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Liu Y, Liu J, Zhang S, Wang J, Sun Z, Sun H, Yang Y, Zheng G, Huang Y, Li M, Zhang Z, Xiao J, Zeng C, Sun C, Qu H, Fang X. A panel sequencing dataset of peripheral blood gene variations in pan-cancer. Sci Data 2024; 11:805. [PMID: 39033182 PMCID: PMC11271301 DOI: 10.1038/s41597-024-03620-6] [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: 10/25/2023] [Accepted: 07/08/2024] [Indexed: 07/23/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) in the peripheral blood is a promising biomarker for cancer diagnosis and prognosis. Somatic mutations identified in cancers have been used to detect therapeutic targets for clinical transformation and individualize drug selection, while germline variants can predict a patient's risk of developing cancer and drug sensitivity. However, no platform has been developed to analyze, calculate, integrate, and friendly visualize these pan-cancer cfDNA mutations deeply. In this work, we performed panel sequencing encompassing 1,115 cancer-related genes across 16,659 cancer patients, spanning 27 cancer types. We detected 496 germline variants in leukocytes and 11,232 somatic mutations in the cfDNA of all patients. CPGV (Cancer Peripheral blood Gene Variations), a database constructed from this dataset, is the first pan-cancer cfDNA database that encompasses somatic mutations, germline variants, and further comparative analyses of mutations across different cancer types. It bears great promise to serve as a valuable resource for cancer research.
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Affiliation(s)
- Yanxia Liu
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Liu
- Yantai Yuhuangding Hospital, Yantai, 264000, China
| | - Shouwei Zhang
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Jinyue Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China
| | - Zhihong Sun
- Yantai Yuhuangding Hospital, Yantai, 264000, China
| | - Huaibo Sun
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Ying Yang
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Guangmin Zheng
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Huang
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Meng Li
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China
| | - Zhaojun Zhang
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China
| | - Jingfa Xiao
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changqing Zeng
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Hongzhu Qu
- China National Center for Bioinformation, Beijing, 100101, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China.
| | - Xiangdong Fang
- China National Center for Bioinformation, Beijing, 100101, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China.
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Galant N, Nicoś M, Kuźnar-Kamińska B, Krawczyk P. Variant Allele Frequency Analysis of Circulating Tumor DNA as a Promising Tool in Assessing the Effectiveness of Treatment in Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2024; 16:782. [PMID: 38398173 PMCID: PMC10887123 DOI: 10.3390/cancers16040782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Despite the different possible paths of treatment, lung cancer remains one of the leading causes of death in oncological patients. New tools guiding the therapeutic process are under scientific investigation, and one of the promising indicators of the effectiveness of therapy in patients with NSCLC is variant allele frequency (VAF) analysis. VAF is a metric characterized as the measurement of the specific variant allele proportion within a genomic locus, and it can be determined using methods based on NGS or PCR. It can be assessed using not only tissue samples but also ctDNA (circulating tumor DNA) isolated from liquid biopsy. The non-invasive characteristic of liquid biopsy enables a more frequent collection of material and increases the potential of VAF analysis in monitoring therapy. Several studies have been performed on patients with NSCLC to evaluate the possibility of VAF usage. The research carried out so far demonstrates that the evaluation of VAF dynamics may be useful in monitoring tumor progression, remission, and recurrence during or after treatment. Moreover, the use of VAF analysis appears to be beneficial in making treatment decisions. However, several issues require better understanding and standardization before VAF testing can be implemented in clinical practice. In this review, we discuss the difficulties in the application of ctDNA VAF analysis in clinical routine, discussing the diagnostic and methodological challenges in VAF measurement in liquid biopsy. We highlight the possible applications of VAF-based measurements that are under consideration in clinical trials in the monitoring of personalized treatments for patients with NSCLC.
