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Nagelberg AL, Sihota TS, Chuang YC, Shi R, Chow JLM, English J, MacAulay C, Lam S, Lam WL, Lockwood WW. Integrative genomics identifies SHPRH as a tumor suppressor gene in lung adenocarcinoma that regulates DNA damage response. Br J Cancer 2024; 131:534-550. [PMID: 38890444 DOI: 10.1038/s41416-024-02755-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Identification of driver mutations and development of targeted therapies has considerably improved outcomes for lung cancer patients. However, significant limitations remain with the lack of identified drivers in a large subset of patients. Here, we aimed to assess the genomic landscape of lung adenocarcinomas (LUADs) from individuals without a history of tobacco use to reveal new genetic drivers of lung cancer. METHODS Integrative genomic analyses combining whole-exome sequencing, copy number, and mutational information for 83 LUAD tumors was performed and validated using external datasets to identify genetic variants with a predicted functional consequence and assess association with clinical outcomes. LUAD cell lines with alteration of identified candidates were used to functionally characterize tumor suppressive potential using a conditional expression system both in vitro and in vivo. RESULTS We identified 21 genes with evidence of positive selection, including 12 novel candidates that have yet to be characterized in LUAD. In particular, SNF2 Histone Linker PHD RING Helicase (SHPRH) was identified due to its frequency of biallelic disruption and location within the familial susceptibility locus on chromosome arm 6q. We found that low SHPRH mRNA expression is associated with poor survival outcomes in LUAD patients. Furthermore, we showed that re-expression of SHPRH in LUAD cell lines with inactivating alterations for SHPRH reduces their in vitro colony formation and tumor burden in vivo. Finally, we explored the biological pathways associated SHPRH inactivation and found an association with the tolerance of LUAD cells to DNA damage. CONCLUSIONS These data suggest that SHPRH is a tumor suppressor gene in LUAD, whereby its expression is associated with more favorable patient outcomes, reduced tumor and mutational burden, and may serve as a predictor of response to DNA damage. Thus, further exploration into the role of SHPRH in LUAD development may make it a valuable biomarker for predicting LUAD risk and prognosis.
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Affiliation(s)
- Amy L Nagelberg
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tianna S Sihota
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Yu-Chi Chuang
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Rocky Shi
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - Justine L M Chow
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - John English
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Calum MacAulay
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Lam
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada.
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, BC, Canada.
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Yatabe Y. Molecular pathology of non-small cell carcinoma. Histopathology 2024; 84:50-66. [PMID: 37936491 DOI: 10.1111/his.15080] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023]
Abstract
Currently, lung cancer is treated by the highest number of therapeutic options and the benefits are based on multiple large-scale sequencing studies, translational research and new drug development, which has promoted our understanding of the molecular pathology of lung cancer. According to the driver alterations, different characteristics have been revealed, such as differences in ethnic prevalence, median age and alteration patterns. Consequently, beyond traditional chemoradiotherapy, molecular-targeted therapy and treatment with immune check-point inhibitors (ICI) also became available major therapeutic options. Interestingly, clinical results suggest that the recently established therapies target distinct lung cancer proportions, particularly between the EGFR/ALK and PD-1/PD-L1-positive subsets, e.g. the kinase inhibitors target driver mutation-positive tumours, whereas driver mutation-negative tumours respond to ICI treatment. These therapeutic efficacy-related differences might be explained by the molecular pathogenesis of lung cancer. Addictive driver mutations promote tumour formation with powerful transformation performance, resulting in a low tumour mutation burden, reduced immune surveillance, and subsequent poor response to ICIs. In contrast, regular tobacco smoke exposure repeatedly injures the proximal airway epithelium, leading to accumulated genetic alterations. In the latter pathway, overgrowth due to alteration and immunological exclusion against neoantigens is initially balanced. However, tumours could be generated from certain clones that outcompete immunological exclusion and outgrow the others. Consequently, this cancer type responds to immune check-point treatment. These pathogenic differences are explained well by the two-compartment model, focusing upon the anatomical and functional composition of distinct cellular components between the terminal respiratory unit and the air-conducting system.
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Affiliation(s)
- Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
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3
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Ohana J, Sandler U, Devary O, Devary Y. Transformation of immunosuppressive mtKRAS tumors into immunostimulatory tumors by Nerofe and Doxorubicin. Oncotarget 2023; 14:688-699. [PMID: 37395796 DOI: 10.18632/oncotarget.28467] [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: 07/04/2023] Open
Abstract
Members of the rat sarcoma viral oncogene (RAS) subfamily KRAS are frequently mutated oncogenes in human cancers and have been identified in pancreatic ductal, colorectal, and lung adenocarcinomas. In this study, we show that a derivative of the hormone peptide Tumor Cell Apoptosis Factor (TCApF), Nerofe™ (dTCApFs), in combination with Doxorubicin (DOX) substantially reduces viability of tumor cells. It was observed that the combination of Nerofe and DOX downregulated KRAS signaling via miR217 upregulation, resulting in enhanced apoptosis of tumor cells. In addition, the combination of Nerofe and DOX also resulted in activation of the immune system against tumor cells, manifested by an increase in the immunostimulatory cytokines IL-2 and IFN-γ as well as the recruitment of NK cells and M1 macrophages to the tumor site.
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Affiliation(s)
- Joel Ohana
- Immune System Key (ISK) Ltd., Jerusalem 9746009, Israel
| | - Uziel Sandler
- Immune System Key (ISK) Ltd., Jerusalem 9746009, Israel
- Department of Bio-Informatics, Lev Academic Center (JCT), Jerusalem 91160, Israel
| | - Orly Devary
- Immune System Key (ISK) Ltd., Jerusalem 9746009, Israel
| | - Yoram Devary
- Immune System Key (ISK) Ltd., Jerusalem 9746009, Israel
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4
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Xu Y, Yan J, Zhou C, Wu L, Wang H, Zhao J, Zhou M, Wang J, Zheng X, Zhang L, Jiang K, Zheng X, Miao Q, Wu S, Zou Z, Lian R, He Y, Chen R, Yang S, Li Y, Chen S, Lin G. Genomic characterisation of de novo EGFR copy number gain and its impact on the efficacy of first-line EGFR-tyrosine kinase inhibitors for EGFR mutated non-small cell lung cancer. Eur J Cancer 2023; 188:81-89. [PMID: 37201385 DOI: 10.1016/j.ejca.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutation generally respond well to epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs). However, genomic characterisation of de novo EGFR copy number gain (CNG) and its impact on the efficacy of first-line EGFR-TKIs remains unclear. METHODS This multicenter, retrospective and real-world study included two cohorts that enroled EGFR mutant NSCLC patients. EGFR CNG was tested by next-generation sequencing of untreated tissue specimens. Cohort 1 detected the impact of EGFR CNG on first-line EGFR-TKIs treatment, and cohort 2 explored the genomic characterisation. RESULTS Cohort 1 enroled 355 patients from four cancer centres between January 2013 and March 2022. The patients were divided into three groups, included the EGFR non-CNG, EGFR CNG, and EGFR uncertain-CNG. No significant difference in progression-free survival (PFS) was found between the three groups (10.0 months vs. 10.8 months vs. 9.9 months, respectively, p = 0.384). Furthermore, the overall response rate was not statistically significant in the EGFR CNG group compared to the EGFR non-CNG or uncertain arm (70.3% vs. 63.2% vs. 54.5%, respectively, p = 0.154). Cohort 2 included 7876 NSCLC patients with 16.4% showing EGFR CNG. Gene mutations such as TP53, IKZF1, RAC1, MYC, MET, CDKN2A/B and alterations of the metabolic-related and ERK signalling pathway were significantly associated with patients with EGFR CNG compared to those without. CONCLUSIONS De novo EGFR CNG had no effect on the efficacy of first-line EGFR-TKI treatment in EGFR mutant NSCLC patients, and tumours with EGFR CNG had more complex genomic profiles than those without.
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Affiliation(s)
- Yiquan Xu
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Jingjing Yan
- Department of Respiratory and Critical Care Medicine, Hebei Petrochina Central Hospital, Langfang, China
| | - Chengzhi Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Lin Wu
- The Second Department of Thoracic Oncology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, China
| | - Haibo Wang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Jun Zhao
- Department of Thoracic Medical Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Maolin Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jingyi Wang
- The Second Department of Thoracic Oncology, the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University/Hunan Cancer Hospital, Changsha, China
| | - Xinlong Zheng
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Longfeng Zhang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Kan Jiang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Xiaobin Zheng
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Qian Miao
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Shiwen Wu
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Zihua Zou
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Rong Lian
- Beijing GenePlus Technology Co., Ltd., Beijing, China
| | - Yuange He
- Beijing GenePlus Technology Co., Ltd., Beijing, China
| | - Rongrong Chen
- Beijing GenePlus Technology Co., Ltd., Beijing, China
| | - Shanshan Yang
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Yujing Li
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Sihui Chen
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China
| | - Gen Lin
- Department of Thoracic Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, China; Fujian Key Laboratory of Advanced Technology for Cancer Screening and Early Diagnosis, Fuzhou, China.
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5
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Bádon ES, Mokánszki A, Mónus A, András C, Méhes G. Clonal diversity in KRAS mutant colorectal adenocarcinoma under treatment: Monitoring of cfDNA using reverse hybridization and DNA sequencing platforms. Mol Cell Probes 2023; 67:101891. [PMID: 36586518 DOI: 10.1016/j.mcp.2022.101891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022]
Abstract
Biological heterogeneity is a key feature of malignancies that significantly contributes to disease progression and therapy resistance. Residual/relapsed tumor foci may represent genetically divergent subclones, which remain uncovered as repeated and multiple tumor sampling is usually limited. The analysis of circulating free DNA (cfDNA) from the peripheral blood plasma (also called a liquid biopsy, LB) is a new achievement that provides an effective tool for follow-up monitoring of cancer-related genetic status. The present study highlights the phenomenon of mutational variability observed in patients with metastatic KRAS mutant colorectal cancer (mCRC) during treatment with bevacizumab in combination in a longitudinal fashion. The prospective study included 490 mCRC patients evaluated between 2020 and 2022 in our institution. Out of the 211 KRAS mutant cases (43.06%) 12 tumors were identified with multiple KRAS gene variants (5.68%). Detailed follow-up investigations were possible in 3 of these patients including the genotyping of the primary and available metastatic tumors, and the peripheral blood cfDNA. cfDNA was collected from three different time points before and between cycles of combined treatment with bevacizumab chemotherapy. KRAS gene variants were identified using reverse-hybridization strips, and next-generation sequencing (NGS), and confirmed by conventional Sanger sequencing. Interestingly, surgery and multiple treatment cycles reorganized the mutational profiles in the selected cases. The effect of the treatments resulted either in the overrepresentation of one of the pre-existing gene variants or in the appearance of new KRAS variants absent in the primary sample, according to the plasma cfDNA findings. Besides the KRAS variants demonstrated by targeted analysis, NGS mutational profiling identified some additional pathogenic variants from the cfDNA samples (including NRAS and MET alterations). In conclusion, plasma cfDNA sampling enables the monitoring of mutational heterogeneity and subclonal dynamics of the actual metastatic tumor mass in mCRC. The pattern of molecular profile potentially reflects a differential drug response determining further progression.
