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Lee B, Chern A, Fu AY, Zhang A, Sha MY. A Highly Sensitive XNA-Based RT-qPCR Assay for the Identification of ALK, RET, and ROS1 Fusions in Lung Cancer. Diagnostics (Basel) 2024; 14:488. [PMID: 38472960 DOI: 10.3390/diagnostics14050488] [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: 01/22/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Lung cancer is often triggered by genetic alterations that result in the expression of oncogenic tyrosine kinases. Specifically, ALK, RET, and ROS1 chimeric receptor tyrosine kinases are observed in approximately 5-7%, 1-2%, and 1-2% of NSCLC patients, respectively. The presence of these fusion genes determines the response to tyrosine kinase inhibitors. Thus, accurate detection of these gene fusions is essential in cancer research and precision oncology. To address this need, we have developed a multiplexed RT-qPCR assay using xeno nucleic acid (XNA) molecular clamping technology to detect lung cancer fusions. This assay can quantitatively detect thirteen ALK, seven ROS1, and seven RET gene fusions in FFPE samples. The sensitivity of the assay was established at a limit of detection of 50 copies of the synthetic template. Our assay has successfully identified all fusion transcripts using 50 ng of RNA from both reference FFPE samples and cell lines. After validation, a total of 77 lung cancer patient FFPE samples were tested, demonstrating the effectiveness of the XNA-based fusion gene assay with clinical samples. Importantly, this assay is adaptable to highly degraded RNA samples with low input amounts. Future steps involve expanding the testing to include a broader range of clinical samples as well as cell-free RNAs to further validate its applicability and reliability.
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Affiliation(s)
- Bongyong Lee
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Andrew Chern
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Andrew Y Fu
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Aiguo Zhang
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
| | - Michael Y Sha
- DiaCarta Inc., 4385 Hopyard Rd., Suite 100, Pleasanton, CA 94588, USA
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Salmani-Javan E, Farhoudi Sefidan Jadid M, Zarghami N. Recent advances in molecular targeted therapy of lung cancer: Possible application in translation medicine. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2024; 27:122-133. [PMID: 38234663 PMCID: PMC10790298 DOI: 10.22038/ijbms.2023.72407.15749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/23/2023] [Indexed: 01/19/2024]
Abstract
Lung cancer is one of the leading causes of death among all cancer deaths. This cancer is classified into two different histological subtypes: non-small cell lung cancer (NSCLC), which is the most common subtype, and small cell lung cancer (SCLC), which is the most aggressive subtype. Understanding the molecular characteristics of lung cancer has expanded our knowledge of the cellular origins and molecular pathways affected by each of these subtypes and has contributed to the development of new therapies. Traditional treatments for lung cancer include surgery, chemotherapy, and radiotherapy. Advances in understanding the nature and specificity of lung cancer have led to the development of immunotherapy, which is the newest and most specialized treatment in the treatment of lung cancer. Each of these treatments has advantages and disadvantages and causes side effects. Today, combination therapy for lung cancer reduces side effects and increases the speed of recovery. Despite the significant progress that has been made in the treatment of lung cancer in the last decade, further research into new drugs and combination therapies is needed to extend the clinical benefits and improve outcomes in lung cancer. In this review article, we discussed common lung cancer treatments and their combinations from the most advanced to the newest.
