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Lazar J, Antal-Szalmas P, Kurucz I, Ferenczi A, Jozsi M, Tornyi I, Muller M, Fekete JT, Lamont J, FitzGerald P, Gall-Debreceni A, Kadas J, Vida A, Tardieu N, Kieffer Y, Jullien A, Guergova-Kuras M, Hempel W, Kovacs A, Kardos T, Bittner N, Csanky E, Szilasi M, Losonczy G, Szondy K, Galffy G, Csada E, Szalontai K, Somfay A, Malka D, Cottu P, Bogos K, Takacs L. Large scale plasma proteome epitome profiling is an efficient tool for the discovery of cancer biomarkers. Mol Cell Proteomics 2023:100580. [PMID: 37211046 PMCID: PMC10319867 DOI: 10.1016/j.mcpro.2023.100580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023] Open
Abstract
Current proteomic technologies focus on the quantification of protein levels, while little effort is dedicated to the development of systems approaches to simultaneously monitor proteome variability and abundance. Protein variants may display different immunogenic epitopes detectable by monoclonal antibodies. Epitope variability results from alternative splicing, posttranslational modifications, processing, degradation, and complex formation and possess dynamically changing availability of interacting surface structures frequently serve as reachable epitopes, and often carry different functions. Thus, it is highly likely, that the presence of some of the accessible epitopes correlate with function under physiological and pathological conditions. To enable the exploration of the impact of protein variation on the immunogenic epitome first; here, we present a robust and analytically validated protein epitome profiling (PEP) technology for characterizing immunogenic epitopes of the plasma. To this end we prepared mAb libraries directed against the normalized human plasma proteome as a complex natural immunogen. Resulting hybridoma supernatants were selected for mAb production and the corresponding hybridomas were cloned. Monoclonal antibodies react with single epitopes, thus profiling with the libraries is expected to profile many epitopes which we define by the mimotopes, as we present here. Screening blood plasma samples from control subjects (n = 558) and cancer patients (n = 598) for merely 69 native epitopes displayed by 20 abundant plasma proteins resulted in distinct cancer-specific epitope panels that showed high accuracy (AUC 0.826-0.966) and specificity for lung, breast, and colon cancer. Deeper profiling (≈290 epitopes of approximately 100 proteins) showed unexpected granularity of the epitope-level expression data and detected neutral and lung-cancer associated epitopes of individual proteins. Biomarker epitope panels selected from a pool of 21 epitopes of 12 proteins were validated in independent clinical cohorts. The results demonstrate the value of PEP as a rich and thus far unexplored source of protein biomarkers with diagnostic potential.
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Affiliation(s)
- Jozsef Lazar
- Biosystems International Kft., Debrecen, Hungary; Biosystems Immunolab Zrt., Debrecen, Hungary.
| | - Peter Antal-Szalmas
- University of Debrecen, Faculty of Medicine, Department of Laboratory Medicine, Debrecen, Hungary; Biosystems Immunolab Zrt., Debrecen, Hungary
| | - Istvan Kurucz
- Biosystems International Kft., Debrecen, Hungary; Biosystems Immunolab Zrt., Debrecen, Hungary
| | | | - Mihaly Jozsi
- Eötvös Loránd University, Department of Immunology and MTA-ELTE Complement Research Group, Department of Immunology, Budapest, Hungary
| | - Ilona Tornyi
- Biosystems Immunolab Zrt., Debrecen, Hungary; University of Debrecen, Faculty of Medicine, Department of Human Genetics, Debrecen, Hungary
| | | | | | - John Lamont
- Randox Laboratories Ltd., Crumlin, United Kingdom
| | | | | | - Janos Kadas
- Biosystems International Kft., Debrecen, Hungary
| | - Andras Vida
- University of Debrecen, Faculty of Medicine, Department of Laboratory Medicine, Debrecen, Hungary
| | | | | | | | | | | | | | - Tamas Kardos
- University of Debrecen, Faculty of Medicine, Department of Pulmonology, Debrecen, Hungary
| | - Nora Bittner
- University of Debrecen, Faculty of Medicine, Department of Pulmonology, Debrecen, Hungary
| | - Eszter Csanky
- Miskolc Semmelweis Hospital and University Hospital, Department of Pulmonology, Miskolc, Hungary
| | - Maria Szilasi
- University of Debrecen, Faculty of Medicine, Department of Pulmonology, Debrecen, Hungary
| | - Gyorgy Losonczy
- Semmelweis University, Faculty of Medicine, Department of Pulmonology, Budapest, Hungary
| | - Klara Szondy
- Semmelweis University, Faculty of Medicine, Department of Pulmonology, Budapest, Hungary
| | - Gabriella Galffy
- Semmelweis University, Faculty of Medicine, Department of Pulmonology, Budapest, Hungary
| | - Edit Csada
- Csongrád County Hospital of Chest Diseases, Deszk, Hungary
| | | | - Attila Somfay
- University of Szeged, Faculty of Medicine, Department of Pulmonology, Deszk, Hungary
| | - David Malka
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Krisztina Bogos
- National Koranyi Institute for Pulmonology, Budapest, Hungary
| | - Laszlo Takacs
- Biosystems International Kft., Debrecen, Hungary; Biosystems Immunolab Zrt., Debrecen, Hungary; University of Debrecen, Faculty of Medicine, Department of Human Genetics, Debrecen, Hungary; Biosystems International SAS, Evry, France.
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Liu B, Hu Z, Ran J, Xie N, Tian C, Tang Y, Ouyang Q. The circulating tumor DNA (ctDNA) alteration level predicts therapeutic response in metastatic breast cancer: Novel prognostic indexes based on ctDNA. Breast 2022; 65:116-123. [PMID: 35926241 PMCID: PMC9356206 DOI: 10.1016/j.breast.2022.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/18/2022] Open
Abstract
Purpose Circulating tumor DNA (ctDNA) has good clinical guiding value for metastatic breast cancer (MBC) patients. This study aimed to apply a novel genetic analysis approach for therapeutic prediction based on ctDNA alterations. Method This nonrandomized, multicenter study recruited 223 MBC patients (NCT05079074). Plasma samples were collected for target-capture deep sequencing of ctDNA at baseline, after the 2nd cycle of treatment, and when progressive disease (PD) was evaluated. Samples were categorized into four levels according to the number of ctDNA alterations: level 1 (no alterations), level 2 (1–2 alterations), level 3 (3–4 alterations) and level 4 (≥5 alterations). According to ctDNA alteration level and variant allele frequency (VAF), a novel ctDNA-level Response Evaluation Criterion in Solid Tumors (ctle-RECIST) was established to assess treatment response and predict progression-free survival (PFS). Results The median PFS in level 1 (6.63 months) patients was significantly longer than that in level 2–4 patients (level 2: 5.70 months; level 3–4: 4.90 months, p < 0.05). After 2 cycles of treatment, based on ctle-RECIST, the median PFS of level-based disease control rate (lev-DCR) patients was significantly longer than that of level-based PD (lev-PD) patients [HR 2.42 (1.52–3.85), p < 0.001]. In addition, we found that ctDNA level assessment could be a good supplement to radiologic assessment. The median PFS in the dual-DCR group tended to be longer than that in the single-DCR group [HR 1.41 (0.93–2.13), p = 0.107]. Conclusion The ctDNA alteration level and ctle-RECIST could be novel biomarkers of prognosis and could complement radiologic assessment in MBC. Based on the number of ctDNA alterations, samples were categorized into four levels: level 1 to level 4. ctDNA alterations differed in different alteration level groups. Higher ctDNA alteration levels (levels 3–4) were associated with a higher probability of liver metastasis. According to ctDNA alteration level and variant allele frequency, a novel ctDNA-level RECIST (ctle-RECIST) was established to assess treatment response. ctle-RECIST can not only independently predict PFS, but also assist radiologic assessment and improve the clinical application value of prediction.
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Affiliation(s)
- Binliang Liu
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Zheyu Hu
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Jialu Ran
- Department of Biostatistics and Bioinformatics, Rollins School of Public Heath, Emory University, Atlanta, GA 30322, USA
| | - Ning Xie
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Can Tian
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China
| | - Yu Tang
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Quchang Ouyang
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, China.
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Liquid biopsy using ascitic fluid and pleural effusion supernatants for genomic profiling in gastrointestinal and lung cancers. BMC Cancer 2022; 22:1020. [PMID: 36167530 PMCID: PMC9513868 DOI: 10.1186/s12885-022-09922-5] [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: 10/08/2021] [Accepted: 07/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background Precision medicine highlights the importance of incorporating molecular genetic testing into standard clinical care. Next-generation sequencing can detect cancer-specific gene mutations, and molecular-targeted drugs can be designed to be effective for one or more specific gene mutations. For patients with special site metastases, it is particularly important to use appropriate samples for genetic profiling. This study aimed to determine whether genomic profiling using ASC and PE is effective in detecting genetic mutations. Methods Tissues, plasma, ascites (ASC) supernatants, and pleural effusion (PE) samples from gastrointestinal cancer patients with peritoneal metastasis and lung cancer patients with pleural metastasis were collected for comprehensive genomic profiling. The samples were subjected to next-generation sequencing using a panel of 59 or 1021 cancer-relevant genes panel. Results A total of 156 tissues, 188 plasma samples, 45 ASC supernatants, and 1 PE samples from 304 gastrointestinal cancer patients and 446 PE supernatants, 122 tissues, 389 plasma samples, and 45 PE sediments from 407 lung cancer patients were analyzed. The MSAF was significantly higher in ASC and PE supernatant than that in plasma ctDNA (50.00% vs. 3.00%, p < 0.0001 and 28.5% vs. 1.30%, p < 0.0001, respectively). The ASC supernatant had a higher actionable mutation rate and more actionable alterations than the plasma ctDNA in 26 paired samples. The PE supernatant had a higher total actionable mutation rate than plasma (80.3% vs. 48.4%, p < 0.05). The PE supernatant had a higher frequency of uncommon variations than the plasma regardless of distant organ metastasis. Conclusion ASC and PE supernatants could be better alternative samples when tumor tissues are not available, especially in patients with only peritoneal or pleural metastases. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09922-5.
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Tian C, Yang J, Xie N, Tang Y, Zhou H, Hu ZY, Ouyang Q. The prognosis and risk factors for capecitabine maintenance treatment in metastatic breast cancer: a retrospective comparative cohort study. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:924. [PMID: 36172110 PMCID: PMC9511179 DOI: 10.21037/atm-22-3828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/31/2022] [Indexed: 11/06/2022]
Abstract
Background Maintenance treatment following efficient chemotherapy can improve the treatment outcomes of patients with metastatic breast cancer (MBC). However, there are no studies for identifying the prognostic factors for patients who could benefit from capecitabine maintenance. Therefore, this study aimed to investigate the prognosis and risk factors of capecitabine maintenance therapy and analysed the circulating tumour DNA (ctDNA) markers that may be related to the treatment response. Methods This study recruited 482 consecutive patients with MBC who achieved clinical benefit from capecitabine-based chemotherapy from 2011 to 2019. A total of 256 patients received subsequent capecitabine maintenance therapy. The baseline clinical factors included age at diagnosis, menopause, neoadjuvant therapy, estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) status and subtypes, prior treatment lines, and prior capecitabine-based treatment response. Treatment outcome (progression-free survival, PFS) was assessed by imaging tools according to RSCIST 1.1 standard during the first two treatment cycles and every 3 weeks thereafter. Univariate and multivariate Cox proportional hazards models were used to analysethe association between capecitabine maintenance treatment and prognosis. Results The median PFS of patients receiving capecitabine maintenance treatment was 21.7 months [95% confidence interval (CI): 15.1-36.3 months]. Capecitabine maintenance showed similar effects as endocrine maintenance or anti-HER2 therapy in hormone receptor (HR)-positive or HER2-positive patients, with adjusted HR of 1.17 (95% CI: 0.81-1.71, P=0.40). In patients with triple-negative breast cancer (TNBC), capecitabine maintenance showed a marginal benefit in PFS. Compared to late-line (≥2) capecitabine maintenance, first-line capecitabine maintenance significantly prolonged median PFS. Compared to other HR/HER2 subtypes, patients with HR-positive and HER2-positive subtypes significantly benefited from capecitabine maintenance treatment. Analysis of ctDNA revealed that among patients receiving capecitabine maintenance, TP53 aberrations were concentrated in patients with short PFS. Conclusions Capecitabine maintenance treatment is associated with longer PFS in patients with MBC, especially those receiving first-line capecitabine-based chemotherapy and those with HR positivity/HER2 positivity. TP53 aberrations may be responsible for the poor response to capecitabine maintenance treatment.