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Affiliation(s)
- Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Csilla András
- Department of Oncology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032, Debrecen, Hungary.
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6
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Peng D, Liang P, Zhong C, Xu P, He Y, Luo Y, Wang X, Liu A, Zeng Z. Effect of EGFR amplification on the prognosis of EGFR-mutated advanced non-small-cell lung cancer patients: a prospective observational study. BMC Cancer 2022; 22:1323. [PMID: 36528578 PMCID: PMC9758842 DOI: 10.1186/s12885-022-10390-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) amplification refers to the copy number increase of EGFR gene, and is often identified as a "bypass" way of Epidermal growth factor receptor Tyrosine kinase inhibitors (EGFR-TKI) resistance. We aimed to explore the effect of EGFR amplification on EGFR mutation treatment-naive advanced non-squamous non-small cell lung cancer (NSCLC) patients. METHODS We conducted a prospective observational study in single center, enrolling advanced non-squamous NSCLC patients receiving Tyrosine kinase inhibitors (TKIs) between March 3, 2019, and February 1, 2022. Next-generation sequencing (NGS) was used to detect genetic alterations in tumor tissue samples. Progression-free survival (PFS) curves were performed using the Kaplan-Meier method. Univariate and multivariate analyses were used to evaluate factors affecting the efficacy of TKIs. RESULTS A total of 117 treatment-naive advanced NSCLC patients were identified in this study. EGFR amplification was found in 22 of 117 (18.8%) patients with EGFR mutations. Of 22 patients with EGFR amplification, 10 patients harbored EGFR 19 del, 11 patients with 21-L858R. The median follow-up time was 22.47 months. The median PFS of the patients with or without EGFR amplification was 8.25 months and 10.67 months, respectively (log-rank test, P = 0.63). In multivariate analysis, EGFR amplification was not an independent prognosis factor for the patients receiving first-line TKIs [HR = 1.38, 95%CI (0.73-2.58), P = 0.321]. Subgroup analysis revealed that EGFR amplification is a risk factor for progression in the brain metastasis population. [HR = 2.28, 95%CI (1.01, 5.14), P = 0.047]. CONCLUSION EGFR amplification is not an independent prognosis factor for PFS in advanced non-squamous NSCLC patients receiving first-line TKIs. However, it is an independent risk factor for PFS in the brain metastasis population.
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Affiliation(s)
- Duanyang Peng
- grid.412455.30000 0004 1756 5980Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi Province PR China ,Jiangxi Key Laboratory of Clinical Translational Cancer Research, Nanchang, Jiangxi Province PR China
| | - Pingan Liang
- grid.412455.30000 0004 1756 5980Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi Province PR China ,Jiangxi Key Laboratory of Clinical Translational Cancer Research, Nanchang, Jiangxi Province PR China
| | - Congying Zhong
- grid.412455.30000 0004 1756 5980Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi Province PR China ,Jiangxi Key Laboratory of Clinical Translational Cancer Research, Nanchang, Jiangxi Province PR China
| | - Peng Xu
- grid.412455.30000 0004 1756 5980Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi Province PR China ,Jiangxi Key Laboratory of Clinical Translational Cancer Research, Nanchang, Jiangxi Province PR China
| | - Yanqing He
- grid.412455.30000 0004 1756 5980Department of Nosocomial Infection Control, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province PR China
| | - Yuxi Luo
- grid.412455.30000 0004 1756 5980Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi Province PR China ,Jiangxi Key Laboratory of Clinical Translational Cancer Research, Nanchang, Jiangxi Province PR China
| | - Xia Wang
- grid.412455.30000 0004 1756 5980Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi Province PR China ,Jiangxi Key Laboratory of Clinical Translational Cancer Research, Nanchang, Jiangxi Province PR China
| | - Anwen Liu
- grid.412455.30000 0004 1756 5980Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi Province PR China ,Jiangxi Key Laboratory of Clinical Translational Cancer Research, Nanchang, Jiangxi Province PR China ,grid.260463.50000 0001 2182 8825Radiation Induced Heart Damage Institute of Nanchang University, Nanchang, Jiangxi Province PR China
| | - Zhimin Zeng
- grid.412455.30000 0004 1756 5980Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, Jiangxi Province PR China ,Jiangxi Key Laboratory of Clinical Translational Cancer Research, Nanchang, Jiangxi Province PR China ,grid.260463.50000 0001 2182 8825Radiation Induced Heart Damage Institute of Nanchang University, Nanchang, Jiangxi Province PR China
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7
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Ge-ge L, Cuicui G, Leiqiang L, Yongcang T, Jiangang M, Yiwen O, Li-zhe S. Case report: A case report and literature review about Pathological transformation of lung adenosquamous cell carcinoma. Front Oncol 2022; 12:1029679. [PMID: 36330480 PMCID: PMC9623338 DOI: 10.3389/fonc.2022.1029679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/30/2022] [Indexed: 11/25/2022] Open
Abstract
Background Lung adenosquamous carcinoma is a relatively rare pathological type in lung cancer. The incidence of gene mutation is lower than that of lung adenocarcinoma. However, the cases of pathological transformation after targeted treatment of EGFR gene mutation are more rare. Case introduction A 55 year old female was diagnosed with lung cancer and underwent surgical treatment.The pathology suggested adenosquamous cell carcinoma. Genetic test was EGFR-L858R. After surgery, she was treated with gefitinib targeted therapy. After 2 years of surgery, she developed brain metastasis. surgery was performed again. The pathology suggested squamous cell carcinoma. She continued to take gefitinib targeted therapy orally. After one month later since brain metastasis, she was found to have heart cavity metastasis and surgery was performed for the third time. Besides, the pathology suggested adenosquamous cell carcinoma. Genetic test was EGFR-p E746_ A750del, T790M (-), and we replaced with the second-generation EGFR-TKI afatinib targeted therapy. Up to now, no recurrence or metastasis has been found. Conclusion We now report a rare case of lung adenosquamous carcinoma with pathological transformation during targeted therapy, which is intended to provide therapeutic ideas for the treatment of lung adenosquamous carcinoma in clinical practice. In addition, we reviewed previously reported tumor heterogeneity in the literature.
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8
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He Q, Liu Z, Wang J. Targeting KRAS in PDAC: A New Way to Cure It? Cancers (Basel) 2022; 14:cancers14204982. [PMID: 36291766 PMCID: PMC9599866 DOI: 10.3390/cancers14204982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic cancer is one of the most intractable malignant tumors worldwide, and is known for its refractory nature and poor prognosis. The fatality rate of pancreatic cancer can reach over 90%. In pancreatic ductal carcinoma (PDAC), the most common subtype of pancreatic cancer, KRAS is the most predominant mutated gene (more than 80%). In recent decades, KRAS proteins have maintained the reputation of being “undruggable” due to their special molecular structures and biological characteristics, making therapy targeting downstream genes challenging. Fortunately, the heavy rampart formed by KRAS has been broken down in recent years by the advent of KRASG12C inhibitors; the covalent inhibitors bond to the switch-II pocket of the KRASG12C protein. The KRASG12C inhibitor sotorasib has been received by the FDA for the treatment of patients suffering from KRASG12C-driven cancers. Meanwhile, researchers have paid close attention to the development of inhibitors for other KRAS mutations. Due to the high incidence of PDAC, developing KRASG12D/V inhibitors has become the focus of attention. Here, we review the clinical status of PDAC and recent research progress in targeting KRASG12D/V and discuss the potential applications.
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Affiliation(s)
- Qianyu He
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun 130021, China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Correspondence: (Z.L.); (J.W.)
| | - Jin Wang
- Department of Chemistry and Physics, Stony Brook University, Stony Brook, NY 11794-3400, USA
- Correspondence: (Z.L.); (J.W.)
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9
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Bonner ER, Harrington R, Eze A, Bornhorst M, Kline CN, Gordish-Dressman H, Dawood A, Das B, Chen L, Pauly R, Williams PM, Karlovich C, Peach A, Howell D, Doroshow J, Kilburn L, Packer RJ, Mueller S, Nazarian J. Circulating tumor DNA sequencing provides comprehensive mutation profiling for pediatric central nervous system tumors. NPJ Precis Oncol 2022; 6:63. [PMID: 36068285 PMCID: PMC9448784 DOI: 10.1038/s41698-022-00306-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/15/2022] [Indexed: 11/11/2022] Open
Abstract
Molecular profiling of childhood CNS tumors is critical for diagnosis and clinical management, yet tissue access is restricted due to the sensitive tumor location. We developed a targeted deep sequencing platform to detect tumor driver mutations, copy number variations, and heterogeneity in the liquid biome. Here, we present the sensitivity, specificity, and clinical relevance of our minimally invasive platform for tumor mutation profiling in children diagnosed with CNS cancer.
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Affiliation(s)
- Erin R Bonner
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.,Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Robin Harrington
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Augustine Eze
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Miriam Bornhorst
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Cassie N Kline
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Adam Dawood
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - Biswajit Das
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Li Chen
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rini Pauly
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - P Mickey Williams
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Chris Karlovich
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amanda Peach
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - D'andra Howell
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - James Doroshow
- Division of Cancer Treatment and Diagnosis, Developmental Therapeutics Clinic/Early Clinical Trials Development Program, National Cancer Institute, Bethesda, MD, USA
| | - Lindsay Kilburn
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Roger J Packer
- Brain Tumor Institute, Children's National Hospital, Washington, DC, USA
| | - Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California San Francisco, San Francisco, CA, USA.,Department of Pediatrics, University Children's Hospital Zürich, Zürich, Switzerland
| | - Javad Nazarian
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA. .,Institute for Biomedical Sciences, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA. .,Department of Pediatrics, University Children's Hospital Zürich, Zürich, Switzerland.
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Molecular Biology and Therapeutic Perspectives for K-Ras Mutant Non-Small Cell Lung Cancers. Cancers (Basel) 2022; 14:cancers14174103. [PMID: 36077640 PMCID: PMC9454753 DOI: 10.3390/cancers14174103] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 12/28/2022] Open
Abstract
In non-small cell lung cancer (NSCLC) the most common alterations are identified in the Kirsten rat sarcoma viral oncogene homolog (KRAS) gene, accounting for approximately 30% of cases in Caucasian patients. The majority of mutations are located in exon 2, with the c.34G > T (p.G12C) change being the most prevalent. The clinical relevance of KRAS mutations in NSCLC was not recognized until a few years ago. What is now emerging is a dual key role played by KRAS mutations in the management of NSCLC patients. First, recent data report that KRAS-mutant lung AC patients generally have poorer overall survival (OS). Second, a KRAS inhibitor specifically targeting the c.34G > T (p.G12C) variant, Sotorasib, has been approved by the U.S. Food and Drug Administration (FDA) and by the European Medicines Agency. Another KRAS inhibitor targeting c.34G > T (p.G12C), Adagrasib, is currently being reviewed by the FDA for accelerated approval. From the description of the biology of KRAS-mutant NSCLC, the present review will focus on the clinical aspects of KRAS mutations in NSCLC, in particular on the emerging efficacy data of Sotorasib and other KRAS inhibitors, including mechanisms of resistance. Finally, the interaction between KRAS mutations and immune checkpoint inhibitors will be discussed.
