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Kucharczyk T, Nicoś M, Kucharczyk M, Kalinka E. NRG1 Gene Fusions-What Promise Remains Behind These Rare Genetic Alterations? A Comprehensive Review of Biology, Diagnostic Approaches, and Clinical Implications. Cancers (Basel) 2024; 16:2766. [PMID: 39123493 PMCID: PMC11311641 DOI: 10.3390/cancers16152766] [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: 07/11/2024] [Revised: 08/01/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) presents a variety of druggable genetic alterations that revolutionized the treatment approaches. However, identifying new alterations may broaden the group of patients benefitting from such novel treatment options. Recently, the interest focused on the neuregulin-1 gene (NRG1), whose fusions may have become a potential predictive factor. To date, the occurrence of NRG1 fusions has been considered a negative prognostic marker in NSCLC treatment; however, many premises remain behind the targetability of signaling pathways affected by the NRG1 gene. The role of NRG1 fusions in ErbB-mediated cell proliferation especially seems to be considered as a main target of treatment. Hence, NSCLC patients harboring NRG1 fusions may benefit from targeted therapies such as pan-HER family inhibitors, which have shown efficacy in previous studies in various cancers, and anti-HER monoclonal antibodies. Considering the increased interest in the NRG1 gene as a potential clinical target, in the following review, we highlight its biology, as well as the potential clinical implications that were evaluated in clinics or remained under consideration in clinical trials.
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Affiliation(s)
- Tomasz Kucharczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland;
| | - Marcin Nicoś
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland;
| | - Marek Kucharczyk
- Department of Zoology and Nature Conservation, Institute of Biology, Maria Curie-Sklodowska University in Lublin, 20-033 Lublin, Poland;
| | - Ewa Kalinka
- Oncology Clinic, Institute of the Polish Mother’s Health Center in Lodz, 93-338 Lodz, Poland;
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Song R, J Sutton G, Li F, Liu Q, Wong JJL. Variable calling of m6A and associated features in databases: a guide for end-users. Brief Bioinform 2024; 25:bbae434. [PMID: 39258883 PMCID: PMC11388104 DOI: 10.1093/bib/bbae434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 07/01/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024] Open
Abstract
N6-methyladenosine (m$^{6}$A) is a widely-studied methylation to messenger RNAs, which has been linked to diverse cellular processes and human diseases. Numerous databases that collate m$^{6}$A profiles of distinct cell types have been created to facilitate quick and easy mining of m$^{6}$A signatures associated with cell-specific phenotypes. However, these databases contain inherent complexities that have not been explicitly reported, which may lead to inaccurate identification and interpretation of m$^{6}$A-associated biology by end-users who are unaware of them. Here, we review various m$^{6}$A-related databases, and highlight several critical matters. In particular, differences in peak-calling pipelines across databases drive substantial variability in both peak number and coordinates with only moderate reproducibility, and the inclusion of peak calls from early m$^{6}$A sequencing protocols may lead to the reporting of false positives or negatives. The awareness of these matters will help end-users avoid the inclusion of potentially unreliable data in their studies and better utilize m$^{6}$A databases to derive biologically meaningful results.
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Affiliation(s)
- Renhua Song
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Gavin J Sutton
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Fuyi Li
- College of Information Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China
- South Australian immunoGENomics Cancer Institute (SAiGENCI), The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Qian Liu
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Maryland Pkwy, NV 89154, United States
- School of Life Sciences, College of Sciences, University of Nevada, Las Vegas, Maryland Pkwy, NV 89154, United States
| | - Justin J-L Wong
- Epigenetics and RNA Biology Laboratory, School of Medical Sciences, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
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Li H, Xu L, Cao H, Wang T, Yang S, Tong Y, Wang L, Liu Q. Analysis on the pathogenesis and treatment progress of NRG1 fusion-positive non-small cell lung cancer. Front Oncol 2024; 14:1405380. [PMID: 38957319 PMCID: PMC11217482 DOI: 10.3389/fonc.2024.1405380] [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: 03/22/2024] [Accepted: 06/06/2024] [Indexed: 07/04/2024] Open
Abstract
Lung cancer persistently leads as the primary cause of morbidity and mortality among malignancies. A notable increase in the prevalence of lung adenocarcinoma has become evident in recent years. Although targeted therapies have shown in treating certain subsets of non-small cell lung cancers (NSCLC), a significant proportion of patients still face suboptimal therapeutic outcomes. Neuregulin-1 (NRG1), a critical member of the NRG gene family, initially drew interest due to its distribution within the nascent ventricular endocardium, showcasing an exclusive presence in the endocardium and myocardial microvessels. Recent research has highlighted NRG1's pivotal role in the genesis and progression across a spectrum of tumors, influencing molecular perturbations across various tumor-associated signaling pathways. This review provides a concise overview of NRG1, including its expression patterns, configuration, and fusion partners. Additionally, we explore the unique features and potential therapeutic strategies for NRG1 fusion-positive occurrences within the context of NSCLC.