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Affiliation(s)
- Can Tian
- Medical Department of Breast Cancer, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China.,Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Jianbo Yang
- The Immunotherapy Research Laboratory, Department of Otolaryngology, University of Minnesota, Minneapolis, MN, USA.,The Cancer Center, Fujian Medical University Union Hospital, Fuzhou, China
| | - Ning Xie
- Medical Department of Breast Cancer, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China.,Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Yu Tang
- Medical Department of Breast Cancer, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China.,Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Haoyu Zhou
- College of Information and Intelligence, Hunan Agricultural University, Changsha, China
| | - Zhe-Yu Hu
- Medical Department of Breast Cancer, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China.,Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Quchang Ouyang
- Medical Department of Breast Cancer, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China.,Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
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TP53 and LRP1B Co-Wild Predicts Improved Survival for Patients with LUSC Receiving Anti-PD-L1 Immunotherapy. Cancers (Basel) 2022; 14:cancers14143382. [PMID: 35884443 PMCID: PMC9320428 DOI: 10.3390/cancers14143382] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/02/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
Immunotherapy brought long-term benefits for partial patients with lung squamous cell carcinoma (LUSC). The predictor of anti-PD-L1 therapy was controversial and limited in LUSC. We aimed to explore novel biomarker for LUSC immunotherapy and the potential mechanism. Five hundred and twenty-five Chinese patients (Geneplus cohort) with LUSC underwent targeted sequencing and were involved to explore the genomic profiling. TP53 and LRP1B were the most frequently recurrent genes and correlated to higher tumor mutational burden (TMB). We observed that LUSC patients with TP53 and LRP1B co-wild (co-wild type) were associated with better survival of anti-PD-L1 therapy compared with TP53 mutant or LRP1B mutant (mutant type) in POPAR/OAK cohort. Copy-number variation (CNV) and whole genome doubling (WGD) data from TCGA LUSC cohort were obtained to assess the CNV events. There were fewer CNV alterations and lower chromosome instability in patients with TP53/LRP1B co-wild compared with those with TP53/LRP1B mutant. RNA expression data from the TCGA LUSC cohort were collected to explore the differences in RNA expression and tumor immune microenvironment (TIME) between mutant and co-wild groups. The TP53/LRP1B co-wild type had a significantly increased proportion of multiple tumor-infiltrating lymphocytes (TILs), including activated CD8 T cell, activated dendritic cell (DC), and effector memory CD8 T cell. Immune-related gene sets including checkpoint, chemokine, immunostimulatory, MHC and receptors were enriched in the co-wild type. In conclusion, TP53/LRP1B co-wild LUSC conferred an elevated response rate in anti-PD-L1 therapy and improved survival, which was associated with a chromosome-stable phenotype and an activated immune microenvironment.
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Peng W, Li B, Li J, Chang L, Bai J, Yi Y, Chen R, Zhang Y, Chen C, Pu X, Jiang M, Li J, Zhong R, Xu F, Chen B, Xu L, Wang N, Huan J, Dai P, Guan Y, Yang L, Xia X, Yi X, Wang J, Yu F, Wu L. Clinical and genomic features of Chinese lung cancer patients with germline mutations. Nat Commun 2022; 13:1268. [PMID: 35273153 PMCID: PMC8913621 DOI: 10.1038/s41467-022-28840-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
Abstract
The germline mutation landscape in Chinese lung cancer patients has not been well defined. In this study, sequencing data of 1,021 cancer genes of 1,794 Chinese lung cancer patients was analyzed. A total of 111 pathogenic or likely pathogenic germline mutations were identified, significantly higher than non-cancer individuals (111/1794 vs. 84/10,588, p < 2.2e-16). BRCA1/2 germline mutations are associated with earlier onset age (median 52.5 vs 60 years-old, p = 0.008). Among 29 cancer disposition genes with germline mutations detected in Chinese cohort and/or TCGA lung cancer cohort, Only 11 from 29 genes are identified in both cohorts and BRCA2 mutations are significantly more common in Chinese cohort (p = 0.015). Chinese patients with germline mutations have different prevalence of somatic KRAS, MET exon 14 skipping and TP53 mutations compared to those without. Our findings suggest potential ethnic and etiologic differences between Western and Asian lung cancer patients.
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Affiliation(s)
- Wenying Peng
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China.,The second department of Oncology, Yunnan Cancer Hospital & The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center, 650000, Kunming, China
| | - Bin Li
- Department of Oncology, Xiangya Hospital, Central South University, 410000, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410000, Changsha, China
| | - Jin Li
- Geneplus-Beijing, 103306, Beijing, China
| | | | - Jing Bai
- Geneplus-Beijing, 103306, Beijing, China
| | - Yuting Yi
- Geneplus-Beijing, 103306, Beijing, China
| | | | | | - Chen Chen
- Geneplus-Beijing, 103306, Beijing, China
| | - Xingxiang Pu
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China
| | - Meilin Jiang
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China
| | - Jia Li
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China
| | - Rui Zhong
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China
| | - Fang Xu
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China
| | - Bolin Chen
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China
| | - Li Xu
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China
| | - Ning Wang
- Department of Oncology, The PLA Rocket Force Characteristic Medical Center, 100088, Beijing, China
| | | | | | | | - Ling Yang
- Geneplus-Beijing, 103306, Beijing, China
| | | | - Xin Yi
- Geneplus-Beijing, 103306, Beijing, China
| | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, 710049, Xi'an, China
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, 410000, Changsha, China.
| | - Lin Wu
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410000, Changsha, China.
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Li M, Ding N, Mi L, Shi Y, Du X, Yi Y, Yang L, Liu W, Zhu J. Liquid biopsy in diffuse large B-cell lymphoma: utility in cell origin determination and survival prediction in Chinese patients. Leuk Lymphoma 2021; 63:608-617. [PMID: 34751093 DOI: 10.1080/10428194.2021.1999441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The utility of circulating tumor DNA (ctDNA) in classifying the cell origin of diffuse large B-cell lymphoma (DLBCL) has not been explored in the Chinese population. In this study, we aimed to investigate the genetic characteristics of DLBCL based on both tumor and ctDNA sequencing and to assess the predictive value of ctDNA in DLBCL. A targeted sequencing panel of 413 genes was applied to tumor biopsies and paired plasma samples obtained from 30 patients with DLBCL before therapeutic intervention (pretreatment). The concordance between plasma genotyping classification and traditional cell-of-origin classification using tumor tissue was 80.0% (20/25). Patients with higher baseline plasma ctDNA levels had poorer survival compared to those with lower ctDNA levels (2-year progression survival rate: 40.0% vs. 80.0%, p = 0.011; 5-year overall survival rate: 30.5% vs. 70.0%, p = 0.004). Collectively, our results demonstrated that pretreatment ctDNA analysis could assist origin determination and prognosis prediction clinically.
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Affiliation(s)
- Miaomiao Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ning Ding
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lan Mi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yunfei Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xinhua Du
- Geneplus-Beijing Institute, Beijing, China
| | - Yuting Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Ling Yang
- Geneplus-Beijing Institute, Beijing, China
| | - Weiping Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jun Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
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Jia N, Chang L, Gao X, Shi X, Dou X, Guan M, Shao Y, Li N, Cheng Y, Ying H, Sun Z, Zhou Y, Zhao L, Zhou J, Bai C. Association of emergence of new mutations in circulating tumuor DNA during chemotherapy with clinical outcome in metastatic colorectal cancer. BMC Cancer 2021; 21:845. [PMID: 34294055 PMCID: PMC8296534 DOI: 10.1186/s12885-021-08309-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/06/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The understanding of molecular changes in mCRC during treatment could be used to personalise therapeutic strategies. The aim of our study was to explore the association of circulating tumour DNA (ctDNA) with clinical outcome in metastatic colorectal cancer (mCRC). METHODS Sequential patients with mCRC receiving standard first-line chemotherapy were included prospectively. Both plasma ctDNA and serum CEA were assessed in samples obtained before treatment and after 4 cycles of chemotherapy (C4). Computed tomography (CT) scans were carried out at baseline and post-C4 (8-10 weeks) and were assessed using Response Evaluation Criteria In Solid Tumours version 1.1 (RECIST v1.1). Target-capture deep sequencing with a panel covering 1021 genes was performed to detected somatic mutations in ctDNA. RESULTS A total of 20 patients were prospectively included and treated with either leucovorin, fluorouracil, and oxaliplatin (FOLFOX) (15/20) or leucovorin, fluorouracil, and irinotecan (FOLFIRI) (5/20). Median follow-up was 6.9 months (range 1.6-26.6). Somatic mutations for baseline ctDNA analysis were identified in 85% (17/20) of the patients. Mutation variations of ctDNA after chemotherapy were tested in 16/20 (80.0%) of the patients. In multivariate analyses, a high baseline molecular tumour burden index (mTBI) in ctDNA was associated with a higher risk of disease progression, as well as emergence of new mutations in ctDNA during chemotherapy. Patients with newly detected mutations had shorter progression-free survival (PFS) compared to those without (median 3.0 versus 7.3 months; hazard ratio (HR), 5.97; 95% confidence interval (CI), 0.70-50.69; P = 0.0003). Fold changes in mTBI from baseline to post-C4 were obtained in 80.0% (16/20) of the patients, which were also related to PFS. Patients with fold reduction in mTBI above 0.8-fold had longer PFS compared to those below (median 9.3 versus 4.1 months; HR, 4.51; 95% CI, 1.29-15.70; P = 0.0008). CONCLUSIONS Newly detected mutations in ctDNA during treatment might potentially be associated with clinical outcome in mCRC and may provide important clinical information.
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Affiliation(s)
- Ning Jia
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | | | - Xin Gao
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohua Shi
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuelin Dou
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Mei Guan
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yajuan Shao
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Ningning Li
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yuejuan Cheng
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Hongyan Ying
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Zhao Sun
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yanping Zhou
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Lin Zhao
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Jianfeng Zhou
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
| | - Chunmei Bai
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 1 Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
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Wang S, Fang Y, Jiang N, Xing S, Li Q, Chen R, Yi X, Zhang Z, Li N. Comprehensive Genomic Profiling of Rare Tumors in China: Routes to Immunotherapy. Front Immunol 2021; 12:631483. [PMID: 33732253 PMCID: PMC7959707 DOI: 10.3389/fimmu.2021.631483] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/18/2021] [Indexed: 01/10/2023] Open
Abstract
Treatment options for rare tumors are limited, and comprehensive genomic profiling may provide useful information for novel treatment strategies and improving outcomes. The aim of this study is to explore the treatment opportunities of patients with rare tumors using immune checkpoint inhibitors (ICIs) that have already been approved for routine treatment of common tumors. We collected immunotherapy-related indicators data from a total of 852 rare tumor patients from across China, including 136 programmed cell death ligand-1 (PD-L1) expression, 821 tumors mutational burden (TMB), 705 microsatellite instability (MSI) and 355 human leukocyte antigen class I (HLA-I) heterozygosity reports. We calculated the positive rates of these indicators and analyzed the consistency relationship between TMB and PD-L1, TMB and MSI, and HLA-I and PD-L1. The prevalence of PD-L1 positive, TMB-H, MSI-, and HLA-I -heterozygous was 47.8%, 15.5%, 7.4%, and 78.9%, respectively. The consistency ratio of TMB and PD-L1, TMB and MSI, and HLA-I and PD-L1 was 54.8% (78/135), 87.3% (598/685), and 47.4% (54/114), respectively. The prevalence of the four indicators varied widely across tumors systems and subtypes. The probability that neuroendocrine tumors (NETs) and biliary tumors may benefit from immunotherapy is high, since the proportion of TMB-H is as high as 50% and 25.4% respectively. The rates of PD-L1 positivity, TMB-H and MSI-H in carcinoma of unknown primary (CUP) were relatively high, while the rates of TMB-H and MSI-H in soft tissue tumors were both relatively low. Our study revealed the distribution of immunotherapeutic indicators in patients with rare tumors in China. Comprehensive genomic profiling may offer novel therapeutic modalities for patients with rare tumors to solve the dilemma of limited treatment options.