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11
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Ai X, Yu Y, Zhao J, Sheng W, Bai J, Fan Z, Liu X, Ji W, Chen R, Lu S. Comprehensive analysis of MET mutations in NSCLC patients in a real-world setting. Ther Adv Med Oncol 2022; 14:17588359221112474. [PMID: 35860830 PMCID: PMC9290171 DOI: 10.1177/17588359221112474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/20/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Aberrant mesenchymal–epithelial transition/hepatocyte growth factor (MET/HGF) regulation presented in a wide variety of human cancers. MET exon 14 skipping, copy number gain (CNG), and kinase domain mutations/arrangements were associated with increased MET activity, and considered to be oncogenic drivers of non-small cell lung cancers (NSCLCs). Methods: We retrospectively analyzed 564 patients with MET alterations. MET alterations were classified into structural mutations or small mutations. MET CNG, exon 14 skipping, gain of function (GOF) mutations, and kinase domain rearrangement were defined as actionable mutations. Results: Six hundred thirty-two MET mutations were identified including 199 CNG, 117 exon 14 skipping, 12 GOF mutations, and 2 actionable fusions. Higher percentage of MET structural alterations (CNG + fusion) were detected in advanced NSCLC patients. Moreover, MET CNG was enriched while exon 14 skipping was rare in epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI)-treated advanced NSCLC patients. Ten of the 12 MET GOF mutations were also in EGFR-TKI-treated patients. Fifteen (68.1%) of the 22 patients treated with crizotinib or savolitinib had a partial response. Interestingly, one patient had a great response to savolitinib with a novel MET exon 14 skipping mutation identified after failure of immune-checkpoint inhibitor. Conclusions: Half of the MET alterations were actionable mutations. MET CNG, exon 14 skipping and GOF mutations had different distribution in different clinical scenario but all defined a molecular subgroup of NSCLCs for which MET inhibition was active.
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Affiliation(s)
- Xinghao Ai
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yongfeng Yu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department I of Thoracic Oncology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Wang Sheng
- Department of Medical Oncology, Xiamen Key Laboratory of Antitumor Drug Transformation Research, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jing Bai
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zaiwen Fan
- Department of Medical Oncology, Air Force Medical Center, PLA, Beijing, China
| | - Xuemei Liu
- Department of Radiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiang Ji
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Rongrong Chen
- Geneplus-Beijing, Floor 9, Building 6, Medical Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, No.241, Huaihai West Road, Shanghai 200032, China
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12
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Xiong Q, Zeng Z, Yang Y, Wang Y, Xu Y, Zhou Y, Liu J, Zhang Z, Qiu M, Zhu Q. KRAS Gene Copy Number as a Negative Predictive Biomarker for the Treatment of Metastatic Rectal Cancer With Cetuximab: A Case Report. Front Oncol 2022; 12:872630. [PMID: 35734602 PMCID: PMC9207953 DOI: 10.3389/fonc.2022.872630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/14/2022] [Indexed: 02/05/2023] Open
Abstract
Background Close to one third of colorectal cancer (CRC) patients are diagnosed with metastatic CRC (mCRC). Patients with wild-type RAS and BRAF usually receive anti-EGFR monoclonal antibody therapy containing cetuximab. Overall, 30–50% of mCRC patients are reported to harbor RAS mutations, and RAS mutation status should be assessed when considering EGFR inhibitor treatment according to mCRC biomarker guidelines. Of note, 0.67–2% of patients with CRC harbored a KRAS amplification. Here we reported a case of advanced rectal cancer with wild-type RAS and BRAF in a male patient who harbored a KRAS amplification during anti-EGFR treatment. Case Presentation A 46-year-old man was diagnosed with rectal adenocarcinoma with liver metastases (cT3NxM1a, stage IVA). After receiving first-line irinotecan- fluorouracil chemotherapy (FOLFIRI) plus cetuximab, second-line capecitabine- oxaliplatin chemotherapy (XELOX) plus bevacizumab, and third-line regorafenib, he rechallenged FOLFIRI and cetuximab for seven cycles, achieving a prolonged survival of at least 5 months. The KRAS copy number of circulating tumor DNA (ctDNA) was assessed during treatment. Notably, apart from serum carbohydrate antigen 199 (CA199) and carcinoembryonic antigen (CEA), the change of plasm Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) copy number appeared to strongly correlate with treatment response. Conclusion Our findings suggest that the dynamic change of KRAS copy number on ctDNA during treatment might be a negative predictive biomarker. Additionally, RAS and BRAF wild-type mCRC patients who are resistant to first-line FOLFIRI plus cetuximab therapy may respond well to the FOLFIRI plus cetuximab “rechallenged” strategy.
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Affiliation(s)
- Qunli Xiong
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhu Zeng
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Yang
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Ya Wang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Yongfeng Xu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Zhou
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinlu Liu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiwei Zhang
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Qiu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Qing Zhu
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, China
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13
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Correia L, Magno R, Xavier JM, de Almeida BP, Duarte I, Esteves F, Ghezzo M, Eldridge M, Sun C, Bosma A, Mittempergher L, Marreiros A, Bernards R, Caldas C, Chin SF, Maia AT. Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant. NPJ Breast Cancer 2022; 8:71. [PMID: 35676284 PMCID: PMC9177727 DOI: 10.1038/s41523-022-00435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
PIK3CA mutations are the most common in breast cancer, particularly in the estrogen receptor-positive cohort, but the benefit of PI3K inhibitors has had limited success compared with approaches targeting other less common mutations. We found a frequent allelic expression imbalance between the missense mutant and wild-type PIK3CA alleles in breast tumors from the METABRIC (70.2%) and the TCGA (60.1%) projects. When considering the mechanisms controlling allelic expression, 27.7% and 11.8% of tumors showed imbalance due to regulatory variants in cis, in the two studies respectively. Furthermore, preferential expression of the mutant allele due to cis-regulatory variation is associated with poor prognosis in the METABRIC tumors (P = 0.031). Interestingly, ER-, PR-, and HER2+ tumors showed significant preferential expression of the mutated allele in both datasets. Our work provides compelling evidence to support the clinical utility of PIK3CA allelic expression in breast cancer in identifying patients of poorer prognosis, and those with low expression of the mutated allele, who will unlikely benefit from PI3K inhibitors. Furthermore, our work proposes a model of differential regulation of a critical cancer-promoting gene in breast cancer.
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Affiliation(s)
- Lizelle Correia
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal
| | - Ramiro Magno
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal
| | - Joana M Xavier
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal
| | - Bernardo P de Almeida
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal
- The Research Institute of Molecular Pathology, Vienna, Austria
| | - Isabel Duarte
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal
| | - Filipa Esteves
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal
- ProRegeM-PhD Program in Mechanisms of Disease and Regenerative Medicine, Universidade do Algarve, Faro, Portugal
| | - Marinella Ghezzo
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal
| | - Matthew Eldridge
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, UK
| | - Chong Sun
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- DKFZ, Heidelberg, Germany
| | - Astrid Bosma
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lorenza Mittempergher
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ana Marreiros
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal
| | - Rene Bernards
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Cancer Centre, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Robinson Way, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
| | - Ana-Teresa Maia
- Faculty of Medicine and Biomedical Sciences (FMCB), Universidade do Algarve, Faro, Portugal.
- Center for Research in Health Technologies and Information Systems (CINTESIS), Universidade do Algarve, Faro, Portugal.
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14
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Reita D, Pabst L, Pencreach E, Guérin E, Dano L, Rimelen V, Voegeli AC, Vallat L, Mascaux C, Beau-Faller M. Direct Targeting KRAS Mutation in Non-Small Cell Lung Cancer: Focus on Resistance. Cancers (Basel) 2022; 14:cancers14051321. [PMID: 35267628 PMCID: PMC8909472 DOI: 10.3390/cancers14051321] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/30/2022] Open
Abstract
Simple Summary KRAS is the most frequently mutated oncogene in non-small cell lung cancers (NSCLC), with a frequency around 30%, and among them KRAS G12C mutation occurs in 11% of cases. KRAS mutations were for a long time considered to be non-targetable alterations or “undruggable”. Direct inhibition is actually developped with switch-II mutant selective covalent KRAS G12C inhibitors with small molecules such as sotorasib or adagrasib preventing conversion of the mutant protein to GTP-bound active state. Little is known about primary or acquired resistance. Acquired resistance does occur and could be related to genetic alterations in the nucleotide exchange function or adaptive mechanisms either in down-stream pathways or in newly expressed KRAS G12C mutation. Mechanisms of resistance could be classified as “on-target” mechanisms, involving KRAS G12C alterations, or “off-target” mechanisms, involving other gene alterations and/or phenotypic changes. Abstract KRAS is the most frequently mutated oncogene in non-small cell lung cancers (NSCLC), with a frequency of around 30%, and encoding a GTPAse that cycles between active form (GTP-bound) to inactive form (GDP-bound). The KRAS mutations favor the active form with inhibition of GTPAse activity. KRAS mutations are often with poor response of EGFR targeted therapies. KRAS mutations are good predictive factor for immunotherapy. The lack of success with direct targeting of KRAS proteins, downstream inhibition of KRAS effector pathways, and other strategies contributed to a focus on developing mutation-specific KRAS inhibitors. KRAS p.G12C mutation is one of the most frequent KRAS mutation in NSCLC, especially in current and former smokers (over 40%), which occurs among approximately 12–14% of NSCLC tumors. The mutated cysteine resides next to a pocket (P2) of the switch II region, and P2 is present only in the inactive GDP-bound KRAS. Small molecules such as sotorasib are now the first targeted drugs for KRAS G12C mutation, preventing conversion of the mutant protein to GTP-bound active state. Little is known about primary or acquired resistance. Acquired resistance does occur and may be due to genetic alterations in the nucleotide exchange function or adaptative mechanisms in either downstream pathways or in newly expressed KRAS G12C mutation.
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Affiliation(s)
- Damien Reita
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
- Bio-Imagery and Pathology (LBP), UMR CNRS 7021, Strasbourg University, 67400 Illkirch-Graffenstaden, France
| | - Lucile Pabst
- Department of Pneumology, Strasbourg University Hospital, CEDEX, 67091 Strasbourg, France; (L.P.); (C.M.)
| | - Erwan Pencreach
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
- Laboratory Streinth (STress REsponse and INnovative THerapy Against Cancer), Université de Strasbourg, Inserm UMR_S 1113, IRFAC, ITI InnoVec, 3 Avenue Molière, 67200 Strasbourg, France
| | - Eric Guérin
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
- Laboratory Streinth (STress REsponse and INnovative THerapy Against Cancer), Université de Strasbourg, Inserm UMR_S 1113, IRFAC, ITI InnoVec, 3 Avenue Molière, 67200 Strasbourg, France
| | - Laurent Dano
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
| | - Valérie Rimelen
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
| | - Anne-Claire Voegeli
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
| | - Laurent Vallat
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
| | - Céline Mascaux
- Department of Pneumology, Strasbourg University Hospital, CEDEX, 67091 Strasbourg, France; (L.P.); (C.M.)