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Affiliation(s)
- Hongyan Li
- Oncology Department of Integrated Traditional Chinese and Western Medicine, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, Liaoning, China
| | - Lina Xu
- Oncology Department of Integrated Traditional Chinese and Western Medicine, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, Liaoning, China
| | - Hongshun Cao
- Oncology Department of Integrated Traditional Chinese and Western Medicine, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, Liaoning, China
| | - Tianyi Wang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, Liaoning, China
| | - Siwen Yang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, Liaoning, China
| | - Yixin Tong
- Oncology Department of Integrated Traditional Chinese and Western Medicine, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, Liaoning, China
| | - Linlin Wang
- Department of Thoracic Surgery, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, Liaoning, China
| | - Qiang Liu
- Oncology Department of Integrated Traditional Chinese and Western Medicine, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, Liaoning, China
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Zhou R, Dai J, Zhou R, Wang M, Deng X, Zhuo Q, Wang Z, Li F, Yao D, Xu Y. Prognostic biomarker NRG2 correlates with autophagy and epithelial‑mesenchymal transition in breast cancer. Oncol Lett 2024; 27:277. [PMID: 38699660 PMCID: PMC11063754 DOI: 10.3892/ol.2024.14410] [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: 12/14/2023] [Accepted: 03/05/2024] [Indexed: 05/05/2024] Open
Abstract
Breast cancer (BRCA) is a leading cause of death in women worldwide, accounting for 31% of female cancer. Autophagy plays a crucial role in cancer progression, however, the function of autophagy-related gene neuroregulatory protein 2 (NRG2) in BRCA and its underlying molecular mechanisms remain unclear. In the present study, the expression of the NRG2 gene in BRCA was significantly down-regulated compared with the normal controls. The low expression level of NRG2 was related to poor survival rate of BRCA. The receiver operating characteristic curve of NRG2 showed a good diagnostic value for distinguishing BRCA from normal tissues (AUC=0.932). GO-KEGG analysis and GSEA enrichment analysis showed that NRG2 and its regulated genes were enriched in autophagy-related and immune-related pathways, and NRG2 was positively correlated with a number of immune cells and immune checkpoint genes. In addition, knockdown of NRG2 significantly promoted the proliferation, invasion and migration of BRCA cells. The autophagy marker, LC3-II and epithelial-mesenchymal transition (EMT) marker, vimentin were increased, while P62 and E-cadherin were decreased in response to NRG2 depletion. The findings of the present study demonstrated that NRG2 acts as a tumor suppressor factor that contributes to the immune escape and anti-tumor immunity inhibition by regulating the pathological process of autophagy and EMT, suggesting that NRG2 could be used as a prognostic biomarker and clinical target for BRCA therapy.
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Affiliation(s)
- Ruijie Zhou
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Jinjin Dai
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Runlong Zhou
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Mengyi Wang
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Xiaotong Deng
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Qing Zhuo
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Zhenrong Wang
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Fan Li
- Wuhan Bio-Raid Biotechnology Co., Ltd., Wuhan, Hubei 430075, P.R. China
| | - Di Yao
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
| | - Yao Xu
- Institute of Biology and Medicine, College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, Hubei 430081, P.R. China
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Xiao Y, Liu P, Wei J, Zhang X, Guo J, Lin Y. Recent progress in targeted therapy for non-small cell lung cancer. Front Pharmacol 2023; 14:1125547. [PMID: 36909198 PMCID: PMC9994183 DOI: 10.3389/fphar.2023.1125547] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
The high morbidity and mortality of non-small cell lung cancer (NSCLC) have always been major threats to people's health. With the identification of carcinogenic drivers in non-small cell lung cancer and the clinical application of targeted drugs, the prognosis of non-small cell lung cancer patients has greatly improved. However, in a large number of non-small cell lung cancer cases, the carcinogenic driver is unknown. Identifying genetic alterations is critical for effective individualized therapy in NSCLC. Moreover, targeted drugs are difficult to apply in the clinic. Cancer drug resistance is an unavoidable obstacle limiting the efficacy and application of targeted drugs. This review describes the mechanisms of targeted-drug resistance and newly identified non-small cell lung cancer targets (e.g., KRAS G12C, NGRs, DDRs, CLIP1-LTK, PELP1, STK11/LKB1, NFE2L2/KEAP1, RICTOR, PTEN, RASGRF1, LINE-1, and SphK1). Research into these mechanisms and targets will drive individualized treatment of non-small cell lung cancer to generate better outcomes.