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Affiliation(s)
- Shuhang Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cell Biology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yuan Fang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ning Jiang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shujun Xing
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qin Li
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Rongrong Chen
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Xin Yi
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Zhiqian Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Cell Biology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ning Li
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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10
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Ye Y, Ding N, Mi L, Shi Y, Liu W, Song Y, Shu S, Zhu J. Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas. Exp Hematol Oncol 2021; 10:9. [PMID: 33546774 PMCID: PMC7866778 DOI: 10.1186/s40164-021-00200-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE To explore the correlation of mutation landscape with clinical outcomes in patients with peripheral T-cell lymphoma (PTCL). METHODS We retrospectively analyzed the clinicopathological and prognosis data of 53 patients with PTCL from November 2011 to December 2017. Targeted next-generation sequencing of a 659-gene panel was performed for tissues from 53 patients with PTCLs. The correlation of mutation landscape with clinical outcomes was analyzed. RESULTS TET2 was the most frequently mutated gene (64%), followed by RHOA (43%), PCLO (23%), DNMT3A (19%), IDH2 (17%), PIEZO1 (17%) and TP53 (15%). When mutated genes were categorized into functional groups, the most common mutations were those involved in epigenetic/chromatin modification (75%), T-cell activation (74%), and the DNA repair/TP53 pathway (64%). TET2/TP53 mutations were significantly associated with positive B symptoms (P = 0.045), and elevated lactate dehydrogenase (LDH) level (P = 0.011). Moreover, TET2/TP53 mutation was a risk factor for PTCL patient survival (HR 3.574, 95% CI 1.069 - 11.941, P = 0.039). The occurrence of JAK/STAT pathway mutations in angioimmunoblastic T-cell lymphoma (AITL) patients conferred a worse progression-free survival (HR 2.366, 95% CI 0.9130-6.129, P = 0.0334). CONCLUSIONS Heterogeneous gene mutations occur in PTCL, some of which have a negative impact on the survival outcome.
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Affiliation(s)
- Yingying Ye
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Ning Ding
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Lan Mi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Yunfei Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Weiping Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Yuqin Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China
| | - Shaokun Shu
- Department of Biomedical Engineering, Peking University, Beijing, 100871, China.
| | - Jun Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Lymphoma, Peking University Cancer Hospital & Institute, Haidian District, No 52, Fucheng Road, Beijing, 100142, China.
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11
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Shi Y, Su H, Song Y, Jiang W, Sun X, Qian W, Zhang W, Gao Y, Jin Z, Zhou J, Jin C, Zou L, Qiu L, Li W, Yang J, Hou M, Xiong Y, Zhou H, Du X, Wang X, Peng B. Circulating tumor DNA predicts response in Chinese patients with relapsed or refractory classical hodgkin lymphoma treated with sintilimab. EBioMedicine 2021; 54:102731. [PMID: 32304999 PMCID: PMC7186760 DOI: 10.1016/j.ebiom.2020.102731] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/17/2020] [Accepted: 03/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Blood-based biomarker such as circulating tumor DNA (ctDNA) has emerged as a promising tool for assessment of response to immunotherapy in solid tumors; But in hematological malignances, evidences are still lacking to support its clinical utility. In current study the feasibility of ctDNA for prediction and monitoring of response to anti-PD-1 therapy in Chinese patients with relapsed or refractory classical Hodgkin lymphoma (r/r cHL) was assessed. Methods A total of 192 plasma samples from 75 patients with r/r cHL were collected at baseline and upon therapeutic evaluation. ctDNA were sequenced by targeting panels capturing frequently mutated genes in cHL and other hematological malignancies and then quantified. Analysis on: 1) Gene mutation profile and association of the gene mutations with progression-free survival; 2) Association of pre- and post-treatment ctDNA variant allelic frequencies with clinical outcome; (3) Correlation of the mutated genes with treatment resistance; were performed. Findings Somatic mutations were detected in 50 out of 61 patients by ctDNA genotyping. The mutations of CHD8 was significantly higher in patients with PFS ≥ 12 months. Baseline ctDNA was significantly higher in responders and a decrease of ctDNA ≥ 40% from baseline indicated superior clinical outcome. Strong agreement between ctDNA dynamic and radiographic response change during therapy was observed in majority of the patients. Furthermore, the mutations of B2M, TNFRSF14 and KDM2B were found to be associated with acquired resistance. Interpretation ctDNA could be an informative biomarker for anti-PD-1 immunotherapy in r/r cHL. Funding This work was supported by Innovent Biologics, Eli Lilly and Companyhttps://doi.org/10.13039/501100002852, China National New Drug Innovation Program (2014ZX09201041-001 and 2017ZX09304015), Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Sciences (CIFMS) (2016-I2M-1-001) and National Key Scientific Program Precision Medicine Research Fund of China (2017YFC0909801). The funders had no role in study design, data collection, data analysis, interpretation or writing.
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Affiliation(s)
- Yuankai Shi
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China.
| | - Hang Su
- The 307th Hospital of Chinese People's Liberation Army, Beijing, China
| | - Yongping Song
- The affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Wenqi Jiang
- Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiuhua Sun
- Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wenbin Qian
- The First Affiliated Hospital, Medical School of Zhejiang University, Hangzhou, China
| | - Wei Zhang
- Peking Union Medical College Hospital, Beijing, China
| | - Yuhuan Gao
- Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhengming Jin
- The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianfeng Zhou
- Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuan Jin
- Cancer Hospital Affiliated to Guangzhou Medical University, Guangzhou, China
| | - Liqun Zou
- West China Hospital, Sichuan University, Chengdu, China
| | - Lugui Qiu
- Blood Institute of Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wei Li
- The First Hospital of Jilin University, Changchun, China
| | | | - Ming Hou
- Qilu Hospital of Shandong University, Jinan, China
| | - Yan Xiong
- Innovent Biologics (Suzhou) Co., Ltd, China
| | - Hui Zhou
- Innovent Biologics (Suzhou) Co., Ltd, China
| | | | - Xiong Wang
- Innovent Biologics (Suzhou) Co., Ltd, China
| | - Bo Peng
- Innovent Biologics (Suzhou) Co., Ltd, China
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12
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Song Z, Yang L, Zhou Z, Li P, Wang W, Cheng G, Chen R, Chang L, Zhang Y, Guan Y, Xia X, Yi X, Zhou R, Chen M. Genomic profiles and tumor immune microenvironment of primary lung carcinoma and brain oligo-metastasis. Cell Death Dis 2021; 12:106. [PMID: 33479213 PMCID: PMC7820277 DOI: 10.1038/s41419-021-03410-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
Brain metastasis (BM) is a common malignant event in lung cancer. Here, we recruited 33 lung cancer patients with brain oligo-metastasis to explore the genomic features and tumor immune microenvironment (TIME) of the lung and BM independently. For genomic profiling, targeted sequencing was performed. We found that high-frequent ZFHX3 occurred in the lung (40%) and brain tumor (28%), which might relate to brain metastasis event; the vast majority of patients had lesions-shared mutations in primary tumor and BM, confirming the common clonal events; and EGFR was the most frequently clonal gene in both lung and BM, indicating its driver capability. To characterize TIME status, we also sequenced the T cell receptor (TCR) repertoires and performed immunohistochemistry (IHC) on CD8+ tumor-infiltrating lymphocytes (TILs) and PD-L1 expression in 28 patients who had paired samples. Through the comparison, the TCR clonality of BM was higher than lung tumor, indicating the distinct pattern of the stronger oligoclonal T cell expansion in BM; the primary tumor had a higher TMB than oligo-BM (13.9 vs 8.7 mutations, p = 0.019); CD8 + TILs of BM were significantly lower than lung tumor (10% vs 30%, p = 0.015), revealing the lower level of cytotoxic T cell infiltration; BM showed statistically equivalent level of PD-L1 compared with lung tumor (p = 0.722). We further investigated the potential biomarkers associated with overall survival (OS) after brain surgery. We found that higher TCR clonality was related to prolonged OS in EGFR-treated patients (HR 0.175, p < 0.001) but the worse outcomes in non-EGFR-treated (HR 2.623, p = 0.034). More CD8+ TILs were an independently positive indicator for OS, in EGFR-treated (HR 0.160, p = 0.001) and non-EGFR-treated patients (HR 0.308, p = 0.009). These findings provide a meaningful molecular and clinical understanding of lung carcinoma and brain oligo-metastasis.
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Affiliation(s)
- Zhengbo Song
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China. .,Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
| | - Ling Yang
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Zhipeng Zhou
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Pansong Li
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Wenxian Wang
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China
| | - Guoping Cheng
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.,Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China
| | | | | | - Yiping Zhang
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Rongrong Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Ming Chen
- Department of Radiotherapy, The Cancer Hospital of the University of Chinese Academy of Science (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China.
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13
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Jiang S, Qin Y, Gui L, Liu P, Jiang H, Liu B, Yang J, Yang S, He X, Zhou S, Du X, Yi Y, Lin J, Shi Y. Genomic Alterations and MYD88 MUT Variant Mapping in Patients with Diffuse Large B-Cell Lymphoma and Response to Ibrutinib. Target Oncol 2020; 15:221-230. [PMID: 32239385 DOI: 10.1007/s11523-020-00710-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is a clinically heterogeneous malignancy. Following front-line immunochemotherapy, 30-40% of DLBCL patients develop relapsed or refractory (r/r) disease, which can be treated with ibrutinib. It has been previously reported that MYD88MUT affects the response to ibrutinib in patients with r/r DLBCL. OBJECTIVE Here, we aimed to gather understanding of MYD88MUT in r/r DLBCL patients and to evaluate its influence on response to ibrutinib. PATIENTS AND METHODS In this study, tissue samples from DLBCL patients (n = 212) were retrospectively collected and sequenced by target-capturing panels of either 413 or 112 genes that are frequently mutated in non-Hodgkin's lymphoma. Sixty patients with MYD88 mutations and available clinical information were included for further analysis. RESULTS Seven MYD88MUT variants were identified, L265P (65.0%, n = 39), S219C (13.3%, n = 8), S243N (8.3%, n = 5), P258L (6.7%, n = 4), F283V (1.7%, n = 1), P141R (1.7%, n = 1), and V217F (1.7%, n = 1). One patient had MYD88 amplification. In addition, mutations in PIM1 (67%, n = 40), IGH fusion (48%, n = 29), CD79B (43%, n = 26), KMT2D (30%, n = 18), and TP53 (27%, n = 17) were identified. For patients with L265P, IRF4 (p = 0.011) was frequently mutated. Otherwise, TET2 (p = 0.016), NOTCH2 (p = 0.044), MET (p = 0.037), SOCS1 (p = 0.011), TNFRSF14 (p = 0.011), EZH2 (p = 0.037), and BCL6 (p < 0.001) mutations were associated with MYD88MUT non-L265P variants. The incidence rate of MYD88MUT L265P was significantly higher with central nervous system involvement (p = 0.034). Four out of nine MYD88MUT patients responded to ibrutinib containing treatment, and this included those with MYD88MUT/CD79BWT. CONCLUSIONS This study adds clinical observations with MYD88MUT patients, further helping to understand the genetic features and possible correlation of MYD88MUT with response to ibrutinib.
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Affiliation(s)
- Shiyu Jiang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Yan Qin
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Lin Gui
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Peng Liu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Hongxin Jiang
- Department of Medical Oncology, Suzhou Municipal Hospital, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, Jiangsu Province, China
| | - Biao Liu
- Department of Pathology, Suzhou Municipal Hospital, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215001, Jiangsu Province, China
| | - Jianliang Yang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Sheng Yang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Xiaohui He
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Shengyu Zhou
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Xinhua Du
- Geneplus-Beijing, Beijing, 102206, China
| | - Yuting Yi
- Geneplus-Beijing, Beijing, 102206, China
| | - Jing Lin
- Burning Rock Biotech, Guangzhou, Guangdong, China
| | - Yuankai Shi
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study On Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
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14
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Wang J, Li R, He Y, Yi Y, Wu H, Liang Z. Next-generation sequencing reveals heterogeneous genetic alterations in key signaling pathways of mismatch repair deficient colorectal carcinomas. Mod Pathol 2020; 33:2591-2601. [PMID: 32620917 DOI: 10.1038/s41379-020-0612-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023]
Abstract
Colorectal carcinoma (CRC) with deficient mismatch repair (dMMR) is an etiologically heterogeneous molecular entity. We investigated the genetic profile, focusing on key signaling pathways and molecular diversity of dMMR CRCs. In this study, next-generation sequencing was applied to 156 consecutive dMMR CRCs and 225 randomly selected proficient MMR (pMMR) CRCs diagnosed between July 2015 and December 2019 at Peking Union Medical College Hospital. Genetic alterations and MLH1 promoter hypermethylation (MLH1me+) were analyzed. Among the most frequently mutated genes, RNF43, ARID1A, PIK3CA, ATM, and BRCA2 mutants were enriched in dMMR CRCs, whereas APC and TP53 mutations were enriched in pMMR CRCs. In dMMR group, RNF43, APC, ARID1A, and BRCA2 mutations were largely microsatellite instability events. WNT pathway was commonly altered regardless of MMR status. Compared to pMMR CRCs, dMMR CRCs had remarkably more prevalent PI3K, RTK-RAS, TGFβ, and DNA damage repair pathway alterations and more multiple mutations in WNT and PI3K pathways. Within dMMR tumors, mutual exclusivity occurred between CTNNB1 mutation and APC or RNF43 mutation, while coexistence existed between BRAF and RNF43 mutation, as well as RAS and APC mutation. MLH1me+ dMMR CRCs had significantly more frequent RNF43 mutations but less frequent KRAS, APC, and CTNNB1 mutations comparing to MLH1-unmethylated dMMR CRCs. RNF43/BRAF comutations were detected in MLH1me+ dMMR CRCs, whereas RAS/APC comutations were largely detected in Lynch syndrome-associated cases. RNF43 mutation was independently associated with MLH1me+ rather than BRAF mutations. dMMR CRCs bearing receptor tyrosine kinase fusion demonstrated no additional RTK-RAS mutations, significantly fewer PI3K alterations and more TGFBR2 mutations than other dMMR tumors. Our study revealed that dMMR CRCs had distinctive gene mutation spectra and signaling pathway interaction patterns compared to proficient mismatch repair (pMMR) CRCs, and molecular heterogeneity was evident for these divergent oncogenic pathways. These findings justify the use of individualized therapy targeted to dMMR CRC subgroups.