- Laboratory Streinth (STress REsponse and INnovative THerapy Against Cancer), Université de Strasbourg, Inserm UMR_S 1113, IRFAC, ITI InnoVec, 3 Avenue Molière, 67200 Strasbourg, France
| | - Michèle Beau-Faller
- Department of Biochemistry and Molecular Biology, Strasbourg University Hospital, CEDEX, 67098 Strasbourg, France; (D.R.); (E.P.); (E.G.); (L.D.); (V.R.); (A.-C.V.); (L.V.)
- Laboratory Streinth (STress REsponse and INnovative THerapy Against Cancer), Université de Strasbourg, Inserm UMR_S 1113, IRFAC, ITI InnoVec, 3 Avenue Molière, 67200 Strasbourg, France
- Correspondence: ; Tel.: +33-3-8812-8457
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15
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Houschyar KS, Borrelli MR, Rein S, Tapking C, Popp D, Puladi B, Ooms M, Schulz T, Maan ZN, Branski LK, Siemers F, Philipp-Dormston WG, Yazdi AS, Duscher D. Wnt ligand expression in malignant melanoma: new insights. EUROPEAN JOURNAL OF PLASTIC SURGERY 2022. [DOI: 10.1007/s00238-022-01941-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Emerging Molecular Dependencies of Mutant EGFR-Driven Non-Small Cell Lung Cancer. Cells 2021; 10:cells10123553. [PMID: 34944063 PMCID: PMC8699920 DOI: 10.3390/cells10123553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) mutations are the molecular driver of a subset of non-small cell lung cancers (NSCLC); tumors that harbor these mutations are often dependent on sustained oncogene signaling for survival, a concept known as “oncogene addiction”. Inhibiting EGFR with tyrosine kinase inhibitors has improved clinical outcomes for patients; however, successive generations of inhibitors have failed to prevent the eventual emergence of resistance to targeted agents. Although these tumors have a well-established dependency on EGFR signaling, there remain questions about the underlying genetic mechanisms necessary for EGFR-driven oncogenesis and the factors that allow tumor cells to escape EGFR dependence. In this review, we highlight the latest findings on mutant EGFR dependencies, co-operative drivers, and molecular mechanisms that underlie sensitivity to EGFR inhibitors. Additionally, we offer perspective on how these discoveries may inform novel combination therapies tailored to EGFR mutant NSCLC.
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Yan H, Yu CC, Fine SA, Youssof AL, Yang YR, Yan J, Karg DC, Cheung EC, Friedman RA, Ying H, Chen EI, Luo J, Miao Y, Qiu W, Su GH. Loss of the wild-type KRAS allele promotes pancreatic cancer progression through functional activation of YAP1. Oncogene 2021; 40:6759-6771. [PMID: 34663879 PMCID: PMC8688281 DOI: 10.1038/s41388-021-02040-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/30/2021] [Accepted: 09/27/2021] [Indexed: 01/02/2023]
Abstract
Human pancreatic ductal adenocarcinoma (PDAC) harboring one KRAS mutant allele often displays increasing genomic loss of the remaining wild-type (WT) allele (known as LOH at KRAS) as tumors progress to metastasis, yet the molecular ramification of this WT allelic loss is unknown. In this study, we showed that the restoration of WT KRAS expression in human PDAC cell lines with LOH at KRAS significantly attenuated the malignancy of PDAC cells both in vitro and in vivo, demonstrating a tumor-suppressive role of the WT KRAS allele. Through RNA-Seq, we identified the HIPPO signaling pathway to be positively regulated by WT KRAS in PDAC cells. In accordance with this observation, PDAC cells with LOH at KRAS exhibited increased nuclear localization and activation of transcriptional co-activator YAP1. Mechanistically, we discovered that WT KRAS expression sequestered YAP1 from the nucleus, through enhanced 14-3-3zeta interaction with phosphorylated YAP1 at S127. Consistently, expression of a constitutively-active YAP1 mutant in PDAC cells bypassed the growth inhibitory effects of WT KRAS. In patient samples, we found that the YAP1-activation genes were significantly upregulated in tumors with LOH at KRAS, and YAP1 nuclear localization predicted poor survival for PDAC patients. Collectively, our results reveal that the WT allelic loss leads to functional activation of YAP1 and enhanced tumor malignancy, which explains the selection advantage of the tumor cells with LOH at KRAS during pancreatic cancer clonal evolution and progression to metastasis, and should be taken into consideration in future therapeutic strategies targeting KRAS.
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Affiliation(s)
- Han Yan
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Pancreas Center & Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Chih-Chieh Yu
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Stuart A Fine
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Ayman Lee Youssof
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Ye-Ran Yang
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Jun Yan
- Department of Pathology, Tianjin First Center Hospital, Tianjin, TJ, China
| | - Dillon C Karg
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Edwin C Cheung
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard A Friedman
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, and Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY, USA
| | - Haoqiang Ying
- Molecular and Cellular Oncology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily I Chen
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pharmacology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Yi Miao
- Pancreas Center & Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wanglong Qiu
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Gloria H Su
- The Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Otolaryngology and Head & Neck Surgery, Columbia University Irving Medical Center, New York, NY, USA.
- Pancreas Center, Columbia University Irving Medical Center, New York, NY, USA.
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18
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Sunaga N, Miura Y, Kasahara N, Sakurai R. Targeting Oncogenic KRAS in Non-Small-Cell Lung Cancer. Cancers (Basel) 2021; 13:cancers13235956. [PMID: 34885068 PMCID: PMC8656763 DOI: 10.3390/cancers13235956] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary v-Ki-ras2 Kirsten rat sarcoma viral oncogene (KRAS) is the most common driver in NSCLC, and targeting oncogenic KRAS is a major challenge in the treatment of non-small-cell lung cancer (NSCLC). While several covalent KRAS G12C inhibitors have emerged as a novel anti-KRAS therapy, the development of combined therapies involving the targeting of oncogenic KRAS plus other targeted drugs is still required given the vast heterogeneity of KRAS-mutated tumors. In this review, we summarize the biological and immunological characteristics of oncogenic KRAS-driven NSCLC and the preclinical and clinical evidence for mutant KRAS-targeted therapies. We also discuss the mechanisms of resistance to KRAS G12C inhibitors and possible therapeutic strategies to overcome this drug resistance. Abstract Recent advances in molecular biology and the resultant identification of driver oncogenes have achieved major progress in precision medicine for non-small-cell lung cancer (NSCLC). v-Ki-ras2 Kirsten rat sarcoma viral oncogene (KRAS) is the most common driver in NSCLC, and targeting KRAS is considerably important. The recent discovery of covalent KRAS G12C inhibitors offers hope for improving the prognosis of NSCLC patients, but the development of combination therapies corresponding to tumor characteristics is still required given the vast heterogeneity of KRAS-mutated NSCLC. In this review, we summarize the current understanding of KRAS mutations regarding the involvement of malignant transformation and describe the preclinical and clinical evidence for targeting KRAS-mutated NSCLC. We also discuss the mechanisms of resistance to KRAS G12C inhibitors and possible combination treatment strategies to overcome this drug resistance.
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Affiliation(s)
- Noriaki Sunaga
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, 3-39-15 Showa-machi, Maebashi 371-8511, Gunma, Japan;
- Correspondence: ; Tel.: +81-27-220-8000
| | - Yosuke Miura
- Department of Respiratory Medicine, Gunma University Graduate School of Medicine, 3-39-15 Showa-machi, Maebashi 371-8511, Gunma, Japan;
| | - Norimitsu Kasahara
- Innovative Medical Research Center, Gunma University Hospital, 3-39-15 Showa-machi, Maebashi 371-8511, Gunma, Japan;
| | - Reiko Sakurai
- Oncology Center, Gunma University Hospital, 3-39-15 Showa-machi, Maebashi 371-8511, Gunma, Japan;
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19
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Label-free enrichment of rare unconventional circulating neoplastic cells using a microfluidic dielectrophoretic sorting device. Commun Biol 2021; 4:1130. [PMID: 34561533 PMCID: PMC8463600 DOI: 10.1038/s42003-021-02651-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023] Open
Abstract
Cellular circulating biomarkers from the primary tumor such as circulating tumor cells (CTCs) and circulating hybrid cells (CHCs) have been described to harbor tumor-like phenotype and genotype. CHCs are present in higher numbers than CTCs supporting their translational potential. Methods for isolation of CHCs do not exist and are restricted to low-throughput, time consuming, and biased methodologies. We report the development of a label-free dielectrophoretic microfluidic platform facilitating enrichment of CHCs in a high-throughput and rapid fashion by depleting healthy peripheral blood mononuclear cells (PBMCs). We demonstrated up to 96.5% depletion of PBMCs resulting in 18.6-fold enrichment of cancer cells. In PBMCs from pancreatic adenocarcinoma patients, the platform enriched neoplastic cells identified by their KRAS mutant status using droplet digital PCR with one hour of processing. Enrichment was achieved in 75% of the clinical samples analyzed, establishing this approach as a promising way to non-invasively analyze tumor cells from patients.
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20
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Reck M, Carbone DP, Garassino M, Barlesi F. Targeting KRAS in non-small-cell lung cancer: recent progress and new approaches. Ann Oncol 2021; 32:1101-1110. [PMID: 34089836 DOI: 10.1016/j.annonc.2021.06.001] [Citation(s) in RCA: 140] [Impact Index Per Article: 46.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/18/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023] Open
Abstract
Rat sarcoma (RAS) is the most frequently mutated oncogene in human cancer, with Kirsten rat sarcoma (KRAS) being the most commonly mutated RAS isoform. Overall, KRAS accounts for 85% of RAS mutations observed in human cancers and is present in 35% of lung adenocarcinomas (LUADs). While the use of targeted therapies and immune checkpoint inhibitors (CPIs) has drastically changed the treatment landscape of advanced non-small-cell lung cancer (NSCLC) in recent years, historic attempts to target KRAS (both direct and indirect approaches) have had little success, and no KRAS-specific targeted therapies have been approved to date for patients in this molecular subset of NSCLC. With the discovery by Ostrem, Shokat, and colleagues of the switch II pocket on the surface of the active and inactive forms of KRAS, we now have an improved understanding of the complex interactions involved in the RAS family of signaling proteins which has led to the development of a number of promising direct KRASG12C inhibitors, such as sotorasib and adagrasib. In previously treated patients with KRASG12C-mutant NSCLC, clinical activity has been shown for both sotorasib and adagrasib monotherapy; these data suggest promising new treatment options are on the horizon. With the stage now set for a new era in the treatment of KRASG12C-mutated NSCLC, many questions remain to be answered in order to further elucidate the mechanisms of resistance, how best to use combination strategies, and if KRASG12C inhibitors will have suitable activity in earlier lines of therapy for patients with advanced/metastatic NSCLC.