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Affiliation(s)
- Natalia Galant
- 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
| | - Barbara Kuźnar-Kamińska
- Department of Pulmonology, Allergology and Respiratory Oncology, Poznan University of Medical Sciences, 61-710 Poznan, Poland;
| | - Paweł Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
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Mao S, Yang S, Liu X, Li X, Wang Q, Zhang Y, Chen J, Wang Y, Gao G, Wu F, Jiang T, Zhang J, Yang Y, Lin X, Zhu X, Zhou C, Ren S. Molecular correlation of response to pyrotinib in advanced NSCLC with HER2 mutation: biomarker analysis from two phase II trials. Exp Hematol Oncol 2023; 12:53. [PMID: 37296463 DOI: 10.1186/s40164-023-00417-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) with HER2 mutation has entered into the era of targeted therapy. However, both anti-HER2 antibody-drug conjugates (ADCs) and tyrosine kinase inhibitors (TKIs) showed moderate objective response rate (ORR) and median progression-free survival (PFS). The aim of this study was to investigate the molecular features of responders to pyrotinib in advanced NSCLC with HER2 mutation. METHODS Patients from our two previous phase II trials were pooled analyzed. Their circulating tumor DNA (ctDNA) were detected by next-generation sequencing (NGS) panels, and the correlation with the efficacy of pyrotinib was investigated. RESULTS This pooled analysis included 75 patients, and 50 of them with baseline plasma samples were finally enrolled with a median age of 57 years old. The overall ORR and median PFS were 28% and 7.0 months respectively. Biomarker analysis showed that 5 patients were ctDNA nonshedding. Patients with TP53 wild type were significantly associated with higher disease control rate (97.1%vs. 68.8%, p = 0.010), PFS (median 8.4 vs. 2.8 months, p = 0.001) and overall survival (OS, median 26.7 vs. 10.4 months, p < 0.001) than those with mutations. ctDNA of nonshedding and clearance exhibited significantly longer PFS (median: 10.2 vs. 9.8 vs. 5.6 months, p = 0.036) and a trend of longer OS (median: 35.3 vs. 18.1 vs. 14.6 months, p = 0.357) than those not. CONCLUSION Patients with TP53 wild type, ctDNA nonshedding, or clearance showed superior efficacy of pyrotinib in patients with HER2-mutated advanced NSCLC, which might be helpful to guide the utility of pyrotinib in clinical setting. TRIAL REGISTRATION The patients were from two registered clinical trials (ClinicalTrials.gov: NCT02535507, NCT02834936).
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Affiliation(s)
- Shiqi Mao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Shuo Yang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Xinyu Liu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Xingya Li
- Second Ward of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, China
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, 450008, China
| | - Yiping Zhang
- Department of Thoracic Oncology, Zhejiang Cancer Hospital, Hangzhou, 310000, China
| | - Jianhua Chen
- Department of Medical Oncology, Cancer Hospital of Central South University, Changsha, 410006, China
| | - Yan Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Guanghui Gao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Fengying Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Jiao Zhang
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Ying Yang
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Xiang Lin
- Jiangsu Hengrui Pharmaceuticals Co., Ltd, Shanghai, China
| | - Xiaoyu Zhu
- Jiangsu Hengrui Pharmaceuticals Co., Ltd, Shanghai, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China.
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China.
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Jiang C, Lu Y, Liu H, Cai G, Peng Z, Feng W, Lin L. Clinical characterization and genomic landscape of gynecological cancers among patients attending a Chinese hospital. Front Oncol 2023; 13:1143876. [PMID: 37064128 PMCID: PMC10101327 DOI: 10.3389/fonc.2023.1143876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
BackgroundGynecological cancers are the most lethal malignancies among females, most of which are associated with gene mutations. Few studies have compared the differences in the genomic landscape among various types of gynecological cancers. In this study, we evaluated the diversity of mutations in different gynecological cancers.MethodsA total of 184 patients with gynecological cancer, including ovarian, cervical, fallopian tube, and endometrial cancer, were included. Next-generation sequencing was performed to detect the mutations and tumor mutational burden (TMB). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses were also conducted.ResultsWe found that 94.57% of patients had at least one mutation, among which single nucleotide variants, insertions and InDels were in the majority. TP53, PIK3CA, PTEN, KRAS, BRCA1, BRCA2, ARID1A, KMT2C, FGFR2, and FGFR3 were the top 10 most frequently mutated genes. Patients with ovarian cancer tended to have higher frequencies of BRCA1 and BRCA2 mutations, and the frequency of germline BRCA1 mutations (18/24, 75.00%) was higher than that of BRCA2 (11/19, 57.89%). A new mutation hotspot in BRCA2 (I770) was firstly discovered among Chinese patients with gynecological cancer. Patients with TP53, PIK3CA, PTEN, and FGFR3 mutations had significantly higher TMB values than those with wild-type genes. A significant cross was discovered between the enriched KEGG pathways of gynecological and breast cancers. GO enrichment revealed that the mutated genes were crucial for the cell cycle, neuronal apoptosis, and DNA repair.ConclusionVarious gynecological cancer types share similarities and differences both in clinical characterization and genomic mutations. Taken together with the results of TMB and enriched pathways, this study provided useful information on the molecular mechanism underlying gynecological cancers and the development of targeted drugs and precision medicine.