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Affiliation(s)
- Elnaz Salmani-Javan
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Farhoudi Sefidan Jadid
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nosratollah Zarghami
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Aydin University, Istanbul, Turkey
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Wang Z, Li L, Wang Y, Li X, Xu Y, Wang M, Liang L, Wu X, Tang M, Li Y, He S, Du J, He L, Sun M, Yang L, Di J, Gai F, Liu D. Sputum cell-free DNA for detection of alterations of multiple driver genes in lung adenocarcinoma. Cancer Cytopathol 2023; 131:110-116. [PMID: 36103360 DOI: 10.1002/cncy.22644] [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: 05/26/2022] [Revised: 06/17/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Sputum cell-free DNA (cfDNA) has been confirmed to be a valued surrogate sample for detection of EGFR mutations in patients with lung adenocarcinoma (LAC). Whether it is suitable for detection of mutations of multiple driver genes has not been reported. METHODS A total of 83 patients with LAC were enrolled and their sputum and paired tumor samples were collected. A next-generation sequencing (NGS)-based 10-gene panel was used to test sputum supernatant-derived cfDNA and paired tumor DNA. The sputum sediments were used for cytological evaluation. RESULTS The total positive rates of hotspot mutations of the 10 driver genes in sputum cfDNA and matched tissue samples were 65.1% and 77.1%, respectively. The overall detection sensitivity of variants in sputum cfDNA was 81.3% (95% confidence interval [CI], 69.2%, 89.5%) and the specificity was 100% (95% CI, 79.1%, 100%). The sensitivities of testing sputum cfDNA from patients with stage IIIB-IV was 87.0% (95% CI, 74.5%, 94.1%); the sensitivities of testing sputum cfDNA from patients with malignant sputum was 92.3% (95% CI, 78.0%, 98.0%); and the sensitivity of testing sputum cfDNA from patients with malignant sputum in stage IIIB-IV were 94.1% (95% CI, 78.9%, 99.0%). CONCLUSIONS This study demonstrated that sputum cfDNA were successfully used for the detection of multiple driver genes by NGS. Sputum cfDNA could be a valuable surrogate clinical sample for all-in-one test of mutations to guide target therapies, especially for patients with advanced LAC and malignant sputum.
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Affiliation(s)
- Zheng Wang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Lin Li
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Yifei Wang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Xiaoguang Li
- Department of Minimally Invasive Tumor Therapies Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Yan Xu
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
| | - Mengzhao Wang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
| | - Li Liang
- Department of Cancer Chemotherapy and Radiation Sickness, Peking University Third Hospital, Beijing, People's Republic of China
| | - Xiaonan Wu
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Min Tang
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Yuanming Li
- Department of Minimally Invasive Tumor Therapies Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Shurong He
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Jun Du
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Lei He
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Mingjun Sun
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Li Yang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Jing Di
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
| | - Fei Gai
- Amoy Diagnostics Co, Ltd, Xiamen, People's Republic of China
| | - Dongge Liu
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing, People's Republic of China
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Kuang Y, Xu P, Wang J, Zheng Y, Sun X, Li Z, Gan R, Li H, Guo Y, Yao F, Zhu C, Ke Z, Tang K. Detecting ALK Rearrangement with RT-PCR: A Reliable Approach Compared with Next-Generation Sequencing in Patients with NSCLC. Mol Diagn Ther 2021; 25:487-494. [PMID: 34133003 PMCID: PMC8249291 DOI: 10.1007/s40291-021-00532-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 11/26/2022]
Abstract
Background Precise detection of anaplastic lymphoma kinase (ALK) rearrangement guides the application of ALK-targeted tyrosine kinase inhibitors (ALK-TKIs) in patients with non-small-cell lung cancer (NSCLC). Next-generation sequencing (NGS) has been widely used in clinics, but DNA-based NGS used to detect fusion genes has delivered false-negative results. However, fusion genes can be successfully detected at the transcription level and with higher sensitivity using RNA-based reverse transcription polymerase chain reaction (RT-PCR). Objective This study compared the performance of RT-PCR and NGS in the detection of echinoderm microtubule-associated protein-like 4 (EML4)-ALK fusion in Chinese patients with NSCLC. Methods Formalin-fixed paraffin-embedded tissues from 153 patients who were pathologically diagnosed as having NSCLC were collected from November 2017 to October 2019. Both DNA/RNA-based NGS and RNA-based RT-PCR were used to detect EML4-ALK fusion. For samples with discordant ALK status results, fluorescence in situ hybridization (FISH) or Sanger sequencing was used to further confirm the ALK status. Results In total, 124 samples were successfully analyzed using both NGS and RT-PCR. For 118 samples, results were consistent between NGS and RT-PCR, with 25 reported as ALK fusion positive and 93 as ALK fusion negative, achieving a concordance rate of 95.16%. Among the six samples with disconcordant results, five were positive using RT-PCR but negative using NGS, and one was positive using NGS but negative using RT-PCR. Four of six cases with disconcordant results (three RT-PCR positive and one NGS positive) were successfully validated using either FISH or Sanger sequencing. Conclusions Compared with NGS, RT-PCR appears to be a reliable method of detecting EML4-ALK fusion in patients with NSCLC. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-021-00532-8.