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Affiliation(s)
- M Reck
- Department of Thoracic Oncology, Lung Clinic Grosshansdorf, Airway Research Center North, German Center for Lung Research, Grosshansdorf, Germany.
| | - D P Carbone
- James Thoracic Oncology Center, The Ohio State University, Columbus, USA
| | - M Garassino
- Department of Medicine, Section Hematology Oncology; The University of Chicago, Chicago, USA
| | - F Barlesi
- Aix Marseille University, Marseille, France; Gustave Roussy Cancer Campus, Villejuif, France
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21
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Sheffels E, Kortum RL. The Role of Wild-Type RAS in Oncogenic RAS Transformation. Genes (Basel) 2021; 12:genes12050662. [PMID: 33924994 PMCID: PMC8146411 DOI: 10.3390/genes12050662] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The RAS family of oncogenes (HRAS, NRAS, and KRAS) are among the most frequently mutated protein families in cancers. RAS-mutated tumors were originally thought to proliferate independently of upstream signaling inputs, but we now know that non-mutated wild-type (WT) RAS proteins play an important role in modulating downstream effector signaling and driving therapeutic resistance in RAS-mutated cancers. This modulation is complex as different WT RAS family members have opposing functions. The protein product of the WT RAS allele of the same isoform as mutated RAS is often tumor-suppressive and lost during tumor progression. In contrast, RTK-dependent activation of the WT RAS proteins from the two non-mutated WT RAS family members is tumor-promoting. Further, rebound activation of RTK–WT RAS signaling underlies therapeutic resistance to targeted therapeutics in RAS-mutated cancers. The contributions of WT RAS to proliferation and transformation in RAS-mutated cancer cells places renewed interest in upstream signaling molecules, including the phosphatase/adaptor SHP2 and the RasGEFs SOS1 and SOS2, as potential therapeutic targets in RAS-mutated cancers.
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22
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Harris KL, Walia V, Gong B, McKim KL, Myers MB, Xu J, Parsons BL. Quantification of cancer driver mutations in human breast and lung DNA using targeted, error-corrected CarcSeq. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:872-889. [PMID: 32940377 PMCID: PMC7756507 DOI: 10.1002/em.22409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/04/2020] [Accepted: 09/12/2020] [Indexed: 05/14/2023]
Abstract
There is a need for scientifically-sound, practical approaches to improve carcinogenicity testing. Advances in DNA sequencing technology and knowledge of events underlying cancer development have created an opportunity for progress in this area. The long-term goal of this work is to develop variation in cancer driver mutation (CDM) levels as a metric of clonal expansion of cells carrying CDMs because these important early events could inform carcinogenicity testing. The first step toward this goal was to develop and validate an error-corrected next-generation sequencing method to analyze panels of hotspot cancer driver mutations (hCDMs). The "CarcSeq" method that was developed uses unique molecular identifier sequences to construct single-strand consensus sequences for error correction. CarcSeq was used for mutational analysis of 13 amplicons encompassing >20 hotspot CDMs in normal breast, normal lung, ductal carcinomas, and lung adenocarcinomas. The approach was validated by detecting expected differences related to tissue type (normal vs. tumor and breast vs. lung) and mutation spectra. CarcSeq mutant fractions (MFs) correlated strongly with previously obtained ACB-PCR mutant fraction (MF) measurements from the same samples. A reconstruction experiment, in conjunction with other analyses, showed CarcSeq accurately quantifies MFs ≥10-4 . CarcSeq MF measurements were correlated with tissue donor age and breast cancer risk. CarcSeq MF measurements were correlated with deviation from median MFs analyzed to assess clonal expansion. Thus, CarcSeq is a promising approach to advance cancer risk assessment and carcinogenicity testing practices. Paradigms that should be investigated to advance this strategy for carcinogenicity testing are proposed.
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Affiliation(s)
- Kelly L. Harris
- US Food and Drug Administration, National Center for Toxicological ResearchDivision of Genetic and Molecular ToxicologyJeffersonArkansasUSA
| | - Vijay Walia
- US Food and Drug Administration, National Center for Toxicological ResearchDivision of Genetic and Molecular ToxicologyJeffersonArkansasUSA
- Present address:
USA
| | - Binsheng Gong
- US Food and Drug AdministrationNational Center for Toxicological Research, Division of Bioinformatics and BiostatisticsJeffersonArkansasUSA
| | - Karen L. McKim
- US Food and Drug Administration, National Center for Toxicological ResearchDivision of Genetic and Molecular ToxicologyJeffersonArkansasUSA
| | - Meagan B. Myers
- US Food and Drug Administration, National Center for Toxicological ResearchDivision of Genetic and Molecular ToxicologyJeffersonArkansasUSA
| | - Joshua Xu
- US Food and Drug AdministrationNational Center for Toxicological Research, Division of Bioinformatics and BiostatisticsJeffersonArkansasUSA
| | - Barbara L. Parsons
- US Food and Drug Administration, National Center for Toxicological ResearchDivision of Genetic and Molecular ToxicologyJeffersonArkansasUSA
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23
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Chung CT, Yeh KC, Lee CH, Chen YY, Ho PJ, Chang KY, Chen CH, Lai YK, Chen CT. Molecular profiling of afatinib-resistant non-small cell lung cancer cells in vivo derived from mice. Pharmacol Res 2020; 161:105183. [PMID: 32896579 DOI: 10.1016/j.phrs.2020.105183] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 01/28/2023]
Abstract
Non-small-cell lung cancer (NSCLC) is a leading cause of cancer-related death worldwide. NSCLC patients with overexpressed or mutated epidermal growth factor receptor (EGFR) related to disease progression are treated with EGFR-tyrosine kinase inhibitors (EGFR-TKIs). Acquired drug resistance after TKI treatments has been a major focus for development of NSCLC therapies. This study aimed to establish afatinib-resistant cell lines from which afatinib resistance-associated genes are identified and the underlying mechanisms of multiple-TKI resistance in NSCLC can be further investigated. Nude mice bearing subcutaneous NSCLC HCC827 tumors were administered with afatinib at different dose intensities (5-100 mg/kg). We established three HCC827 sublines resistant to afatinib (IC50 > 1 μM) with cross-resistance to gefitinib (IC50 > 5 μM). cDNA microarray revealed several of these sublines shared 27 up- and 13 down-regulated genes. The mRNA expression of selective novel genes - such as transmembrane 4 L six family member 19 (TM4SF19), suppressor of cytokine signaling 2 (SOCS2), and quinolinate phosphoribosyltransferase (QPRT) - are responsive to afatinib treatments only at high concentrations. Furthermore, c-MET amplification and activations of a subset of tyrosine kinase receptors were observed in all three resistant cells. PHA665752, a c-MET inhibitor, remarkably increased the sensitivity of these resistant cells to afatinib (IC50 = 12-123 nM). We established afatinib-resistant lung cancer cell lines and here report genes associated with afatinib resistance in human NSCLC. These cell lines and the identified genes serve as useful investigational tools, prognostic biomarkers of TKI therapies, and promising molecule targets for development of human NSCLC therapeutics.
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Affiliation(s)
- Cheng-Ta Chung
- Graduate Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan; Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Kai-Chia Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chia-Huei Lee
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Yun-Yu Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Pai-Jiun Ho
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Kai-Yen Chang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chieh-Hsin Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Yiu-Kay Lai
- Graduate Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan.
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan.
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24
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Owen S, Lo TW, Fouladdel S, Zeinali M, Keller E, Azizi E, Ramnath N, Nagrath S. Simultaneous Single Cell Gene Expression and EGFR Mutation Analysis of Circulating Tumor Cells Reveals Distinct Phenotypes in NSCLC. ADVANCED BIOSYSTEMS 2020; 4:e2000110. [PMID: 32700450 PMCID: PMC7883301 DOI: 10.1002/adbi.202000110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/08/2020] [Indexed: 12/31/2022]
Abstract
While cancer cell populations are known to be highly heterogeneous within a tumor, the current gold standard of tumor profiling is through a tumor biopsy. These biopsies are invasive and prone to missing these clones due to spatial heterogeneity, and this bulk analysis approach can miss information from rare subpopulations. To noninvasively investigate tumor cell heterogeneity, a streamlined workflow is developed to scrutinize rare cells, such as circulating tumor cells (CTCs), for simultaneous analysis of mutations and gene expression profiles at the single cell level. This powerful workflow overcomes low-input limitations of single cell analysis techniques. The utility of this multiplexed workflow to unravel inter- and intra-patient heterogeneity is demonstrated using non-small-cell lung cancer (NSCLC) CTCs (n = 58) from six epidermal growth factor receptor (EGFR) mutant positive NSCLC patients. CTCs are isolated using a high-throughput microfluidic technology, the Labyrinth, and their EGFR mutation status and gene expression profiles are characterized.
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Affiliation(s)
- Sarah Owen
- Department of Chemical Engineering, North Campus Research Complex (NCRC) B028-G068W, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, North Campus Research Complex (NCRC) B010-A175, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Ting-Wen Lo
- Department of Chemical Engineering, North Campus Research Complex (NCRC) B028-G068W, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, North Campus Research Complex (NCRC) B010-A175, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Shamileh Fouladdel
- Biointerfaces Institute, North Campus Research Complex (NCRC) B010-A175, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, 1500 E. Medical Center Drive, Ann Arbor, Michigan, 48109-5330, USA
| | - Mina Zeinali
- Department of Chemical Engineering, North Campus Research Complex (NCRC) B028-G068W, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, North Campus Research Complex (NCRC) B010-A175, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Evan Keller
- Biointerfaces Institute, North Campus Research Complex (NCRC) B010-A175, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center , 1500 East Medical Center Drive, CCGC 6-303, Ann Arbor, MI, 48109-0944, USA
- Department of Urology, A. Alfred Taubman Health Care Center, 1500 E. Medical Center Drive, Ann Arbor, Michigan, 48109-5330, USA
- Unit of Laboratory Animal Medicine, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
| | - Ebrahim Azizi
- Biointerfaces Institute, North Campus Research Complex (NCRC) B010-A175, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, 1500 E. Medical Center Drive, Ann Arbor, Michigan, 48109-5330, USA
| | - Nithya Ramnath
- Department of Internal Medicine, 1500 E. Medical Center Drive, Ann Arbor, Michigan, 48109-5330, USA
- Rogel Cancer Center , 1500 East Medical Center Drive, CCGC 6-303, Ann Arbor, MI, 48109-0944, USA
| | - Sunitha Nagrath
- Department of Chemical Engineering, North Campus Research Complex (NCRC) B028-G068W, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, North Campus Research Complex (NCRC) B010-A175, 2800 Plymouth Road, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center , 1500 East Medical Center Drive, CCGC 6-303, Ann Arbor, MI, 48109-0944, USA
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25
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Bádon ES, Mokánszki A, Mónus A, András C, Damjanovich L, Méhes G. Quadruplicate Synchronous Adenocarcinoma of the Colon with Distant Metastases-Long-Term Molecular Follow-Up by KRAS and TP53 Mutational Profiling. Diagnostics (Basel) 2020; 10:diagnostics10060407. [PMID: 32560038 PMCID: PMC7345140 DOI: 10.3390/diagnostics10060407] [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: 04/29/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 12/18/2022] Open
Abstract
Anatomically independent tumor foci represent biologically distinct neoplasias, potentially featured by different progressivity and treatment responsiveness. To demonstrate the biological complexity, a metastatic colon adenocarcinoma patient originally presenting with four independent primary tumors of the right colon half and altogether eight distant metastases was followed by molecular testing. Next-generation sequencing results highlighted the mutational profile of the individual primaries and the dynamics of the different gene variants observed during follow-up. The four primary colon tumors presented with four different KRAS genotypes, one of them with a wild-type and three with pathogenic variants, without overlap. These were the following: c.35G > A; p.Gly12Asp with 40.6% variant allele frequency (VAF); c.34G > T; p.Gly12Cys with 16.2% VAF and c.35G > T; p.Gly12Val with 15.1% VAF. In metastatic tumors, with one exception where no mutation was detected, only the KRAS c.34G > T; p.Gly12Cys mutation could be detected. TP53 gene variants were variable in the primary tumors, with a single dominant variant evolving in the follow-up metastases (c.820G > T; p.Val274Phe). Genetic profiling of individually developing synchronous malignancies uncovers the clonal relations of metastatic tumors. NGS gene panels provide a solution to follow the dynamics of key oncogene variants during the course of the disease and greatly contribute to therapy optimization.