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Affiliation(s)
- Jing Wang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruiyu Li
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yangzhige He
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuting Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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15
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Jia R, Zhao CH, Li PS, Liu RR, Zhang Y, Chen HE, Chang LP, Gong YH, Guan YF, Yi X, Xu JM. Post-radiation circulating tumor DNA as a prognostic factor in locally advanced esophageal squamous cell carcinoma. Oncol Lett 2020; 21:68. [PMID: 33365079 PMCID: PMC7716704 DOI: 10.3892/ol.2020.12329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a highly malignant and deadly tumor. Radiation therapy is one of the primary treatments for locally advanced ESCC. However, the biomarkers for prognosis of definitive radiation remain undefined. Peripheral blood circulating tumor (ct)DNA provides information of tumor genetic alterations and has been confirmed as a potential non-invasive biomarker for several types of cancer. The present study investigated the clinical implications of ctDNA detection in patients with ESCC and receiving definitive radiation therapy. Patients with locally advanced ESCC were retrospectively recruited. Plasma samples were collected before, during and following radiation therapy. Next-generation sequencing was performed to identify somatic mutations in 180 genes. A total of 69 baseline and post-radiation plasma samples were collected from 25 patients. A total of 59 non-silent single nucleotide variants were present in 33 genes. All pre-radiation and 58.3% (14/24) of post-radiation samples had at least one mutation. Patients with lymph node metastases (LNM) exhibited a higher number of pre-radiation mutations compared with those without LNM. The variables, progression-free survival (PFS) and overall survival (OS) of the patients with one baseline mutation were not significantly different compared with that in patients with more than one baseline mutation. Patients with initial ctDNA-positive post-radiation samples exhibited significantly reduced PFS (P=0.047) and OS (P=0.005) compared with that in patients with ctDNA-negative samples. The post-radiation plasma ctDNA status was an independent prognostic factor from univariate and multivariate analyses. Dynamic monitoring of ctDNA during follow-up was examined. The results indicated that ctDNA was a predictive and prognostic marker in patients with ESCC and receiving definitive radiation therapy, which may guide subsequent treatment.
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Affiliation(s)
- Ru Jia
- Department of Gastrointestinal Oncology, The Fifth Medical Centre, Chinese People's Liberation Army General Hospital, Fengtai, Beijing 100071, P.R. China
| | - Chuan-Hua Zhao
- Department of Gastrointestinal Oncology, The Fifth Medical Centre, Chinese People's Liberation Army General Hospital, Fengtai, Beijing 100071, P.R. China
| | - Pan-Song Li
- Geneplus-Beijing Institute, Changping, Beijing 102206, P.R. China
| | - Rong-Rui Liu
- Department of Gastrointestinal Oncology, The Fifth Medical Centre, Chinese People's Liberation Army General Hospital, Fengtai, Beijing 100071, P.R. China
| | - Yun Zhang
- Department of Gastrointestinal Oncology, The Fifth Medical Centre, Chinese People's Liberation Army General Hospital, Fengtai, Beijing 100071, P.R. China
| | - Hai-E Chen
- Department of Gastrointestinal Oncology, The Fifth Medical Centre, Chinese People's Liberation Army General Hospital, Fengtai, Beijing 100071, P.R. China
| | - Lian-Peng Chang
- Geneplus-Beijing Institute, Changping, Beijing 102206, P.R. China
| | - Yu-Hua Gong
- Geneplus-Beijing Institute, Changping, Beijing 102206, P.R. China
| | - Yan-Fang Guan
- Geneplus-Beijing Institute, Changping, Beijing 102206, P.R. China
| | - Xin Yi
- Geneplus-Beijing Institute, Changping, Beijing 102206, P.R. China
| | - Jian-Ming Xu
- Department of Gastrointestinal Oncology, The Fifth Medical Centre, Chinese People's Liberation Army General Hospital, Fengtai, Beijing 100071, P.R. China
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16
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Li L, Zhou W, Li Q, Li P, Yang L, Xia X, Yi X, Wan D. Tumor-derived mutations in postoperative plasma of colorectal cancer with microsatellite instability. Transl Oncol 2020; 14:100945. [PMID: 33190041 PMCID: PMC7674603 DOI: 10.1016/j.tranon.2020.100945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/22/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022] Open
Abstract
The mutation in postoperative plasma (molecular residues) was an independently prognostic factor in colorectal cancer (CRC). The status of postoperative plasma mutation of microsatellite instability (MSI) CRC has not been systematically examined. In this study, we enrolled 30 MSI and 46 microsatellite stability (MSS) CRCs, and performed next generation sequencing on surgical tissues, postoperative plasma, and plasma during follow-up. Compared with MSS, MSI tumors had dissimilar genomic profiles, higher tumor mutation burden (TMB), and more frameshift mutations. In the postoperative plasma, more MSI CRCs were detected with tumor-derived mutations (77% in MSI vs 33% in MSS, p < 0.001). The numbers of postoperative mutations were proportional to MSI tissues (Spearman r = 0.47, p = 0.023), while not for MSS. More proportion of postoperative plasma samples of MSI CRCs harbored frameshift mutations than MSS (p = 0.007). For the follow-up plasma, 93% (14 out of 15) MSI CRCs harbored tumor-derived mutations; 33% (4/12) MSS were mutation-positive, lower than MSI (p = 0.003). Thus, considering that MSI CRC had extremely distinct mutational characteristics in tumor and postoperative plasma compared with MSS CRC, we propose that the prognostic value of molecular residue identification in postoperative plasma needs to be independently evaluated in MSI and MSS CRCs.
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Affiliation(s)
- Liren Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, P. R. China; Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P. R. China.
| | - Wenhao Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, P. R. China; Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P. R. China.
| | - Qian Li
- Geneplus-Beijing, Beijing 102206, P. R. China.
| | - Pansong Li
- Geneplus-Beijing, Beijing 102206, P. R. China.
| | - Ling Yang
- Geneplus-Beijing, Beijing 102206, P. R. China.
| | - Xuefeng Xia
- Geneplus-Beijing, Beijing 102206, P. R. China.
| | - Xin Yi
- Geneplus-Beijing, Beijing 102206, P. R. China.
| | - Desen Wan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, Guangdong 510060, P. R. China; Department of Colorectal Surgery, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong 510060, P. R. China.
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17
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Yi Z, Rong G, Guan Y, Li J, Chang L, Li H, Liu B, Wang W, Guan X, Ouyang Q, Li L, Zhai J, Li C, Li L, Xia X, Yang L, Qian H, Yi X, Xu B, Ma F. Molecular landscape and efficacy of HER2-targeted therapy in patients with HER2-mutated metastatic breast cancer. NPJ Breast Cancer 2020; 6:59. [PMID: 33145402 PMCID: PMC7603305 DOI: 10.1038/s41523-020-00201-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) protein overexpression or gene amplification is an important predictive biomarker for identifying patients with breast cancer, who may benefit from HER2-targeted therapy. However, little is known about the molecular landscape and efficacy of HER2-targeted therapy in patients with HER2-mutated metastatic breast cancer. We analysed the HER2 mutation features of 1184 patients with invasive breast cancer. In addition, a single-arm, prospective, phase-II study (NCT03412383) of pyrotinib was conducted in patient with metastatic HER2 amplification-negative, mutation-positive breast cancer. Peripheral blood was collected from each patient and circulating tumour DNA (ctDNA) sequencing was performed using a 1021 gene panel. HER2 mutations were detected in 8.9% (105/1184) of patients. The HER2 amplification-positive patients had a higher mutation frequency than the HER2 amplification-negative patients (19.5% vs. 4.8%, P < 0.001). A multivariate Cox regression analysis indicated that patients with HER2 mutations had a shorter progression-free survival (PFS) than HER2 wild-type patients (median PFS 4.7 months vs. 11.0 months, hazard ratio 2.65, 95% confidence interval 1.25-5.65, P = 0.011). Ten HER2 amplification-negative, mutation-positive patients who received pyrotinib monotherapy were ultimately included in the efficacy analysis. The median PFS was 4.9 months. The objective response rate (complete response + partial response) was 40.0% and the clinical benefit rate (complete response + partial response + stable disease over 24 weeks) was 60%. In conclusion, a HER2 gene mutation analysis is potentially useful to identify biomarkers of trastuzumab resistance in HER2 amplification-positive patients. Patients with HER2-mutated, non-amplified metastatic breast cancers may benefit from pyrotinib.
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Affiliation(s)
- Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Guohua Rong
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing, China
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University, 28 West Xianning Road, Xi’an, Shanxi 710048 China
| | - Jin Li
- Geneplus-Beijing Institute, Beijing, China
| | | | - Hui Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Binliang Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Wenna Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Quchang Ouyang
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, 410013 China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Jingtong Zhai
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Lifeng Li
- Geneplus-Beijing Institute, Beijing, China
| | | | - Ling Yang
- Geneplus-Beijing Institute, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing, China
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University, 28 West Xianning Road, Xi’an, Shanxi 710048 China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
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18
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Hu ZY, Liu L, Xie N, Lu J, Liu Z, Tang Y, Wang Y, Yang J, Ouyang Q. Germline PALB2 Mutations in Cancers and Its Distinction From Somatic PALB2 Mutations in Breast Cancers. Front Genet 2020; 11:829. [PMID: 33193564 PMCID: PMC7482549 DOI: 10.3389/fgene.2020.00829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/09/2020] [Indexed: 12/27/2022] Open
Abstract
PALB2 is an important BRCAx candidate for familial breast cancers (FBC). PALB2 pathogenic variants (PVs) may not to conform to "two hit" paradigm. However, a recent study demonstrates that in the majority PALB2 germline mutant breast cancers, the loss of heterozygosity (LOH) and somatic point mutations are the "second hit." This study aimed to investigate the second hits in germline PALB2 mutations in breast cancers. We screened out 28 germline PALB2-mutation carriers among 480 familial cancer patients (including 143 FBC patients) in Geneplus database pool. Of the 143 patients with FBC, 10 had mono-allelic PALB2 germline mutations. All these germline PALB2 mutations were high-risk stop-gain, frameshift, or splicing mutations that concentrated in EX5-EX9 and might led to truncated proteins, severe functional defects and malignant phenotype. The hotspots were c.1057A[3 > 2] and c.3114-1G > A. Other mutations included c.389delA, c.2068C > T, c.2167_2168delAT, c.2629delT and c.2968G > T. Only one FBC patient has PALB2 somatic mutation and two patients had LOH of PALB2. All germline PALB2 mutations were high-risk mutations, whereas the somatic PALB2 mutations were moderate-risk missense mutations. We also distinguished PALB2 "novel mutations" from "reported mutations." In conclusion, germline PALB2 mutation should be put into the context of future screening.
