of a missense mutation in the MH1 domain of SMAD4 may be responsible for the loss of function in suppressing tumor progression. Missense SMAD4 mutations, therefore, could be useful prognostic determinants for patients affected by HNSCCs. This report is the first study where NGS analysis based on multiplex-PCR is used to demonstrate the imminent occurrence of missense SMAD4 mutations in HNSCC cells. The gene analysis that we performed may support the identification of SMAD4 mutations as a diagnostic marker or even as a potential therapeutic target in head and neck cancer. Moreover, the analytic strategy proposed for the detection of mutations in the SMAD4 gene may be validated as a platform to assist mutation screening.
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Affiliation(s)
- Li-Han Lin
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Kuo-Wei Chang
- Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Dentistry, Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan
| | - Hui-Wen Cheng
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chung-Ji Liu
- School of Dentistry, Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan.,Department of Oral and Maxillofacial Surgery, Taipei MacKay Memorial Hospital, Taipei, Taiwan
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Lin SC, Lin LH, Yu SY, Kao SY, Chang KW, Cheng HW, Liu CJ. FAT1 somatic mutations in head and neck carcinoma are associated with tumor progression and survival. Carcinogenesis 2019; 39:1320-1330. [PMID: 30102337 DOI: 10.1093/carcin/bgy107] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/08/2018] [Indexed: 02/06/2023] Open
Abstract
In recent years, the incidence and mortality rates of head and neck squamous cell carcinoma (HNSCC) have increased worldwide. Therefore, understanding genomic alterations in HNSCC carcinogenesis is crucial for appropriate diagnosis and therapy. Protocadherin FAT1, which encodes 4588 amino acid residues, regulates complex mechanisms to promote oncogenesis or suppression of malignancies. Multiplex PCR-based next-generation sequencing (NGS) revealed FAT1 somatic mutations. The clinicopathologic implications of FAT1 in HNSCC were investigated using expression assays, and the functional role of FAT1 in HNSCC pathogenesis was determined using ectopic expression and knockdown experiments. Approximately 29% patients with HNSCC harbored damaging FAT1 mutations. InVEx algorithm identified FAT1 as a significant functional mutation burden. Each type of mutation (missense, nonsense and frameshift) accounted for nearly one-third of deleterious mutations. FAT1 mutations correlated with lower FAT1 expression in tumors. The knockdown of the endogenous expression of FAT1 and exogenous expression of crucial FAT1 domains unequivocally indicated that FAT1 suppressed the migration and invasion capability of HNSCC cells. Functional analysis suggested that nonsense mutations in FAT1 result in the loss of the suppression of tumor progression. FAT1 mutations and downregulation defined nodal involvement, lymphovascular permeation and tumor recurrence. In addition, FAT1 mutations and downregulation are independent predictors of poor disease-free survival in patients with HNSCC. This study is the first to perform multiplex PCR-based NGS to indicate marked non-synonymous FAT1 mutations in HNSCC, which are prognostic indicators. The gene analysis strategy proposed for detecting FAT1 mutations may be a valid method for mutation screening.
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Affiliation(s)
- Shu-Chun Lin
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Stomatology Department, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Li-Han Lin
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Ssu-Yu Yu
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan
| | - Shou-Yen Kao
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Stomatology Department, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Kuo-Wei Chang
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Stomatology Department, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Hui-Wen Cheng
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chung-Ji Liu
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Department of Oral and Maxillofacial Surgery, MacKay Memorial Hospital, Taipei, Taiwan
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