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Affiliation(s)
- Emese Sarolta Bádon
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (E.S.B.); (A.M.); (A.M.)
| | - Attila Mokánszki
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (E.S.B.); (A.M.); (A.M.)
| | - Anikó Mónus
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (E.S.B.); (A.M.); (A.M.)
| | - Csilla András
- Department of Oncology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - László Damjanovich
- Department of Surgery, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Gábor Méhes
- Department of Pathology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary; (E.S.B.); (A.M.); (A.M.)
- Correspondence:
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26
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Saito Y, Koya J, Araki M, Kogure Y, Shingaki S, Tabata M, McClure MB, Yoshifuji K, Matsumoto S, Isaka Y, Tanaka H, Kanai T, Miyano S, Shiraishi Y, Okuno Y, Kataoka K. Landscape and function of multiple mutations within individual oncogenes. Nature 2020; 582:95-99. [PMID: 32494066 DOI: 10.1038/s41586-020-2175-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/13/2020] [Indexed: 01/09/2023]
Abstract
Sporadic reports have described cancer cases in which multiple driver mutations (MMs) occur in the same oncogene1,2. However, the overall landscape and relevance of MMs remain elusive. Here we carried out a pan-cancer analysis of 60,954 cancer samples, and identified 14 pan-cancer and 6 cancer-type-specific oncogenes in which MMs occur more frequently than expected: 9% of samples with at least one mutation in these genes harboured MMs. In various oncogenes, MMs are preferentially present in cis and show markedly different mutational patterns compared with single mutations in terms of type (missense mutations versus in-frame indels), position and amino-acid substitution, suggesting a cis-acting effect on mutational selection. MMs show an overrepresentation of functionally weak, infrequent mutations, which confer enhanced oncogenicity in combination. Cells with MMs in the PIK3CA and NOTCH1 genes exhibit stronger dependencies on the mutated genes themselves, enhanced downstream signalling activation and/or greater sensitivity to inhibitory drugs than those with single mutations. Together oncogenic MMs are a relatively common driver event, providing the underlying mechanism for clonal selection of suboptimal mutations that are individually rare but collectively account for a substantial proportion of oncogenic mutations.
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Affiliation(s)
- Yuki Saito
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Junji Koya
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Mitsugu Araki
- Department of Clinical System Onco-Informatics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasunori Kogure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Sumito Shingaki
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Mariko Tabata
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Marni B McClure
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kota Yoshifuji
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Hematology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shigeyuki Matsumoto
- Medical Sciences Innovation Hub Program, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| | - Yuta Isaka
- Research and Development Group for In Silico Drug Discovery, Center for Cluster Development and Coordination, Foundation for Biomedical Research and Innovation, Kobe, Japan
| | - Hiroko Tanaka
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takanori Kanai
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuichi Shiraishi
- Center for Cancer Genomics and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Yasushi Okuno
- Department of Clinical System Onco-Informatics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Tokyo, Japan.
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27
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Maeda S, Ohka F, Okuno Y, Aoki K, Motomura K, Takeuchi K, Kusakari H, Yanagisawa N, Sato S, Yamaguchi J, Tanahashi K, Hirano M, Kato A, Shimizu H, Kitano Y, Yamazaki S, Yamashita S, Takeshima H, Shinjo K, Kondo Y, Wakabayashi T, Natsume A. H3F3A mutant allele specific imbalance in an aggressive subtype of diffuse midline glioma, H3 K27M-mutant. Acta Neuropathol Commun 2020; 8:8. [PMID: 32019606 PMCID: PMC7001313 DOI: 10.1186/s40478-020-0882-4] [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: 12/03/2019] [Accepted: 01/18/2020] [Indexed: 11/12/2022] Open
Abstract
Diffuse midline glioma, H3 K27M-mutant is a lethal brain tumor located in the thalamus, brain stem, or spinal cord. H3 K27M encoded by the mutation of a histone H3 gene such as H3F3A plays a pivotal role in the tumorigenesis of this type of glioma. Although several studies have revealed comprehensive genetic and epigenetic profiling, the prognostic factors of these tumors have not been identified to date. In various cancers, oncogenic driver genes have been found to exhibit characteristic copy number alterations termed mutant allele specific imbalance (MASI). Here, we showed that several diffuse midline glioma, H3 K27M-mutant exhibited high variant allele frequency (VAF) of the mutated H3F3A gene using droplet digital polymerase chain reaction (ddPCR) assays. Whole-genome sequencing (WGS) revealed that these cases had various copy number alterations that affected the mutant and/or wild-type alleles of the H3F3A gene. We also found that these MASI cases showed a significantly higher Ki-67 index and poorer survival compared with those in the lower VAF cases (P < 0.05). Our results indicated that the MASI of the H3F3A K27M mutation was associated with the aggressive phenotype of the diffuse midline glioma, H3 K27M-mutant via upregulation of the H3 K27M mutant protein, resulting in downregulation of H3K27me3 modification.
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28
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Harris KL, Myers MB, McKim KL, Elespuru RK, Parsons BL. Rationale and Roadmap for Developing Panels of Hotspot Cancer Driver Gene Mutations as Biomarkers of Cancer Risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:152-175. [PMID: 31469467 PMCID: PMC6973253 DOI: 10.1002/em.22326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 05/24/2023]
Abstract
Cancer driver mutations (CDMs) are necessary and causal for carcinogenesis and have advantages as reporters of carcinogenic risk. However, little progress has been made toward developing measurements of CDMs as biomarkers for use in cancer risk assessment. Impediments for using a CDM-based metric to inform cancer risk include the complexity and stochastic nature of carcinogenesis, technical difficulty in quantifying low-frequency CDMs, and lack of established relationships between cancer driver mutant fractions and tumor incidence. Through literature review and database analyses, this review identifies the most promising targets to investigate as biomarkers of cancer risk. Mutational hotspots were discerned within the 20 most mutated genes across the 10 deadliest cancers. Forty genes were identified that encompass 108 mutational hotspot codons overrepresented in the COSMIC database; 424 different mutations within these hotspot codons account for approximately 63,000 tumors and their prevalence across tumor types is described. The review summarizes literature on the prevalence of CDMs in normal tissues and suggests such mutations are direct and indirect substrates for chemical carcinogenesis, which occurs in a spatially stochastic manner. Evidence that hotspot CDMs (hCDMs) frequently occur as tumor subpopulations is presented, indicating COSMIC data may underestimate mutation prevalence. Analyses of online databases show that genes containing hCDMs are enriched in functions related to intercellular communication. In its totality, the review provides a roadmap for the development of tissue-specific, CDM-based biomarkers of carcinogenic potential, comprised of batteries of hCDMs and can be measured by error-correct next-generation sequencing. Environ. Mol. Mutagen. 61:152-175, 2020. Published 2019. This article is a U.S. Government work and is in the public domain in the USA. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Kelly L. Harris
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Meagan B. Myers
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Karen L. McKim
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
| | - Rosalie K. Elespuru
- Division of Biology, Chemistry and Materials ScienceCDRH/OSEL, US Food and Drug AdministrationSilver SpringMaryland
| | - Barbara L. Parsons
- Division of Genetic and Molecular ToxicologyNational Center for Toxicological Research, US Food and Drug AdministrationJeffersonArkansas
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29
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Calculating the Tumor Nuclei Content for Comprehensive Cancer Panel Testing. J Thorac Oncol 2020; 15:130-137. [DOI: 10.1016/j.jtho.2019.09.081] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/15/2019] [Accepted: 09/24/2019] [Indexed: 11/17/2022]
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30
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Robbrecht DG, Atrafi F, van Riet J, Eskens FA, van Diest PJ, Cuppen EP, van Leenders GJ, van de Werken HJ, Lolkema MP. Unique Case of a Rare Mesenchymal Tumor Harboring a Somatic c.119delC VHL Mutation. JCO Precis Oncol 2019; 3:1-8. [DOI: 10.1200/po.18.00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Florence Atrafi
- Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Job van Riet
- Erasmus University Medical Center, Rotterdam, the Netherlands
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31
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Yoshioka T, Shien K, Takeda T, Takahashi Y, Kurihara E, Ogoshi Y, Namba K, Torigoe H, Sato H, Tomida S, Yamamoto H, Soh J, Fujiwara T, Toyooka S. Acquired resistance mechanisms to afatinib in HER2-amplified gastric cancer cells. Cancer Sci 2019; 110:2549-2557. [PMID: 31162771 PMCID: PMC6676122 DOI: 10.1111/cas.14089] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/22/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022] Open
Abstract
Cancer treatment, especially that for breast and lung cancer, has entered a new era and continues to evolve, with the development of genome analysis technology and the advent of molecular targeted drugs including tyrosine kinase inhibitors. Nevertheless, acquired drug resistance to molecular targeted drugs is unavoidable, creating a clinically challenging problem. We recently reported the antitumor effect of a pan-HER inhibitor, afatinib, against human epidermal growth factor receptor 2 (HER2)-amplified gastric cancer cells. The purpose of the present study was to identify the mechanisms of acquired afatinib resistance and to investigate the treatment strategies for HER2-amplified gastric cancer cells. Two afatinib-resistant gastric cancer cell lines were established from 2 HER2-amplified cell lines, N87 and SNU216. Subsequently, we investigated the molecular profiles of resistant cells. The activation of the HER2 pathway was downregulated in N87-derived resistant cells, whereas it was upregulated in SNU216-derived resistant cells. In the N87-derived cell line, both MET and AXL were activated, and combination treatment with afatinib and cabozantinib, a multikinase inhibitor that inhibits MET and AXL, suppressed the cell growth of cells with acquired resistance both in vitro and in vivo. In the SNU216-derived cell line, YES1, which is a member of the Src family, was remarkably activated, and dasatinib, a Src inhibitor, exerted a strong antitumor effect in these cells. In conclusion, we identified MET and AXL activation in addition to YES1 activation as novel mechanisms of afatinib resistance in HER2-driven gastric cancer. Our results also indicated that treatment strategies targeting individual mechanisms of resistance are key to overcoming such resistance.