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Affiliation(s)
- Zhe-Yu Hu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Liping Liu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Ning Xie
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Jun Lu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | | | - Yu Tang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Yikai Wang
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Jianbo Yang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Fujian Medical University Union Hospital, Fuzhou, China.,Department of Otolaryngology, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Quchang Ouyang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
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19
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Zhang B, Chen Y, Dai P, Yu H, Ma J, Chen C, Zhang Y, Guan Y, Chen R, Liu T, Wang J, Yang L, Yi X, Xia X, Ma H. Oncogenic mutations within the β3-αC loop of EGFR/ERBB2/BRAF/MAP2K1 predict response to therapies. Mol Genet Genomic Med 2020; 8:e1395. [PMID: 32757330 PMCID: PMC7549570 DOI: 10.1002/mgg3.1395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/31/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
Background β3‐αC loop is a highly conserved structural domain across oncogene families, which is a switch for kinase activity. There have been numerous researches on mutations within β3‐αC loop in EGFR, but relatively less in ERBB2, BRAF, and MAP2K1. In addition, previous studies mainly focus on β3‐αC deletion in EGFR, which is the most common type affecting kinase activity and driving lung cancer. Other mutation types are not well studied. Methods Here we analyzed the profile of β3‐αC loop mutations in a total of 10,000 tumor biopsy and/or ctDNA patient samples using hybridization capture‐based next‐generation sequencing. Results We identified 1616 mutations within β3‐αC loop in this cohort. Most mutations were located in EGFR, with less percentage in ERBB2, BRAF, and MAP2K1. EGFR β3‐αC deletions occurred at a high percentage of 96.7% and were all drug‐relevant. We also detected rare EGFR β3‐αC insertions and point mutations, most of which were related to EGFR TKIs resistance. ERBB2 β3‐αC deletions were only found in breast cancers and sensitive to EGFR/ERBB2 inhibitor. Moreover, BRAF and MAP2K1 mutations within β3‐αC loop also demonstrated drugs relevance. Conclusion Our study showed that oncogenic mutations within the β3‐αC loop of ERBB2, MAP2K1, and BRAF are analogous to that of EGFR, which have profound effect on drug response. Understanding the mutation profile within the β3‐αC loop is critical for targeted therapies.
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Affiliation(s)
- Biao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yongsheng Chen
- Geneplus-Beijing, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Pingping Dai
- Geneplus-Beijing, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Haoda Yu
- Department of Respiratory Medicine, Wuxi People's Hospital, Wuxi, China
| | | | - Chen Chen
- Geneplus-Beijing, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Yan Zhang
- Geneplus-Beijing, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Yanfang Guan
- Geneplus-Beijing, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | | | - Tao Liu
- Geneplus-Beijing, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | | | - Xin Yi
- Geneplus-Beijing, Beijing, China
| | | | - Haitao Ma
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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20
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Chen Q, Ouyang D, Anwar M, Xie N, Wang S, Fan P, Qian L, Chen G, Zhou E, Guo L, Gu X, Ding B, Yang X, Liu L, Deng C, Xiao Z, Li J, Wang Y, Zeng S, Hu J, Zhou W, Qiu B, Wang Z, Weng J, Liu M, Li Y, Tang T, Wang J, Zhang H, Dai B, Tang W, Wu T, Xiao M, Li X, Liu H, Li L, Yi W, Ouyang Q. Effectiveness and Safety of Pyrotinib, and Association of Biomarker With Progression-Free Survival in Patients With HER2-Positive Metastatic Breast Cancer: A Real-World, Multicentre Analysis. Front Oncol 2020; 10:811. [PMID: 32528890 PMCID: PMC7263174 DOI: 10.3389/fonc.2020.00811] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/24/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Pyrotinib, an irreversible pan-ERBB inhibitor, has shown promising antitumour activity, and acceptable tolerability. This research was conducted to evaluate the actual use and effectiveness of pyrotinib in China, therefore, contributed to solve the problem of real-world data scarcity. Methods: In this retrospective study, 168 patients who received pyrotinib treatment for HER2-positive metastatic breast cancer (MBC) in Hunan Province from June 2018 to August 2019 were included. Progression-free survival (PFS), tumor mutation burden (TMB), and drug-related adverse events (AEs) after pyrotinib administration were analyzed. Results: The median PFS (mPFS) time in the 168 participants was 8.07 months. The mPFS times in patients with pyrotinib in second-line therapy (n = 65) and third-or-higher-line therapy (n = 94) were 8.10 months and 7.60 months, respectively. Patients with brain metastases achieved 8.80 months mPFS time. In patients with pyrotinib in third-or-higher-line therapy, patients who had previously used lapatinib still got efficacy but showed a shorter mPFS time (6.43 months) than patients who had not (8.37 months). TMB was measured in 28 patients, K-M curve (P = 0.0024) and Multivariate Cox analysis (P = 0.0176) showed a significant negative association between TMB and PFS. Diarrhea occurred in 98.2% of participants (in any grade) and 19.6% in grade 3-4 AEs. Conclusion: Pyrotinib is highly beneficial to second-or-higher-line patients or HER2-positive MBC patients with brain metastases. Pyrotinib seems to be a feasible strategy both in combination of chemotherapeutic drugs or as a replacement of lapatinib if diseases progressed. TMB could be a potential predictor for evaluating pyrotinib's effectiveness in HER2-positive MBC.
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Affiliation(s)
- Qitong Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Dengjie Ouyang
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.,Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Munawar Anwar
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ning Xie
- Department of Breast Internal Medicine, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Shouman Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Peizhi Fan
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital, Changsha, China
| | - Liyuan Qian
- Department of Breast and Thyroid Surgery, Central South University Third Xiangya Hospital, Changsha, China
| | - Gannong Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Enxiang Zhou
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lei Guo
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaowen Gu
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital, Changsha, China
| | - Boni Ding
- Department of Breast and Thyroid Surgery, Central South University Third Xiangya Hospital, Changsha, China
| | - Xiaohong Yang
- Department of Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Cental South University, Changsha, China
| | - Liping Liu
- Department of Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Cental South University, Changsha, China
| | - Chao Deng
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Zhi Xiao
- Department of Breast Internal Medicine, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jing Li
- Department of Breast Medical Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Cental South University, Changsha, China
| | - Yunqi Wang
- Department of Traditional Chinese Medicine, The Affiliated Cancer Hospital of Xiangya School of Medicine, Cental South University, Changsha, China
| | - Shan Zeng
- Department of Internal Medicine - Oncology, Xiangya Hospital Central South University, Changsha, China
| | - Jinhui Hu
- Department of Breast Surgery, The First Hospital Hunan University of Chinese Medicine, Changsha, China
| | - Wei Zhou
- Department of Breast and Thyroid Surgery, The Affiliated ZhuZhou Hospital of Xiangya School of Medicine Central South University, Zhuzhou, China
| | - Bo Qiu
- Department of Oncology, The Affiliated ZhuZhou Hospital of Xiangya School of Medicine Central South University, Zhuzhou, China
| | - Zhongming Wang
- Department of Breast Surgery, The Third People's Hospital of Yongzhou, Yongzhou, China
| | - Jie Weng
- Department of Oncology, The First People's Hospital of Yueyang, Yueyang, China
| | - Mingwen Liu
- Department of Breast and Thyroid Surgery, The First People's Hospital of Xiangtan City, Xiangtan, China
| | - Yi Li
- Department of Oncology, The Third People's Hospital of Changde, Changde, China
| | - Tiegang Tang
- Department of Oncology, Xiangtan Central Hospital, Xiangtan, China
| | - Jianguo Wang
- Department of General Surgery, Xiangtan Central Hospital, Xiangtan, China
| | - Hui Zhang
- Department of Oncology, Central Hospital of Shaoyang, Shaoyang, China
| | - Bin Dai
- Department of Breast and Thyroid Surgery, Central Hospital of Shaoyang, Shaoyang, China
| | - Wuping Tang
- Department of Breast Surgery, Shaoyang Hospital of Traditional Chinese Medicine, Shaoyang, China
| | - Tao Wu
- Department of Oncology, The First People's Hospital of Changde, Changde, China
| | - Maoliang Xiao
- Department of Oncology, The Third Hospital of Hunan University of Chinese Medicine, Zhuzhou, China
| | - Xiantao Li
- Department of Oncology, The Central Hospital of Yiyang, Yiyang, China
| | - Hailong Liu
- Department of Internal Medicine - Oncology, The First People's Hospital of Chenzhou, Chenzhou, China
| | - Lai Li
- Department of Breast and Thyroid Surgery, The People's Hospital of Xiangtan County, Xiangtan, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Quchang Ouyang
- Department of Breast Internal Medicine, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
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21
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Xie N, Tian C, Wu H, Yang X, Liu L, Li J, Xiao H, Gao J, Lu J, Hu X, Cao M, Shui Z, Tang Y, Wang X, Yang J, Hu ZY, Ouyang Q. FGFR aberrations increase the risk of brain metastases and predict poor prognosis in metastatic breast cancer patients. Ther Adv Med Oncol 2020; 12:1758835920915305. [PMID: 32499836 PMCID: PMC7243401 DOI: 10.1177/1758835920915305] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
Background: The survival status of patients with breast cancer and brain metastasis (BCBM) receiving current treatments is poor. Method: We designed a real-world study to investigate using patients’ clinical and genetic aberrations to forecast the prognoses of BCBM patients. We recruited 146 BCBM patients and analyzed their clinical features to evaluate the overall survival (OS). For genetic testing, 30 BCBM and 165 non-brain-metastatic (BM) metastatic breast cancer (MBC) patients from Hunan Cancer Hospital, and 86 BCBM and 1416 non-BM MBC patients from the Geneplus database who received circulating tumor DNA testing, were compared and analyzed. Results: Ki67 >14% and >3 metastatic brain tumors were significant risk factors associated with poor OS, while chemotherapy and brain radiotherapy were beneficial factors for better OS. Compared with non-BM MBC patients, BCBM patients had more fibroblast growth factor receptor (FGFR) aberrations. The combination of FGFR, TP53 and FLT1 aberrations plus immunohistochemistry HER2-positive were associated with an increased risk of brain metastasis (AUC = 77.13%). FGFR aberration alone was not only a predictive factor (AUC = 67.90%), but also a significant risk factor for poor progression-free survival (Logrank p = 0.029). FGFR1 aberration was more frequent than other FGFR family genes in BCBM patients, and FGFR1 aberration was significantly higher in BCBM patients than non-BM MBC patients. Most FGFR1-amplified MBC patients progressed within 3 months of the late-line (>2 lines) treatment. Conclusion: A group of genetic events, including FGFR, TP53 and FLT1 genetic aberrations, and HER2-positivity, forecasted the occurrence of BM in breast cancers. FGFR genetic aberration alone predicted poor prognosis.
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Affiliation(s)
- Ning Xie
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Can Tian
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Hui Wu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Xiaohong Yang
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Liping Liu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Jing Li
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Huawu Xiao
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Jianxiang Gao
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Jun Lu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Xuming Hu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Min Cao
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Zhengrong Shui
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Yu Tang
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China
| | - Xiao Wang
- ICF, 3 Corporate Square NE., Atlanta, GA, USA
| | - Jianbo Yang
- Department of Otolaryngology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - Zhe-Yu Hu
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, No. 283, Tongzipo Road, Changsha, 410013, P.R. China
| | - Quchang Ouyang
- Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, No. 283, Tongzipo Road, Changsha, 410013, P.R. China
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22
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Wang S, Chen R, Tang Y, Yu Y, Fang Y, Huang H, Wu D, Fang H, Bai Y, Sun C, Yu A, Fan Q, Gu D, Yi X, Li N. Comprehensive Genomic Profiling of Rare Tumors: Routes to Targeted Therapies. Front Oncol 2020; 10:536. [PMID: 32373528 PMCID: PMC7186305 DOI: 10.3389/fonc.2020.00536] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/25/2020] [Indexed: 01/24/2023] Open
Abstract
Comprehensive Genomic Profiling may be informative for novel treatment strategies and to improve outcomes for patients with rare tumors. This study aims to discover opportunities for use of targeted therapies already approved for routine use in patients with rare tumors. Solid tumors with an incidence lower than 2.5/100,000 per year was defined as rare tumors in China after comprehensive analysis based on epidemiological data and current availability of standardized treatment. Genomic data of rare tumors from the public database cBioPortal were compared with that of the Chinese population for targetable genomic alterations (TGAs). TGAs were defined as mutations of ALK, ATM, BRAF, BRCA1, BRCA2, CDKN2A, EGFR, ERBB2, FGFR1,2,3, KIT, MET, NF1, NTRK1,2,3, PIK3CA, PTEN, RET, and ROS1 with level 1 to 4 of evidence according to the OncoKB knowledge database. Genomic data of 4,901 patients covering 63 subtypes of rare tumor from cBioPortal were used as the western cohort. The Chinese cohort was comprised of next generation sequencing (NGS) data of 1,312 patients from across China covering 67 subtypes. Forty-one subtypes were common between the two cohorts. The accumulative prevalence of TGAs was 20.40% (1000/4901) in cBioPortal cohort, and 53.43% (701/1312) in Chinese cohort (p < 0.001). Among those 41 overlapping subtypes, it was still significantly higher in Chinese cohort compared with cBioPortal cohort (54.1%% vs. 26.1%, p < 0.001). Generally, targetable mutations in BRAF, BRCA2, CDKN2A, EGFR, ERBB2, KIT, MET, NF1, ROS1 were ≥3 times more frequent in Chinese cohort compared with that of the cBioPortal cohort. Cancer of unknown primary tumor type, gastrointestinal stromal tumor, gallbladder cancer, intrahepatic cholangiocarcinoma, and sarcomatoid carcinoma of the lung were the top 5 tumor types with the highest number of TGAs per tumor. The incidence of TGAs in rare tumors was substantial worldwide and was even higher in our Chinese rare tumor population. Comprehensive genomic profiling may offer novel treatment paradigms to address the limited options for patients with rare tumors.