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Affiliation(s)
- Cen Jiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yiyi Lu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hua Liu
- Department of Obstetrics & Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Gang Cai
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhao Peng
- Genecast Biotechnology Co., Ltd., Wuxi, China
| | - Weiwei Feng
- Department of Obstetrics & Gynecology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Weiwei Feng, ; Lin Lin,
| | - Lin Lin
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Weiwei Feng, ; Lin Lin,
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Rajana N, Mounika A, Chary PS, Bhavana V, Urati A, Khatri D, Singh SB, Mehra NK. Multifunctional hybrid nanoparticles in diagnosis and therapy of breast cancer. J Control Release 2022; 352:1024-1047. [PMID: 36379278 DOI: 10.1016/j.jconrel.2022.11.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022]
Abstract
Breast cancer is the most prevalent non-cutaneous malignancy in women, with greater than a million new cases every year. In the last decennium, numerous diagnostic and treatment approaches have been enormously studied for Breast cancer. Among the different approaches, nanotechnology has appeared as a promising approach in preclinical and clinical studies for early diagnosis of primary tumors and metastases and eradicating tumor cells. Each of these nanocarriers has its particular advantages and drawbacks. Combining two or more than two constituents in a single nanocarrier system leads to the generation of novel multifunctional Hybrid Nanocarriers with improved structural and biological properties. These novel Hybrid Nanocarriers have the capability to overcome the drawbacks of individual constituents while having the advantages of those components. Various hybrid nanocarriers such as lipid polymer hybrid nanoparticles, inorganic hybrid nanoparticles, metal-organic hybrid nanoparticles, and hybrid carbon nanocarriers are utilized for the diagnosis and treatment of various cancers. Certainly, Hybrid Nanocarriers have the capability to encapsulate multiple cargos, targeting agents, enhancement in encapsulation, stability, circulation time, and structural disintegration compared to non-hybrid nanocarriers. Many studies have been conducted to investigate the utilization of Hybrid nanocarriers in breast cancer for imaging platforms, photothermal and photodynamic therapy, chemotherapy, gene therapy, and combinational therapy. In this review, we mainly discussed in detailed about of preparation techniques and toxicological considerations of hybrid nanoparticles. This review also discussed the role of hybrid nanocarriers as a diagnostic and therapeutic agent for the treatment of breast cancer along with alternative treatment approaches apart from chemotherapy including photothermal and photodynamic therapy, gene therapy, and combinational therapy.
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Affiliation(s)
- Naveen Rajana
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Aare Mounika
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Padakanti Sandeep Chary
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Valamla Bhavana
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Anuradha Urati
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Dharmendra Khatri
- Department of Biological science, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Shashi Bala Singh
- Department of Biological science, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Neelesh Kumar Mehra
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India.
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Zhao X, Wang J, Zhu R, Zhang J, Zhang Y. DLX6-AS1 activated by H3K4me1 enhanced secondary cisplatin resistance of lung squamous cell carcinoma through modulating miR-181a-5p/miR-382-5p/CELF1 axis. Sci Rep 2021; 11:21014. [PMID: 34697393 PMCID: PMC8546124 DOI: 10.1038/s41598-021-99555-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023] Open
Abstract
Cisplatin (CDDP) based chemotherapy is widely used as the first-line strategy in treating non-small cell lung cancer (NSCLC), especially lung squamous cell carcinoma (LUSC). However, secondary cisplatin resistance majorly undermines the cisplatin efficacy leading to a worse prognosis. In this respect, we have identified the role of the DLX6-AS1/miR-181a-5p/miR-382-5p/CELF1 axis in regulating cisplatin resistance of LUSC. qRT-PCR and Western blot analysis were applied to detect gene expression. Transwell assay was used to evaluate the migration and invasion ability of LUSC cells. CCK-8 assay was used to investigate the IC50 of LUSC cells. Flow cytometry was used to test cell apoptosis rate. RNA pull-down and Dual luciferase reporter gene assay were performed to evaluate the crosstalk. DLX6-AS1 was aberrantly high expressed in LUSC tissues and cell lines, and negatively correlated with miR-181a-5p and miR-382-5p expression. DLX6-AS1 expression was enhanced by H3K4me1 in cisplatin resistant LUSC cells. Besides, DLX6-AS1 knockdown led to impaired IC50 of cisplatin resistant LUSC cells. Furthermore, DLX6-AS1 interacted with miR-181a-5p and miR-382-5p to regulate CELF1 expression and thereby mediated the cisplatin sensitivity of cisplatin resistant LUSC cells. DLX6-AS1 induced by H3K4me1 played an important role in promoting secondary cisplatin resistance of LUSC through regulating the miR-181a-5p/miR-382-5p/CELF1 axis. Therefore, targeting DLX6-AS1 might be a novel way of reversing secondary cisplatin resistance in LUSC.
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Affiliation(s)
- Xu Zhao
- Department of Radiation Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Jizhao Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No.277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Rui Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No.277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Jing Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No.277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Yunfeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No.277, Yanta West Road, Xi'an, 710061, Shaanxi, China.
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