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Affiliation(s)
- Takahiro Yoshioka
- Departments of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kazuhiko Shien
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Tatsuaki Takeda
- Department of Clinical Pharmacy, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yuta Takahashi
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Eisuke Kurihara
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yusuke Ogoshi
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kei Namba
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hidejiro Torigoe
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroki Sato
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Shuta Tomida
- Bioinformatics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiromasa Yamamoto
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Junichi Soh
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toshiyoshi Fujiwara
- Departments of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Shinichi Toyooka
- General Thoracic Surgery, Breast and Endocrinological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Zito Marino F, Bianco R, Accardo M, Ronchi A, Cozzolino I, Morgillo F, Rossi G, Franco R. Molecular heterogeneity in lung cancer: from mechanisms of origin to clinical implications. Int J Med Sci 2019; 16:981-989. [PMID: 31341411 PMCID: PMC6643125 DOI: 10.7150/ijms.34739] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/05/2019] [Indexed: 12/13/2022] Open
Abstract
Molecular heterogeneity is a frequent event in cancer responsible of several critical issues in diagnosis and treatment of oncologic patients. Lung tumours are characterized by high degree of molecular heterogeneity associated to different mechanisms of origin including genetic, epigenetic and non-genetic source. In this review, we provide an overview of recognized mechanisms underlying molecular heterogeneity in lung cancer, including epigenetic mechanisms, mutant allele specific imbalance, genomic instability, chromosomal aberrations, tumor mutational burden, somatic mutations. We focus on the role of spatial and temporal molecular heterogeneity involved in therapeutic implications in lung cancer patients.
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Affiliation(s)
| | - Roberto Bianco
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Marina Accardo
- Pathology Unit, University of Campania “L. Vanvitelli”, Naples, Italy
| | - Andrea Ronchi
- Pathology Unit, University of Campania “L. Vanvitelli”, Naples, Italy
| | | | - Floriana Morgillo
- Medical Oncology, Department of Precision Medicine, University of Campania “L. Vanvitelli”, Naples, Italy
| | - Giulio Rossi
- Pathology Unit, Hospital S. Maria delle Croci, Azienda Romagna, Ravenna, Italy
| | - Renato Franco
- Pathology Unit, University of Campania “L. Vanvitelli”, Naples, Italy
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33
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Smith CJ, Perfetti TA. In vitro cobalt-stimulated hypoxia-inducible factor-1 overexpression does not correlate with cancer risk from cobalt exposure in humans. TOXICOLOGY RESEARCH AND APPLICATION 2019. [DOI: 10.1177/2397847319850167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Carr J Smith
- Albemarle Corporation, Mobile, AL, USA
- Department of Nurse Anesthesia, Florida State University, Tallahassee, FL, USA
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34
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To C, Jang J, Chen T, Park E, Mushajiang M, De Clercq DJH, Xu M, Wang S, Cameron MD, Heppner DE, Shin BH, Gero TW, Yang A, Dahlberg SE, Wong KK, Eck MJ, Gray NS, Jänne PA. Single and Dual Targeting of Mutant EGFR with an Allosteric Inhibitor. Cancer Discov 2019; 9:926-943. [PMID: 31092401 DOI: 10.1158/2159-8290.cd-18-0903] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 03/29/2019] [Accepted: 05/01/2019] [Indexed: 12/14/2022]
Abstract
Allosteric kinase inhibitors offer a potentially complementary therapeutic strategy to ATP-competitive kinase inhibitors due to their distinct sites of target binding. In this study, we identify and study a mutant-selective EGFR allosteric inhibitor, JBJ-04-125-02, which as a single agent can inhibit cell proliferation and EGFRL858R/T790M/C797S signaling in vitro and in vivo. However, increased EGFR dimer formation limits treatment efficacy and leads to drug resistance. Remarkably, osimertinib, an ATP-competitive covalent EGFR inhibitor, uniquely and significantly enhances the binding of JBJ-04-125-02 for mutant EGFR. The combination of osimertinib and JBJ-04-125-02 results in an increase in apoptosis, a more effective inhibition of cellular growth, and an increased efficacy in vitro and in vivo compared with either single agent alone. Collectively, our findings suggest that the combination of a covalent mutant-selective ATP-competitive inhibitor and an allosteric EGFR inhibitor may be an effective therapeutic approach for patients with EGFR-mutant lung cancer. SIGNIFICANCE: The clinical efficacy of EGFR tyrosine kinase inhibitors (TKI) in EGFR-mutant lung cancer is limited by acquired drug resistance, thus highlighting the need for alternative strategies to inhibit EGFR. Here, we identify a mutant EGFR allosteric inhibitor that is effective as a single agent and in combination with the EGFR TKI osimertinib.This article is highlighted in the In This Issue feature, p. 813.
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Affiliation(s)
- Ciric To
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jaebong Jang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Ting Chen
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Mierzhati Mushajiang
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Dries J H De Clercq
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Man Xu
- Belfer Center for Applied Cancer Science, Boston, Massachusetts
| | - Stephen Wang
- Belfer Center for Applied Cancer Science, Boston, Massachusetts
| | - Michael D Cameron
- Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida
| | - David E Heppner
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Bo Hee Shin
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Thomas W Gero
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Annan Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Suzanne E Dahlberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kwok-Kin Wong
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Boston, Massachusetts
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Nathanael S Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Belfer Center for Applied Cancer Science, Boston, Massachusetts
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35
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Smith CJ, Perfetti TA, King JA. Indirect oxidative stress from pulmonary inflammation exceeds direct oxidative stress from chemical damage to mitochondria. TOXICOLOGY RESEARCH AND APPLICATION 2019. [DOI: 10.1177/2397847319842845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Carr J Smith
- Albemarle Corporation, Charlotte, NC, USA
- Department of Nurse Anesthesia, Florida State University, Tallahassee, FL, USA
| | | | - Judy A King
- Department of Pathology and Translational Pathobiology, LSU Health Shreveport, Shreveport, LA, USA
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36
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Guo L, Chen Z, Xu C, Zhang X, Yan H, Su J, Yang J, Xie Z, Guo W, Li F, Wu Y, Zhou Q. Intratumoral heterogeneity of EGFR-activating mutations in advanced NSCLC patients at the single-cell level. BMC Cancer 2019; 19:369. [PMID: 31014278 PMCID: PMC6480785 DOI: 10.1186/s12885-019-5555-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 03/31/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Intratumoral epidermal growth factor receptor (EGFR) mutational heterogeneity is yet controversial in non-small cell lung cancer (NSCLC) patients. Single-cell analysis provides the genetic profile of single cancer cells and an in-depth understanding of the heterogeneity of a tumor. METHODS Firstly, single H1975 cells harboring the EGFR L858R mutation were submitted to flow cytometry isolation, nested polymerase chain reaction (nested-PCR) amplification, and direct DNA sequencing to assess the feasibility of single-cell direct DNA sequencing. Then, the single cells of patients with lung adenocarcinoma receiving gefitinib were captured by laser capture microdissection and analyzed by the above methods to identify the intratumoral heterogeneity of the EGFR L858R mutant. Three patients with progression-free survival (PFS) > 14 months were categorized as the long PFS group, and 3 patients with PFS < 6 months as the short PFS group. The correlation between the abundance of EGFR L858R mutant and PFS was analyzed. RESULTS 104 single H1975 cells were isolated. 100/104 were amplified by nested-PCR and confirmed by direct sequencing. We captured 135 tumor cells from the tissues of six patients. 120 single tumor cells were successfully amplified and sequenced. The rate of EGFR exon 21 mutation was only 77.5% (93/120). Furthermore, the rate of mutation in exon 21 of EGFR was significantly higher in the long PFS group than in the short PFS group (86.4 ± 4.9% vs. 68.9 ± 2.8%, P = 0.021). CONCLUSION Our study suggested the intratumoral heterogeneity of EGFR-activating mutations in lung adenocarcinoma confirmed on the single-cell level, which might be associated with EGFR-TKIs response in lung adenocarcinoma patients harboring the EGFR L858R mutation.
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Affiliation(s)
- Longhua Guo
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China.,Department of Medical Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, 63 Huangtang Road, Meizhou, 514031, People's Republic of China
| | - Zhihong Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Chongrui Xu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Xuchao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Honghong Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Jian Su
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Jinji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Zhi Xie
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Weibang Guo
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Feng Li
- Department of Medical Oncology, Cancer Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-Sen University, 63 Huangtang Road, Meizhou, 514031, People's Republic of China
| | - Yilong Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China.
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China.
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Sato H, Soh J, Aoe K, Fujimoto N, Tanaka S, Namba K, Torigoe H, Shien K, Yamamoto H, Tomida S, Tao H, Okabe K, Kishimoto T, Toyooka S. Droplet digital PCR as a novel system for the detection of microRNA‑34b/c methylation in circulating DNA in malignant pleural mesothelioma. Int J Oncol 2019; 54:2139-2148. [PMID: 30942424 DOI: 10.3892/ijo.2019.4768] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/08/2019] [Indexed: 11/06/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare malignancy arising from the pleura that is difficult to diagnose, contributing to its dismal prognosis. Previously, we reported that the degree of microRNA (miR)‑34b/c methylation in circulating DNA is associated with the development of MPM. Herein, we present a newly developed droplet digital PCR (ddPCR)‑based assay for the detection of miR‑34b/c methylation in circulating DNA in patients with MPM. We originally prepared two probes within a short amplicon of 60 bp, designing one from the positive strand and the other from the complementary strand. The two probes functioned cooperatively, and our established assay detected DNA methylation accurately in the preliminary validation. We subsequently verified this assay using clinical samples. Serum samples from 35 cases of MPM, 29 cases of pleural plaque and 10 healthy volunteers were collected from 3 different institutions and used in this study. We divided the samples into 2 groups (group A, n=33; group B, n=41). A receiver‑operating characteristic curve analysis using the samples in group A determined the optimal cut‑off value for the diagnosis of MPM, with a sensitivity of 76.9% and a specificity of 90%. On the other hand, the use of the same criterion yielded a sensitivity of 59.1% and a specificity of 100% in group B, and corresponding values of 65.7 and 94.9% for the entire cohort, indicating a moderate sensitivity and a high specificity. In addition, when the analysis was focused on stage II or more advanced MPM, the sensitivity improved to 81.8%, suggesting the possibility that the methylated allele frequency in MPM may be associated with the stage of disease progression. On the whole, the findings of this study indicate that miR‑34b/c methylation in circulating DNA is a promising biomarker for the prediction of disease progression in patients with MPM.