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Affiliation(s)
- Shuhang Wang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rongrong Chen
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Yu Tang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Yu
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Fang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huiyao Huang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dawei Wu
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hong Fang
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Bai
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Sun
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Anqi Yu
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Fan
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dejian Gu
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Xin Yi
- Department of Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Ning Li
- Clinical Cancer Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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23
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Lan J, Lu Y, Guan Y, Chang L, Yu Z, Qian H. Identification of circulating tumor DNA using a targeted 545-gene next generation sequencing panel in patients with gastric cancer. Oncol Lett 2020; 19:2251-2257. [PMID: 32194723 PMCID: PMC7039113 DOI: 10.3892/ol.2020.11305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 06/05/2019] [Indexed: 12/26/2022] Open
Abstract
Gastric cancer (GC) is characterized by unique genetic aberrations. Some of these mutations may be used to predict tumor prognosis or to guide patient therapy. Cell-free circulating tumor DNA (ctDNA) has been considered a promising alternative to biopsy to identify genome aberrations. However, no standardized methods to detect ctDNA variations in patients with GC are currently available. In the present study, the targeted sequencing of 545 genes was used to identify somatic alterations in tissues and matched plasma samples of nine patients with GC. Driver gene mutations were detected in matched tissues and plasma ctDNA. The mutated reads concordance rate of ctDNA in GC tissues with matched tissues was 45%. A true positive copy number gain of human epidermal growth factor receptor 2 in plasma from patients with GC was identified. Furthermore, the ctDNA fraction in plasma cell-free DNA (cfDNA) was positively correlated with metastasis lymph node number and with lactate dehydrogenase level. In conclusion, results from the present study suggested that targeted sequencing of plasma ctDNA may be considered a potential option for the clinical monitoring of GC.
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Affiliation(s)
- Jing Lan
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Yaping Lu
- Research and Development Department, Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Yanfang Guan
- Research and Development Department, Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Lianpeng Chang
- Research and Development Department, Geneplus-Beijing Institute, Beijing 102206, P.R. China
| | - Zhengyuan Yu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
| | - Haixin Qian
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, P.R. China
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24
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Xu Y, She Y, Li Y, Li H, Jia Z, Jiang G, Liang L, Duan L. Multi-omics analysis at epigenomics and transcriptomics levels reveals prognostic subtypes of lung squamous cell carcinoma. Biomed Pharmacother 2020; 125:109859. [PMID: 32036209 DOI: 10.1016/j.biopha.2020.109859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/05/2019] [Accepted: 12/23/2019] [Indexed: 01/26/2023] Open
Abstract
In this study, we identified prognostic biomarkers for lung squamous cell carcinoma (LUSC) by integrating multiple sets of DNA copy number variants (CNV) and methylation variant (MET) data, and performing qPCR and immunohistochemical identification. We examined the expression of CNV and MET in 368 LUSC patients. Gene expression associated with DNA copy number or DNA methylation was identified and four LUSC gene subtypes were defined based on these correlations. The prognosis overall survival (OS) of the iC1 subtype was significantly lower than that in the iC2 and iC4 subtypes. We assessed the immune scores of each subtype and found that the six immune cell scores of the iC3 subtype were significantly higher than the other subtypes (p < 0.01). Three genes associated with prognosis, NFE2L2, ASAH2, and RIMBP2, were identified by comparing the expression of CNV and MET in subtypes. Analysis of mutational differences between subtypes revealed a group of genes with significant mutations between the iC1 and iC4 subtypes. The number of mutations in the NFE2L2 gene in LUSC was significantly higher than that in other genes, and the gene was prognostic. The number of mutations was significantly higher in the best iC4 subtype than the iC1 subtype with the worst prognosis; the other two genes, ASAH2 and RIMBP2, were only found in the worst prognosis of the iC1 subtype. This comprehensive multi-omics analysis of genomics, epigenomics, and transcriptomics data provides new insights into the molecular mechanisms of LUSC and may be helpful in identifying biomolecular markers for early disease diagnosis.
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Affiliation(s)
- Yong Xu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Yunlang She
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China
| | - Yaqiang Li
- Department of Orthopaedic Surgery, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Hao Li
- Research Institute of Plastic Surgery, Weifang Medical College, Weifang, Shandong, PR China
| | - Zihao Jia
- Research Institute of Plastic Surgery, Weifang Medical College, Weifang, Shandong, PR China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China.
| | - Leilei Liang
- Department of Surgery, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China.
| | - Liang Duan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, PR China.
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25
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Tang C, Lee WC, Reuben A, Chang L, Tran H, Little L, Gumbs C, Wargo J, Futreal A, Liao Z, Xia X, Yi X, Swisher SG, Heymach JV, Gomez D, Zhang J. Immune and Circulating Tumor DNA Profiling After Radiation Treatment for Oligometastatic Non-Small Cell Lung Cancer: Translational Correlatives from a Mature Randomized Phase II Trial. Int J Radiat Oncol Biol Phys 2020; 106:349-357. [DOI: 10.1016/j.ijrobp.2019.10.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/02/2019] [Accepted: 10/10/2019] [Indexed: 12/31/2022]
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26
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Tang Y, Li J, Xie N, Yang X, Liu L, Wu H, Tian C, He Y, Wang X, He Q, Hu ZY, Ouyang Q. PIK3CA gene mutations in the helical domain correlate with high tumor mutation burden and poor prognosis in metastatic breast carcinomas with late-line therapies. Aging (Albany NY) 2020; 12:1577-1590. [PMID: 31980592 PMCID: PMC7053638 DOI: 10.18632/aging.102701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/27/2019] [Indexed: 12/15/2022]
Abstract
Nearly half of metastatic breast cancers (MBC) have genetic aberrations in the PI3K/AKT pathway. To investigate the distinct effect of these aberrations on MBC, 193 MBC patients who progressed after the early line (≤2) salvage treatment voluntarily received next generation sequencing (NGS) for a panel of 1,021 genes. 93 (48%) patients had genetic aberrations in the PI3K/AKT pathway. The number of patients with PIK3CA mutations in kinase domain (KD), helical domain (HD) and other domain (OD), were 36 (18.7%), 26 (13.5%), 10 (5.2%), respectively. 21 (10.9%) patients had mutations in PI3K/AKT pathway genes other than PIK3CA (P/A). Compared to PI3K/AKT-wild type (WT) patients, PIK3CA-HD patients had a significantly shorter progression-free survival (PFS) (Logrank p-value < 0.0001). PIK3CA-KD, PIK3CA-OD and other P/A mutations showed similar PFS to WT patients (Logrank p-value = 0.63). PIK3CA-HD patients had a distinct ctDNA mutation profile to patients with other PI3K/AKT mutations. PIK3CA-HD patients had a higher rate of FGFR and NF1 aberrations. In addition, more PIK3CA-HD carriers were TMB-high. Cox regression analyses suggested that PIK3CA-HD mutations, FGFR aberrations and high TMB were all significant risk factors for poor PFS. In conclusion, future research needs to focus more on the treatment strategies targeting PIK3CA-HD mutations.
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Affiliation(s)
- Yu Tang
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | - Jing Li
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | - Ning Xie
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | - Xiaohong Yang
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | - Liping Liu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | - Hui Wu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | - Can Tian
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | - Ying He
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,The 2nd Department of Breast Cancer Surgical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | | | - Qiongzhi He
- Beijing Geneplus Institute, Beijing 102200, China
| | - Zhe-Yu Hu
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
| | - Quchang Ouyang
- The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Hunan Cancer Hospital, Changsha 410000, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410000, China
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27
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Geeurickx E, Hendrix A. Targets, pitfalls and reference materials for liquid biopsy tests in cancer diagnostics. Mol Aspects Med 2019; 72:100828. [PMID: 31711714 DOI: 10.1016/j.mam.2019.10.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/12/2022]
Abstract
Assessment of cell free DNA (cfDNA) and RNA (cfRNA), circulating tumor cells (CTC) and extracellular vesicles (EV) in blood or other bodily fluids can enable early cancer detection, tumor dynamics assessment, minimal residual disease detection and therapy monitoring. However, few liquid biopsy tests progress towards clinical application because results are often discordant and challenging to reproduce. Reproducibility can be enhanced by the development and implementation of standard operating procedures and reference materials to identify and correct for pre-analytical variables. In this review we elaborate on the technological considerations, pre-analytical variables and the use and availability of reference materials for the assessment of liquid biopsy targets in blood and highlight initiatives towards the standardization of liquid biopsy testing.
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Affiliation(s)
- Edward Geeurickx
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, 9000, Ghent, Belgium; Cancer Research Institute Ghent, 9000, Ghent, Belgium
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and Repair, Ghent University, 9000, Ghent, Belgium; Cancer Research Institute Ghent, 9000, Ghent, Belgium.
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28
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Zhuo M, Guan Y, Yang X, Hong L, Wang Y, Li Z, Chen R, Abbas HA, Chang L, Gong Y, Wu N, Zhong J, Chen W, Chen H, Dong Z, Zhu X, Li J, Wang Y, An T, Wu M, Wang Z, Wang J, Roarty EB, Rinsurongkawong W, Lewis J, Roth JA, Swisher SG, Lee JJ, Heymach JV, Wistuba II, Kalhor N, Yang L, Yi X, Futreal PA, Glisson BS, Xia X, Zhang J, Zhao J. The Prognostic and Therapeutic Role of Genomic Subtyping by Sequencing Tumor or Cell-Free DNA in Pulmonary Large-Cell Neuroendocrine Carcinoma. Clin Cancer Res 2019; 26:892-901. [PMID: 31694833 DOI: 10.1158/1078-0432.ccr-19-0556] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/20/2019] [Accepted: 10/28/2019] [Indexed: 12/15/2022]
Abstract
PURPOSE The optimal systemic treatment for pulmonary large-cell neuroendocrine carcinoma (LCNEC) is still under debate. Previous studies showed that LCNEC with different genomic characteristics might respond differently to different chemotherapy regimens. In this study, we sought to investigate genomic subtyping using cell-free DNA (cfDNA) analysis in advanced LCNEC and assess its potential prognostic and predictive value. EXPERIMENTAL DESIGN Tumor DNA and cfDNA from 63 patients with LCNEC were analyzed by target-captured sequencing. Survival and response analyses were applied to 54 patients with advanced stage incurable disease who received first-line chemotherapy. RESULTS The mutation landscape of frequently mutated cancer genes in LCNEC from cfDNA closely resembled that from tumor DNA, which led to a 90% concordance in genomic subtyping. The 63 patients with LCNEC were classified into small-cell lung cancer (SCLC)-like and non-small cell lung cancer (NSCLC)-like LCNEC based on corresponding genomic features derived from tumor DNA and/or cfDNA. Overall, patients with SCLC-like LCNEC had a shorter overall survival than those with NSCLC-like LCNEC despite higher response rate (RR) to chemotherapy. Furthermore, treatment with etoposide-platinum was associated with superior response and survival in SCLC-like LCNEC compared with pemetrexed-platinum and gemcitabine/taxane-platinum doublets, while treatment with gemcitabine/taxane-platinum led to a shorter survival compared with etoposide-platinum or pemetrexed-platinum in patients with NSCLC-like LCNEC. CONCLUSIONS Genomic subtyping has potential in prognostication and therapeutic decision-making for patients with LCNEC and cfDNA analysis may be a reliable alternative for genomic profiling of LCNEC.