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Affiliation(s)
- Yukun Kuang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Peihang Xu
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Jiyu Wang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Yifan Zheng
- Department of Pharmacy, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xue Sun
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Zimu Li
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - RunJing Gan
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Huixia Li
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Yubiao Guo
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China
| | - Fei Yao
- Amoy Diagnostics Co., Ltd., Xiamen, China
| | | | - Zunfu Ke
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Kejing Tang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. .,Institute of Pulmonary Diseases, Sun Yat-sen University, Guangzhou, China.
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The Prevalence of the EML4-ALK Fusion Gene in Cytology Specimens from Patients with Lung Adenocarcinoma. Pulm Med 2020; 2020:3578748. [PMID: 33425389 PMCID: PMC7773471 DOI: 10.1155/2020/3578748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/12/2020] [Accepted: 12/16/2020] [Indexed: 12/25/2022] Open
Abstract
Background Under the National Comprehensive Cancer Network (NCCN) guidelines for non-small-cell lung carcinoma (NSCLC), anaplastic lymphoma kinase (ALK) gene rearrangement is required to be assessed. However, data showing the prevalence of the ALK rearrangement is still deficient and is not yet available in Indonesia. This study used direct smear preparation from transthoracic needle specimens that are minimally invasive. The main objective of the study is to identify the prevalence of the ALK fusion rearrangement gene in cytological specimens. Materials and Methods A total of 35 direct smear preparations diagnosed as lung adenocarcinoma and EGFR mutation negative were involved in this study. The samples were taken between 2017 and 2019. These samples were examined for EML4-ALK fusion rearrangement gene using qRT-PCR. The EML4-ALK rearrangement status was determined by qRT-PCR with high-resolution melting (HRM) analysis. Results A total of 28 (80%) samples were from males, and 7 samples were from females. Seven (20% 95% CI: 8.4%-36.9%) samples were EML4-ALK rearrangement positive. The average age of the patients was 63.5 years old. The most common sites of metastasis in this study were pleural cavity, bone, liver, and CNS. Conclusions qRT-PCR successfully identified EML4-ALK fusion rearrangement in direct smear preparations of lung adenocarcinoma. Direct smear samples can be used for EML4-ALK rearrangement detection using qRT-PCR. The EML4-ALK rearrangement gene has high prevalence in selected lung adenocarcinoma and EGFR mutation-negative populations. ALK inhibitors in lung cancer can be openly considered for use in Indonesian patients to improve the outcome of this subset of patients.
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Tao H, Shi L, Zhou A, Li H, Gai F, Huang Z, Che N, Liu Z. Distribution of EML4-ALK fusion variants and clinical outcomes in patients with resected non-small cell lung cancer. Lung Cancer 2020; 149:154-161. [PMID: 33017727 DOI: 10.1016/j.lungcan.2020.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVES The molecular profiles and prognosis of anaplastic lymphoma kinase (ALK) fusion and resectable non-small cell lung cancer (NSCLC) remain unclear. This study aimed to explore the distribution of ALK fusion variants and prognostic factors in patients with surgically resected NSCLC. MATERIAL AND METHODS Among the 93 ALK positive surgical patients screened by immunohistochemistry (IHC) or real-time polymerase chain reaction (RT-PCR), 63 patients were confirmed as ALK rearrangement by next-generation sequencing (NGS), including 55 cases of stage I-III and 8 cases of stage IV. Medical records were retrospectively reviewed, the distribution of ALK fusion variants and prognostic factors were analyzed. RESULTS All of the 55 early stage patients were histological adenocarcinoma. No other fusion types were found except for echinoderm microtubule-associated protein-like 4- anaplastic lymphoma kinase (EML4-ALK). EML4-ALK variant 1 (E13:A20; 25/55, 45.5 %) was the predominant variant type, followed by EML4-ALK variant 3 (E6:A20; 19/55, 34.5 %) and variant 2 (E20:A20; 8/55, 14.5 %). Concomitant mutations occurred in 22 patients (22/55, 40.0 %), which involved in 32 co-mutations from 12 kinds of mutated genes. TP53 mutations were most common in coexisting mutations (13/32, 40.6 %). TP53 mutations were less frequently occurred in variant 1 group (3/25, 12.0 %) than in non-variant 1 group (10/30, 33.3 %, P = 0.064). The median disease-free survival (DFS) of the 55 patients was 22.1 months, and the median overall survival (OS) was not mature at the time of analysis. Multivariable analysis showed that stage T3 and EML4-ALK variant 3 were independent prognostic factors for shorter DFS. Neither TP53 mutations nor any coexisting mutations were related to prognosis. CONCLUSIONS This study illustrated the patterns of EML4-ALK fusion variants and gene profiles in patients with resected NSCLC. Advanced T stage and EML4-ALK variant 3 were associated with worse prognosis. The role of TP53 mutations in prognosis is worthy of further study.