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Affiliation(s)
- Yanxia Xiao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Pu Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Jie Wei
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Xin Zhang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Jun Guo
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China
| | - Yajun Lin
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital, National Center of Gerontology of National Health Commission, Beijing, China.,Peking University Fifth School of Clinical Medicine, Beijing, China
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Cheng X, Wei Y, Zhang Z, Wang F, He J, Wang R, Xu Y, Keerman M, Zhang S, Zhang Y, Bi J, Yao J, He M. Plasma PFOA and PFOS Levels, DNA Methylation, and Blood Lipid Levels: A Pilot Study. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:17039-17051. [PMID: 36374530 DOI: 10.1021/acs.est.2c04107] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Exposure to perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) is associated with blood lipids in adults, but the underlying mechanisms remain unclear. This pilot study aimed to investigate the associations between PFOA or PFOS and epigenome-wide DNA methylation and assess the mediating effect of DNA methylation on the PFOA/PFOS-blood lipid association. We measured plasma PFOA/PFOS and leukocyte DNA methylation in 98 patients enrolled from the hospital between October 2018 and August 2019. The median plasma PFOA/PFOS levels were 0.85 and 2.29 ng/mL. Plasma PFOA and PFOS levels were significantly associated with elevated total cholesterol (TC) and low-density lipoprotein cholesterol (LDL) levels. There were 63/87 CpG positions and 8/11 differentially methylated regions (DMRs) associated with plasma PFOA/PFOS levels, respectively. In addition, 5 CpG positions (annotated to AFF3, CREB5, NRG2, USF2, and intergenic region) and one DMR annotated to IRF6 may mediate the association between plasma PFOA/PFOS and LDL levels (mediated proportion from 7.29 to 46.77%); two CpG positions may mediate the association between plasma PFOA/PFOS and TC levels (annotated to CREB5 and USF2, mediated proportion is around 30%). The data suggest that PFOA/PFOS exposure alters DNA methylation. More importantly, the association of PFOA/PFOS with lipid indicators was partly mediated by DNA methylation changes in lipid metabolism-related genes.
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Affiliation(s)
- Xu Cheng
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Yue Wei
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Zefang Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Fei Wang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
- Department of Occupational Health and Environmental Health, School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Jia He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Ruixin Wang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Yali Xu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Mulatibieke Keerman
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Shiyang Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Ying Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Jiao Bi
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Jinqiu Yao
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan 430030, China
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Patient Selection Approaches in FGFR Inhibitor Trials-Many Paths to the Same End? Cells 2022; 11:cells11193180. [PMID: 36231142 PMCID: PMC9563413 DOI: 10.3390/cells11193180] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 12/16/2022] Open
Abstract
Inhibitors of fibroblast growth factor receptor (FGFR) signaling have been investigated in various human cancer diseases. Recently, the first compounds received FDA approval in biomarker-selected patient populations. Different approaches and technologies have been applied in clinical trials, ranging from protein (immunohistochemistry) to mRNA expression (e.g., RNA in situ hybridization) and to detection of various DNA alterations (e.g., copy number variations, mutations, gene fusions). We review, here, the advantages and limitations of the different technologies and discuss the importance of tissue and disease context in identifying the best predictive biomarker for FGFR targeting therapies.
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Zhang C, Mei W, Zeng C. Oncogenic Neuregulin 1 gene (NRG1) fusions in cancer: A potential new therapeutic opportunities. Biochim Biophys Acta Rev Cancer 2022; 1877:188707. [PMID: 35247506 DOI: 10.1016/j.bbcan.2022.188707] [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: 02/06/2022] [Revised: 02/27/2022] [Accepted: 02/27/2022] [Indexed: 10/19/2022]
Abstract
It is widely established that chromosomal rearrangements induce oncogenesis in solid tumors. However, discovering chromosomal rearrangements that are targetable and actionable remains a difficulty. Targeting gene fusion or chromosomal rearrangement seems to be a powerful strategy to address malignancies characterized by gene rearrangement. Oncogenic NRG1 fusions are relatively rare drivers that infrequently occur across most tumor types. NRG1 fusions exhibit unique biological properties and are difficult to identify owing to their large intronic regions. NRG1 fusions can be detected using a variety of techniques, including fluorescence in situ hybridization, immunohistochemistry, or next-generation sequencing (NGS), with NGS-based RNA sequencing being the most sensitive. Previous studies have shown that NRG1 fusion protein induces tumorigenesis, and numerous therapies targeting the ErbB signaling pathway, such as ErbB kinase inhibitors and monoclonal antibodies, have initially demonstrated encouraging anticancer efficacy in malignant tumors carrying NRG1 fusions. In this review, we present the characteristics and prevalence of NRG1 fusions in solid tumors. Additionally, we discuss the laboratory approaches for diagnosing NRG1 gene fusions. More importantly, we outline promising strategies for treating malignancies with NRG1 fusion.
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Affiliation(s)
- Congwang Zhang
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen 518110, China
| | - Wuxuan Mei
- Clinical Medical College, Hubei University of Science and Technology, Xianning, Hubei 437100, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen 518110, China.
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