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Affiliation(s)
- Minglei Zhuo
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yanfang Guan
- GenePlus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xue Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Lingzhi Hong
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuqi Wang
- GenePlus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Zhongwu Li
- Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Runzhe Chen
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hussein A Abbas
- Hematology and Oncology Fellowship Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lianpeng Chang
- GenePlus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Yuhua Gong
- GenePlus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Nan Wu
- Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jia Zhong
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | | | - Hanxiao Chen
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zhi Dong
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiang Zhu
- Department of Pathology, School of Basic Medical Sciences, Third Hospital, Peking University Health Science Center, Beijing, China
| | - Jianjie Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuyan Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Tongtong An
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Meina Wu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ziping Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Emily B Roarty
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Waree Rinsurongkawong
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeff Lewis
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jack A Roth
- Department of Thoracic Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen G Swisher
- Department of Thoracic Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ling Yang
- GenePlus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Xin Yi
- GenePlus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China.,Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bonnie S Glisson
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | | | - Jianjun Zhang
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Zhao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital & Institute, Beijing, China.
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29
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Zhang L, Liu Z, Li J, Huang T, Wang Y, Chang L, Zheng W, Ma Y, Chen F, Gong X, Yuan Q, Teaw S, Fang X, Song T, Huo L, Li X, Xia X, Liu Z, Wu J. Genomic analysis of primary and recurrent gliomas reveals clinical outcome related molecular features. Sci Rep 2019; 9:16058. [PMID: 31690770 PMCID: PMC6831607 DOI: 10.1038/s41598-019-52515-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Tremendous efforts have been made to explore biomarkers for classification and grading on gliomas. The goal of this study was to identify more molecular features that are associated with clinical outcomes by comparing the genomic profiles of primary and recurrent gliomas and determine potential recurrence leading factors that are significantly enriched in relapse tumors. Hybrid capture based next generation sequencing (NGS) analysis was performed on 64 primary and 17 recurrent glioma biopsies. Copy number variation (CNV) was more frequent in recurrent tumors and CDKN2A/B loss was significantly enriched. In addition, overall mutations in cell cycle pathway are more common in relapse tumors. The patterns of gene sets, including IDH1/TERT and IDH1/TP53 exhibited significant difference between the groups. Survival analysis uncovered the worse disease-free survival (DFS) and overall survival (OS) associated with altered copy number and excessive activation of CELL CYCLE pathway. High Tumor Mutation Burden (TMB) was also a biomarker with great potential for poor prognosis. The assessment of genomic characteristics in primary versus recurrent gliomas aids the discovery of potential predictive biomarkers. The prognostic value of TMB in gliomas was raised for the first time.
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Affiliation(s)
- Longbo Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States
| | - Zhiqiang Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jin Li
- Geneplus-Beijing, Beijing, China
| | - Tianxiang Huang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ying Wang
- Department of Emergency, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | | | | | - Yujie Ma
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Fenghua Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuan Gong
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianying Yuan
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, United States
| | - Shannon Teaw
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States
| | - Xinqi Fang
- Xiangya Medical School, Central South University, Changsha, Hunan, China
| | - Tao Song
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lei Huo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xi Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | | | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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30
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Xing P, Han X, Wang S, Liu Y, Yang S, Hao X, Wang Y, Liu P, Li J, Wang L, Chang L, Guan Y, Zhang Z, Wu D, Yao J, Yi X, Shi Y. Co-mutational assessment of circulating tumour DNA (ctDNA) during osimertinib treatment for T790M mutant lung cancer. J Cell Mol Med 2019; 23:6812-6821. [PMID: 31393074 PMCID: PMC6787503 DOI: 10.1111/jcmm.14565] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/19/2019] [Accepted: 06/23/2019] [Indexed: 02/06/2023] Open
Abstract
Osimertinib is designed to target the secondary resistant EGFR T790M mutant and has shown outstanding clinical efficacy. However, the prognostic prediction of osimertinib patients is a big problem in clinical practice. The resistance mechanism of osimertinib is also not fully understood. NGS and a 1021 gene capture panel were used to analyse the somatic mutation profile of thirty‐six lung adenocarcinoma patients' serial ctDNA samples. Progression‐free survival of subgroup patients is analysed. Patients harbour TP53 mutations and patients with higher TMB value in pre‐treatment samples showed a shorter PFS. Moreover, compared to CT evaluation, ctDNA changes generally correlated with treatment responses in most patients. Novel resistance mechanisms are discovered including EGFR mutations and alternative activation pathway. Our results implied a broad potential of ctDNA as an adjuvant tool in practical clinical management of NSCLC patients. ctDNA could help with clinical practice during osimertinib treatment, regarding monitoring tumour response, detecting development of heterogeneity, identifying potential resistance mechanisms, predicting treatment efficacy and patient outcome.
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Affiliation(s)
- Puyuan Xing
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohong Han
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Clinical Laboratory, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sha Wang
- Geneplus-Beijing, Beijing, China
| | - Yutao Liu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sheng Yang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuezhi Hao
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Wang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Liu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junling Li
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Wang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | - Zhishang Zhang
- Department of Clinical Laboratory, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Di Wu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiarui Yao
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, China
| | - Yuankai Shi
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Ma F, Guan Y, Yi Z, Chang L, Li Q, Chen S, Zhu W, Guan X, Li C, Qian H, Xia X, Yang L, Zhang J, Husain H, Liao Z, Futreal A, Huang J, Yi X, Xu B. Assessing tumor heterogeneity using ctDNA to predict and monitor therapeutic response in metastatic breast cancer. Int J Cancer 2019; 146:1359-1368. [PMID: 31241775 DOI: 10.1002/ijc.32536] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/18/2019] [Accepted: 06/12/2019] [Indexed: 12/12/2022]
Abstract
Tumor heterogeneity was associated with treatment outcome of metastatic cancers but few studies have examined whether tumor heterogeneity in circulating tumor DNA (ctDNA) can be used to predict treatment outcome. ctDNA analysis was performed in 37 HER2-positive metastatic breast cancer patients treated with pyrotinib. Patients with high tumor heterogeneity had significantly worse PFS outcomes, with a median PFS of 30.0 weeks vs. 60.0 weeks for patients with low tumor heterogeneity (hazard ratio [HR], 2.9; p = 0.02). Patients with trunk resistance mutations receiving pyrotinib monotherapy had worse outcomes (HR, 4.5; p = 0.03), with a median PFS of 7.8 weeks vs. 27.4 weeks for those with branch resistance mutations or without any resistance mutations in baseline ctDNA. Longitudinal monitoring of 21 patients during treatment showed that the molecular tumor burden index ([mTBI] a measure of the percentage of ctDNA in samples) was positively correlated with tumor size as evaluated by computed tomography (p < 0.0001, Pearson r = 0.52) and detected disease progression 8-16 weeks earlier. Our current findings suggested that ctDNA could be used to assess tumor heterogeneity and predict treatment outcomes. Furthermore, the mTBI is better for assessing therapeutic response than single gene mutations and might supplement the current therapeutic response evaluation system.
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Affiliation(s)
- Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanfang Guan
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lianpeng Chang
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Qiao Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Chen
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenjie Zhu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuefeng Xia
- Houston Methodist Research Institute, Weill Cornell School of Medicine, Houston, TX
| | - Ling Yang
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX.,Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hatim Husain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Zhongxing Liao
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Yi
- Geneplus-Beijing, Beijing, China.,Geneplus-Beijing Institute, Beijing, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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32
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Wang J, Yi Y, Xiao Y, Dong L, Liang L, Teng L, Ying JM, Lu T, Liu Y, Guan Y, Pang J, Zhou L, Lu J, Zhang Z, Liu X, Liang X, Zeng X, Yi X, Zhou W, Xia X, Yang L, Zhang J, Kopetz S, Futreal PA, Wu H, Liang Z. Prevalence of recurrent oncogenic fusion in mismatch repair-deficient colorectal carcinoma with hypermethylated MLH1 and wild-type BRAF and KRAS. Mod Pathol 2019; 32:1053-1064. [PMID: 30723297 DOI: 10.1038/s41379-019-0212-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 12/31/2018] [Accepted: 12/31/2018] [Indexed: 01/04/2023]
Abstract
Oncogenic fusions are rare in colorectal carcinomas, but may be important for prognosis and therapy. An effective strategy for screening targetable oncogenic fusions in colorectal carcinomas is needed. Here, we investigate molecular genetic alterations in colorectal carcinomas based on their DNA mismatch repair status, and to effectively screen for targetable oncogenic fusions in colorectal carcinomas. In this retrospective study, the initial cohort included 125 consecutive mismatch repair-deficient and 238 randomly selected mismatch repair-proficient colorectal carcinomas diagnosed between July 2015 and December 2017 at Peking Union Medical College Hospital. Targeted sequencing was performed. MLH1 promoter hypermethylation analysis was further employed for subgrouping dMMR colorectal carcinomas. Clinicopathological characteristics, molecular features, and survival outcome of colorectal carcinomas harboring oncogenic fusions were assessed. A multicenter cohort comprised of 227 colorectal carcinomas with dual loss of MLH1/PMS2 was used to validate the efficacy of the proposed screening strategy for oncogenic fusions. Of the 363 patients in the initial cohort, 11(3.0%) harbored oncogenic fusions and were all mismatch repair-deficient colorectal carcinomas with hypermethylated MLH1 and wild-type BRAF and KRAS, comprising 55% (11/20) of this subgroup. These patients with oncogenic fusions showed poorer 3-year cancer-specific survival compared with other Stage III/IV mismatch repair-deficient colorectal carcinoma patients (40% vs. 97%), and significantly higher CD274(PD-L1) expression in tumor cells compared with other dMMR colorectal carcinoma patients (46% vs. 6.1%, P < 0.001). An easy-to-perform and cost-efficient strategy for screening targetable fusions was proposed based on the current molecular testing algorithms for colorectal carcinomas, and validated in an independent multicenter cohort. In conclusion, oncogenic fusions were highly enriched and frequently detected in mismatch repair-deficient colorectal carcinomas with MLH1 hypermethylation and wild-type BRAF and KRAS, and were associated with poor prognosis and high tumor CD274(PD-L1) expression.
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Affiliation(s)
- Jing Wang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuting Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Yi Xiao
- Department of Surgery, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Dong
- Departments of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Guangzhou, Guangdong, China
| | - Lianghong Teng
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Jian Ming Ying
- Departments of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Lu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanyuan Liu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Junyi Pang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lianrui Zhou
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junliang Lu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiwen Zhang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoding Liu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaolong Liang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuan Zeng
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Weixun Zhou
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xuefeng Xia
- Houston Methodist Research Institute, Houston, TX, USA
| | - Ling Yang
- Geneplus-Beijing Institute, Beijing, China
| | - Jianjun Zhang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Huanwen Wu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhiyong Liang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Yi Z, Ma F, Liu B, Guan X, Li L, Li C, Qian H, Xu B. Everolimus in hormone receptor-positive metastatic breast cancer: PIK3CA mutation H1047R was a potential efficacy biomarker in a retrospective study. BMC Cancer 2019; 19:442. [PMID: 31088410 PMCID: PMC6515626 DOI: 10.1186/s12885-019-5668-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/01/2019] [Indexed: 02/08/2023] Open
Abstract
Background Everolimus, an inhibitor of mammalian target of rapamycin (mTOR), has been shown to increase the efficacy of endocrine therapies in hormone receptor (HR)-positive metastatic breast cancer. However, because breast cancer is a highly heterogeneous disease, the responses of different patients to everolimus may vary. Therefore, we performed this study to better select patients who will benefit most from or be resistant to everolimus. Methods Patients with HR-positive breast cancer who were treated with everolimus at the Cancer Hospital, Chinese Academy of Medical Sciences from February 2014 to March 2017 were enrolled in the present study. Mutations in ctDNA were assayed in 1021 tumor-related genes via gene panel target capture-based next-generation sequencing. Results In total, 120 patients with metastatic breast cancer who were treated with everolimus were enrolled in the present study. The median progression-free survival (PFS) of all patients was 5.1 months (95% confidence interval [CI] 3.9–6.3 months). No difference in survival was observed between patients who received endocrine drugs used in previous treatment regimens and patients who did not receive these drugs (median PFS 5.2 and 5.1 months, respectively, p > 0.05). Additionally, we did not find any difference in outcomes between patients who had primary resistance to previously used endocrine drugs and patients who had nonprimary resistance to previous treatments (p > 0.05). Multivariate analysis showed that < 3 metastatic sites, < 2 lines of previous endocrine therapy, < 2 lines of previous chemotherapy, and treatment with everolimus combined with fulvestrant were associated with improved survival (p < 0.05). Sixteen patients underwent ctDNA analysis before everolimus treatment. The frequency of PIK3CA gene mutations was 62.5%, and H1047R was the most frequently detected mutation. Patients with the PIK3CA/H1047R mutation had longer PFS than patients with wild-type or other mutant forms of PIK3CA, and the median PFS in these two groups of patients was 8.8 and 4.1 months, respectively (p < 0.05). Conclusions Our data suggest that patients who receive more lines of chemotherapy or endocrine therapy are less likely to benefit from everolimus. For everolimus combination therapy, we can even select endocrine drugs that gave rise to primary resistance in previous treatments. Additionally, the PIK3CA/H1047R mutation may be a potential biomarker of sensitivity to everolimus. Electronic supplementary material The online version of this article (10.1186/s12885-019-5668-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zongbi Yi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
| | - Binliang Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
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Zhou D, Ouyang Q, Liu L, Liu J, Tang Y, Xiao M, Wang Y, He Q, Hu ZY. Chemotherapy Modulates Endocrine Therapy-Related Resistance Mutations in Metastatic Breast Cancer. Transl Oncol 2019; 12:764-774. [PMID: 30893632 PMCID: PMC6423490 DOI: 10.1016/j.tranon.2019.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 01/07/2023] Open
Abstract
PURPOSE: Accumulation of PIK3CA, ESR1, and GATA3 mutations results in resistance to endocrine therapy in breast cancer patients; however, the response of these genes to chemotherapy is unclear. Therefore, we sought to evaluate the genetic response of circulating tumor DNA (ctDNA) to chemotherapy in metastatic breast cancer patients. METHODS: The mutation frequency of 1021 genes was examined prior to chemotherapy in ctDNA of 44 estrogen receptor–positive metastatic breast cancer patients. These genes were evaluated again in a subset of patients (n=24) following chemotherapy. Mutation frequency was defined as the percentage of mutations found in ctDNA compared to total cell-free DNA. RESULTS: Prior to chemotherapy, PIK3CA was the most commonly mutated gene, with mutation found in 22 of the metastatic breast cancer patients. Following chemotherapy, 16 patients exhibited progressive disease (PD), and 8 patients experienced no progression (non-PD). PIK3CA mutation frequency increased in 56.25% (9/16) of the PD patients but decreased in 62.5% (5/8) of the non-PD patients. As a result, more PD patients exhibited increased PIK3CA mutation frequency than non-PD patients (56.25% vs 0%, P=.002). Further, ESR1 and GATA3 mutations correlated with PIK3CA mutation. Interestingly, patients receiving the mTOR inhibitor everolimus exhibited a lower progression rate (0% vs 62.5%, P=.001), and the combination of everolimus and chemotherapy effectively suppressed PIK3CA, ESR1, and GATA3 gene mutations. CONCLUSION: Together, these results suggest that mTOR inhibition may be a useful chemotherapy adjuvant to suppress chemotherapy-induced gene mutations that render tumors resistant to endocrine therapy in metastatic breast cancer patients with PD.