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Affiliation(s)
- Hong Tao
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Liang Shi
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Aoxue Zhou
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hongxia Li
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Fei Gai
- Amoy Diagnostics Co., Ltd, Xiamen, China
| | - Zhan Huang
- Amoy Diagnostics Co., Ltd, Xiamen, China
| | - Nanying Che
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
| | - Zhe Liu
- Department of Oncology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
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Pan T, Li YG, Li KY, Chen C, Xu K, Yuan DY, Zou B, Meng Z. Identification of a novel fusion gene, TRIM52-RACK1, in oral squamous cell carcinoma. Mol Cell Probes 2020; 52:101568. [PMID: 32251686 DOI: 10.1016/j.mcp.2020.101568] [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: 03/04/2020] [Revised: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 11/25/2022]
Abstract
Gene fusion is caused by the linkage of previously separate genes or sequences. Recently, an increasing number of novel fusion genes have been identified and associated with tumor progression, and several of them have been suggested as promising targets for tumor therapy. However, there are hardly any studies reporting the association of fusion genes with the progression of oral squamous cell carcinoma (OSCC). In this study, we identified a total of 11 fused genes in OSCC cells. We further analyzed the structure of one fused gene, TRIM52-RACK1, and detected its function in tumor progression in vitro. We found that TRIM52-RACK1 was caused by a deletion of 181,257,187-181,247,386 at 5q35.3 and it promoted OSCC cell proliferation, migration, and invasion. Therefore, TRIM52-RACK1 can be a promising target for tumor therapy in OSCC.
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Affiliation(s)
- Tao Pan
- Key Lab of Precision Biomedicine & Department of Stomatology, Liaocheng People's Hospital, College of Stomatology, Shandong First Medical University, China
| | - Yong-Guo Li
- Key Lab of Precision Biomedicine & Department of Stomatology, Liaocheng People's Hospital, College of Stomatology, Shandong First Medical University, China; Medical College, Liaocheng University, China
| | - Ke-Yi Li
- Key Lab of Precision Biomedicine & Department of Stomatology, Liaocheng People's Hospital, College of Stomatology, Shandong First Medical University, China; Medical College, Liaocheng University, China
| | - Cheng Chen
- Key Lab of Precision Biomedicine & Department of Stomatology, Liaocheng People's Hospital, College of Stomatology, Shandong First Medical University, China; Medical College, Liaocheng University, China
| | - Kai Xu
- Key Lab of Precision Biomedicine & Department of Stomatology, Liaocheng People's Hospital, College of Stomatology, Shandong First Medical University, China; Medical College, Liaocheng University, China
| | - Dao-Ying Yuan
- Key Lab of Precision Biomedicine & Department of Stomatology, Liaocheng People's Hospital, College of Stomatology, Shandong First Medical University, China; Medical College, Liaocheng University, China
| | - Bo Zou
- Key Lab of Precision Biomedicine & Department of Stomatology, Liaocheng People's Hospital, College of Stomatology, Shandong First Medical University, China.
| | - Zhen Meng
- Key Lab of Precision Biomedicine & Department of Stomatology, Liaocheng People's Hospital, College of Stomatology, Shandong First Medical University, China; Medical College, Liaocheng University, China.
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