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Affiliation(s)
- Dabo Zhou
- The Affiliated Cancer Hospital of Xiangya Medical School, Central South University / Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Quchang Ouyang
- The Affiliated Cancer Hospital of Xiangya Medical School, Central South University / Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China.
| | - Liping Liu
- The Affiliated Cancer Hospital of Xiangya Medical School, Central South University / Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Jingyu Liu
- The Affiliated Cancer Hospital of Xiangya Medical School, Central South University / Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Yu Tang
- The Affiliated Cancer Hospital of Xiangya Medical School, Central South University / Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Mengjia Xiao
- The Affiliated Cancer Hospital of Xiangya Medical School, Central South University / Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Yikai Wang
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, 33022, USA
| | - Qiongzhi He
- Geneplus Beijing Institute, Beijing 102206, China
| | - Zhe-Yu Hu
- The Affiliated Cancer Hospital of Xiangya Medical School, Central South University / Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, 410013, China; Department of Breast Cancer Medical Oncology, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China.
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The cornerstone of integrating circulating tumor DNA into cancer management. Biochim Biophys Acta Rev Cancer 2018; 1871:1-11. [PMID: 30419316 DOI: 10.1016/j.bbcan.2018.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/23/2018] [Accepted: 11/07/2018] [Indexed: 12/26/2022]
Abstract
Recent circulating tumor DNA (ctDNA) research has demonstrated its potential as a non-invasive biomarker for cancer. However, the deployment of ctDNA assays in routine clinical practice remains challenging owing to variability in analytical approaches and the assessment of clinical significance. A well-developed, analytically valid ctDNA assay is a prerequisite for integrating ctDNA into cancer management, and an appropriate analytical technology is crucial for the development of a ctDNA assay. Other determinants including pre-analytical procedures, test validation, internal quality control (IQC), and continual proficiency testing (PT) are also important for the accuracy of ctDNA assays. In the present review, we will focus on the most widely used ctDNA detection technologies and the key quality management measures used to assure the accuracy of ctDNA assays. The aim of this review is to provide useful information for technology selection during ctDNA assay development and assure a reliable test result in clinical practice.
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Hu ZY, Xie N, Tian C, Yang X, Liu L, Li J, Xiao H, Wu H, Lu J, Gao J, Hu X, Cao M, Shui Z, Xiao M, Tang Y, He Q, Chang L, Xia X, Yi X, Liao Q, Ouyang Q. Identifying Circulating Tumor DNA Mutation Profiles in Metastatic Breast Cancer Patients with Multiline Resistance. EBioMedicine 2018; 32:111-118. [PMID: 29807833 PMCID: PMC6020712 DOI: 10.1016/j.ebiom.2018.05.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/10/2018] [Accepted: 05/10/2018] [Indexed: 12/27/2022] Open
Abstract
Purpose In cancer patients, tumor gene mutations contribute to drug resistance and treatment failure. In patients with metastatic breast cancer (MBC), these mutations increase after multiline treatment, thereby decreasing treatment efficiency. The aim of this study was to evaluate gene mutation patterns in MBC patients to predict drug resistance and disease progression. Method A total of 68 MBC patients who had received multiline treatment were recruited. Circulating tumor DNA (ctDNA) mutations were evaluated and compared among hormone receptor (HR)/human epidermal growth factor receptor 2 (HER2) subgroups. Results The baseline gene mutation pattern (at the time of recruitment) varied among HR/HER2 subtypes. BRCA1 and MED12 were frequently mutated in triple negative breast cancer (TNBC) patients, PIK3CA and FAT1 mutations were frequent in HR+ patients, and PIK3CA and ERBB2 mutations were frequent in HER2+ patients. Gene mutation patterns also varied in patients who progressed within either 3 months or 3–6 months of chemotherapy treatment. For example, in HR+ patients who progressed within 3 months of treatment, the frequency of TERT mutations significantly increased. Other related mutations included FAT1 and NOTCH4. In HR+ patients who progressed within 3–6 months, PIK3CA, TP53, MLL3, ERBB2, NOTCH2, and ERS1 were the candidate mutations. This suggests that different mechanisms underlie disease progression at different times after treatment initiation. In the COX model, the ctDNA TP53 + PIK3CA gene mutation pattern successfully predicted progression within 6 months. Conclusion ctDNA gene mutation profiles differed among HR/HER2 subtypes of MBC patients. By identifying mutations associated with treatment resistance, we hope to improve therapy selection for MBC patients who received multiline treatment. Doctors felt difficult to design effective regimen for MBC patients after multi-line treatment. ctDNA testing provide potential treatment targets and reflect treatment response of tumors. ctDNA gene mutation pattern varies among four HR/HER2 subgroups. The gene mutation patterns also varied between resistant patients and sensitive patients. In COX model, ctDNA gene mutation pattern could successfully predict progression within 6 months.
In this study, we clarified the baseline ctDNA mutation pattern for metastatic breast cancer patients. We also selected out treatment-resistance related mutations by ctDNA testing. Here, we showed that PIK3CA were significantly related to HR+. Moreover, in this study, we also showed a plenty of other rare mutations, including DDR2, CDK12, etc. For different HR/HER2 subtypes, MED12 was frequent in TNBC samples, FAT1 was frequent in HR+ samples, and DDR2 was frequent in HER2+ samples. These findings need further intensive investigations in larger samples.
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Affiliation(s)
- Zhe-Yu Hu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Central Laboratory, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Ning Xie
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Can Tian
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Xiaohong Yang
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Liping Liu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Jing Li
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Huawu Xiao
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Hui Wu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Jun Lu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Jianxiang Gao
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Xuming Hu
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Min Cao
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Zhengrong Shui
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Mengjia Xiao
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Yu Tang
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China
| | - Qiongzhi He
- Geneplus-Beijing Institute, Beijing 102206, China
| | | | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Qianjin Liao
- Geneplus-Beijing Institute, Beijing 102206, China
| | - Quchang Ouyang
- Hunan Cancer Hospital, and the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China; Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha 410013, China; Department of Breast Cancer Medical Oncology, The Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha 410013, China.
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Wang Y, Li L, Han R, Jiao L, Zheng J, He Y. Clinical analysis by next-generation sequencing for NSCLC patients with MET amplification resistant to osimertinib. Lung Cancer 2018; 118:105-110. [PMID: 29571987 DOI: 10.1016/j.lungcan.2018.02.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/08/2018] [Accepted: 02/09/2018] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The efficacy of osimertinib was compromised by the development of resistance mechanisms, such as MET amplification. However, cohort studies of osimertinib resistance mechanism, and the correlation of MET and progression-free survival (PFS) after osimertinib resistance have been poorly investigated. OBJECTIVES This study was carried out to study the acquired MET amplification after osimertinib resistance in advanced lung adenocarcinoma patients, and interrogate the correlation of clinical prognosis and MET amplification. METHODS We performed capture-based sequencing on longitudinal plasma and tissue samples obtained before osimertinib treatment and after resistance development from lung adenocarcinoma patients to investigate the underlying resistance mechanism. We also investigated the correlation of MET amplification and patient prognosis after osimertinib resistance using Kaplan-Meier analysis. RESULTS Paired biopsies before osimertinib treatment and after the resistance development revealed underlying resistance mechanisms. In addition, a cohort of 13 patients who developed disease progression after osimertinib resistance was investigated. Patients with MET amplification after osimertinib resistance commonly had inferior median progression-free survival (mPFS) than patients without MET amplification appearance or increase (3.5 months vs. 9.9 months, p = .117). Patients in MET amplification group also displayed poor median overall survival (mOS) compared to MET amplification negative group (15.6 months vs. 30.7 months, p = .885). Furthermore, combinatorial treatment of first/third-generation EGFR-TKI and crizotinib was efficaciously administrated into two patients with newly acquired MET amplification after osimertinib resistance. Partial responses were achieved by them, both clinically and radiographically. CONCLUSIONS We investigated the osimertinib resistance mechanism in a small cohort of lung adenocarcinoma patients, and demonstrated MET amplification was correlated with inferior PFS/OS after osimertinib treatment. Moreover, we reported the first clinical evidence of efficacy generated by combination of first-generation EGFR-TKI icotinib and crizotinib after the resistance to osimertinib.
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Affiliation(s)
- Yubo Wang
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Li Li
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Rui Han
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Lin Jiao
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Jie Zheng
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China
| | - Yong He
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing, PR China.
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39
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Yi Z, Ma F, Li C, Chen R, Yuan L, Sun X, Guan X, Li L, Liu B, Guan Y, Qian H, Xu B. Landscape of somatic mutations in different subtypes of advanced breast cancer with circulating tumor DNA analysis. Sci Rep 2017; 7:5995. [PMID: 28729728 PMCID: PMC5519668 DOI: 10.1038/s41598-017-06327-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/12/2017] [Indexed: 01/28/2023] Open
Abstract
It is particularly important to provide precise therapies and understand tumor heterogeneity based on the molecular typing of mutational landscape. However, the landscape of somatic mutations in different subtypes of advanced breast cancer (ABC) is largely unknown. We applied target-region capture deep sequencing to determine the frequency and spectrum of common cancer-related gene mutations in circulating tumor DNA (ctDNA) among different ABC subtypes and analyze their association with clinical features. In this retrospective study of 100 female advanced breast cancer patients, 96 (96.0%) had somatic genomic alterations in ctDNA, including copy number variants and point mutations. The results revealed that different subtypes of ABC have distinct features in terms of genetic alterations. Multivariate regression analyses revealed that the number of somatic mutations increased with the line of endocrine therapy and the fractions of trunk mutations was positive associated with the line of target therapy.
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Affiliation(s)
- Zongbi Yi
- Department of Medical Oncology, National Cancer Center/Cancer hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/Cancer hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Chunxiao Li
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | | | - Lifang Yuan
- Department of Medical Oncology, Huanxing Cancer Hospital, Beijing, 100005, China
| | - Xiaoying Sun
- Department of Medical Oncology, Huanxing Cancer Hospital, Beijing, 100005, China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/Cancer hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/Cancer hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Binliang Liu
- Department of Medical Oncology, National Cancer Center/Cancer hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | | | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/Cancer hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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