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Affiliation(s)
- Hiroki Sato
- Department of General Thoracic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Junichi Soh
- Department of General Thoracic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Keisuke Aoe
- Department of Medical Oncology, National Hospital Organization, Yamaguchi‑Ube Medical Center, Ube, Yamaguchi 755‑0241, Japan
| | - Nobukazu Fujimoto
- Department of Respiratory Medicine, Okayama Rosai Hospital, Okayama 702‑8055, Japan
| | - Shin Tanaka
- Department of General Thoracic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Kei Namba
- Department of General Thoracic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Hidejiro Torigoe
- Department of General Thoracic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Kazuhiko Shien
- Department of General Thoracic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Hiromasa Yamamoto
- Department of General Thoracic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Shuta Tomida
- Department of Bioinformatics, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
| | - Hiroyuki Tao
- Department of Clinical Research, National Hospital Organization, Yamaguchi‑Ube Medical Center, Ube, Yamaguchi 755‑0241, Japan
| | - Kazunori Okabe
- Department of Clinical Research, National Hospital Organization, Yamaguchi‑Ube Medical Center, Ube, Yamaguchi 755‑0241, Japan
| | - Takumi Kishimoto
- Department of Respiratory Medicine, Okayama Rosai Hospital, Okayama 702‑8055, Japan
| | - Shinichi Toyooka
- Department of General Thoracic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700‑8558, Japan
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Rodriguez-Meira A, Buck G, Clark SA, Povinelli BJ, Alcolea V, Louka E, McGowan S, Hamblin A, Sousos N, Barkas N, Giustacchini A, Psaila B, Jacobsen SEW, Thongjuea S, Mead AJ. Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing. Mol Cell 2019; 73:1292-1305.e8. [PMID: 30765193 PMCID: PMC6436961 DOI: 10.1016/j.molcel.2019.01.009] [Citation(s) in RCA: 182] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 11/07/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022]
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for resolving transcriptional heterogeneity. However, its application to studying cancerous tissues is currently hampered by the lack of coverage across key mutation hotspots in the vast majority of cells; this lack of coverage prevents the correlation of genetic and transcriptional readouts from the same single cell. To overcome this, we developed TARGET-seq, a method for the high-sensitivity detection of multiple mutations within single cells from both genomic and coding DNA, in parallel with unbiased whole-transcriptome analysis. Applying TARGET-seq to 4,559 single cells, we demonstrate how this technique uniquely resolves transcriptional and genetic tumor heterogeneity in myeloproliferative neoplasms (MPN) stem and progenitor cells, providing insights into deregulated pathways of mutant and non-mutant cells. TARGET-seq is a powerful tool for resolving the molecular signatures of genetically distinct subclones of cancer cells.
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Affiliation(s)
- Alba Rodriguez-Meira
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Gemma Buck
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, Medical Research Council, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Benjamin J Povinelli
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Veronica Alcolea
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Eleni Louka
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Simon McGowan
- Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Angela Hamblin
- National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nikolaos Sousos
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Nikolaos Barkas
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Alice Giustacchini
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Bethan Psaila
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Sten Eirik W Jacobsen
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Department of Cell and Molecular Biology, Wallenberg Institute for Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden; Karolinska University Hospital, Stockholm, Sweden; Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Supat Thongjuea
- Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam J Mead
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; National Institute for Health Research Biomedical Research Centre, University of Oxford, Oxford, UK.
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Chen-Yin O, Vu T, Grunwald JT, Toledano M, Zimak J, Toosky M, Shen B, Zell JA, Gratton E, Abram T, Zhao W. An ultrasensitive test for profiling circulating tumor DNA using integrated comprehensive droplet digital detection. LAB ON A CHIP 2019; 19:993-1005. [PMID: 30735225 PMCID: PMC6559803 DOI: 10.1039/c8lc01399c] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Current cancer detection systems lack the required sensitivity to reliably detect minimal residual disease (MRD) and recurrence at the earliest stages when treatment would be most effective. To address this issue, we present a novel liquid biopsy approach that utilizes an integrated comprehensive droplet digital detection (IC3D) digital PCR system which combines microfluidic droplet partitioning, fluorescent multiplex PCR chemistry, and our rapid 3D, large-volume droplet counting technology. The IC3D ddPCR assay can detect cancer-specific, ultra-rare genomic targets due to large sample input and high degree of partitioning. We first demonstrate our droplet digital PCR assay can robustly detect common cancer mutants including KRAS G12D spiked in wild-type genomic background or isolated from patient samples with 100% specificity. We then demonstrate that the IC3D ddPCR system can detect oncogenic KRAS G12D mutant alleles against a background of wild-type genomes at a sensitivity of 0.00125-0.005% with a false positive rate of 0% which is 50 to 1000× more sensitive than existing commercial liquid biopsy ddPCR and qPCR platforms, respectively. In addition, our technology can uniquely enable detection of circulating tumor cells using their genetic markers without a pre-enrichment step, and analysis of total tumor DNA isolated from blood samples, which will increase clinical sensitivity and specificity, and minimize inter-assay variability. Therefore, our technology holds the potential to provide clinicians with a powerful decision-making tool to monitor and treat MRD with unprecedented sensitivity for earlier stage intervention.
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Affiliation(s)
- Ou Chen-Yin
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Tam Vu
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Michael Toledano
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
| | - Melody Toosky
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Byron Shen
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Jason A. Zell
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
- Division of Hematology/Oncology, University of California Irvine Medical Center, Orange, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, USA
| | - Tim Abram
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
- Division of Hematology/Oncology, University of California Irvine Medical Center, Orange, USA
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Ding G, Wang J, Ding P, Wen Y, Yang L. Case report: HER2 amplification as a resistance mechanism to crizotinib in NSCLC with MET exon 14 skipping. Cancer Biol Ther 2019; 20:837-842. [PMID: 30744539 DOI: 10.1080/15384047.2019.1566049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) harboring MET exon 14 skipping can benefit from crizotinib treatment. Currently, the main resistance mechanisms to crizotinib are MET D1228N and Y1230C mutations. We reported a case of a Chinese NSCLC patient with MET exon 14 skipping detected by targeted next-generation sequencing (NGS) achieved clinical and imaging remission after crizotinib treatment. Then, amplification of multiple genes such as erb-b2 receptor tyrosine kinase 2 (HER2) was detected when disease progressed, indicating novel resistance mechanisms to crizotinib. Ultimately the patient died from cancer-related factors. This was the first NSCLC case with MET exon 14 skipping which reported the HER2 gene amplification at the time of progression during crizotinib treatment, indicating that bypass mechanisms contribute to the development of acquired resistance to MET inhibitors.
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Affiliation(s)
- Guanggui Ding
- a Department of Thoracic Surgery , Shenzhen People's Hospital, Second Clinical Medical College of Jinan University
| | - Jian Wang
- a Department of Thoracic Surgery , Shenzhen People's Hospital, Second Clinical Medical College of Jinan University
| | - Peikun Ding
- a Department of Thoracic Surgery , Shenzhen People's Hospital, Second Clinical Medical College of Jinan University
| | - Yuxin Wen
- a Department of Thoracic Surgery , Shenzhen People's Hospital, Second Clinical Medical College of Jinan University
| | - Lin Yang
- a Department of Thoracic Surgery , Shenzhen People's Hospital, Second Clinical Medical College of Jinan University
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Integrative Genomic Analyses Identifies GGA2 as a Cooperative Driver of EGFR-Mediated Lung Tumorigenesis. J Thorac Oncol 2018; 14:656-671. [PMID: 30578931 DOI: 10.1016/j.jtho.2018.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/29/2018] [Accepted: 12/01/2018] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Targeted therapies for lung adenocarcinoma (LUAD) have improved patient outcomes; however, drug resistance remains a major problem. One strategy to achieve durable response is to develop combination-based therapies that target both mutated oncogenes and key modifiers of oncogene-driven tumorigenesis. This is based on the premise that mutated oncogenes, although necessary, are not sufficient for malignant transformation. We aimed to uncover genetic alterations that cooperate with mutant EGFR during LUAD development. METHODS We performed integrative genomic analyses, combining copy number, gene expression and mutational information for over 500 LUAD tumors. Co-immunoprecipitation and Western blot analysis were performed in LUAD cell lines to confirm candidate interactions while RNA interference and gene overexpression were used for in vitro and in vivo functional assessment. RESULTS We identified frequent amplifications/deletions of chromosomal regions affecting the activity of genes specifically in the context of EGFR mutation, including amplification of the mutant EGFR allele and deletion of dual specificity phosphatase 4 (DUSP4), which have both previously been reported. In addition, we identified the novel amplification of a segment of chromosome arm 16p in mutant-EGFR tumors corresponding to increased expression of Golgi Associated, Gamma Adaptin Ear Containing, ARF Binding Protein 2 (GGA2), which functions in protein trafficking and sorting. We found that GGA2 interacts with EGFR, increases EGFR protein levels and modifies EGFR degradation after ligand stimulation. Furthermore, we show that overexpression of GGA2 enhances EGFR mediated transformation while GGA2 knockdown reduces the colony and tumor forming ability of EGFR mutant LUAD. CONCLUSIONS These data suggest that overexpression of GGA2 in LUAD tumors results in the accumulation of EGFR protein and increased EGFR signaling, which helps drive tumor progression. Thus, GGA2 plays a cooperative role with EGFR during LUAD development and is a potential therapeutic target for combination-based strategies in LUAD.
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Xu Y, Su Z, Li J, Wang Q, Meng G, Zhang Y, Yang W, Zhang J, Gao P. Role of RNA-binding protein 5 in the diagnosis and chemotherapeutic response of lung cancer. Oncol Lett 2018; 17:2013-2019. [PMID: 30675268 DOI: 10.3892/ol.2018.9818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/04/2018] [Indexed: 01/16/2023] Open
Abstract
Lung cancer remains one of the leading causes of cancer-associated mortality in the world. Lung carcinogenesis is frequently associated with deletions or the loss of heterozygosity at the critical chromosomal region 3p21.3, where RNA-binding protein 5 (RBM5) is localized. RBM5 regulates cell growth, cell cycle progression and apoptosis in cell homeostasis. In the lungs, altered RBM5 protein expression leads to alterations in cell growth and apoptosis, with subsequent lung pathogenesis and varied responses to treatment in patients with lung cancer. Detection of RBM5 expression may be a tumor marker for diagnosis, prediction and treatment response in lung cancer, and may be developed as a potential therapeutic target for drug resistant lung cancer. This review discusses the most recent progress on the role of RBM5 in lung cancer.
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Affiliation(s)
- Yanling Xu
- Department of Respiratory Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China.,Department of Geriatrics and General Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Zhenzhong Su
- Department of Respiratory Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Junyao Li
- Department of Respiratory Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Qi Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Guangping Meng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Yu Zhang
- Department of Geriatrics and General Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Wen Yang
- Department of Geriatrics and General Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Jie Zhang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Peng Gao
- Department of Respiratory Medicine, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
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Bronchioloalveolar lung tumors induced in “mice only” by non-genotoxic chemicals are not useful for quantitative assessment of pulmonary adenocarcinoma risk in humans. TOXICOLOGY RESEARCH AND APPLICATION 2018. [DOI: 10.1177/2397847318816617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Chemicals classified as known human carcinogens by International Agency for Research on Cancer (IARC) show a low level of concordance between rodents and humans for induction of pulmonary carcinoma. Rats and mice exposed via inhalation for 2 years show a low level of concordance in both tumor development and organ site location. In 2-year inhalation studies using rats and mice, when pulmonary tumors are seen in only male or female mice or both, but not in either sex of rat, there is a high probability that the murine pulmonary tumor has been produced via Clara cell or club cell (CC) metabolism of the inhaled chemical to a cytotoxic metabolite. Cytotoxicity-induced mitogenesis increases mutagenesis via amplification of the background mutation rate. If the chemical being tested is also negative in the Ames Salmonella mutagenicity assay, and only mouse pulmonary tumors are induced, the probability that this pulmonary tumor is not relevant to human lung cancer risk goes even higher. Mice have a larger percentage of CCs in their distal airways than rats, and a much larger percentage than in humans. The CCs of mice have a much higher concentration of metabolic enzymes capable of metabolizing xenobiotics than CCs in either rats or humans. A principal threat to validity of extrapolating from the murine model lies in the unique capacity of murine CCs to metabolize a significant spectrum of xenobiotics which in turn produces toxicants not seen in rat or human pulmonary pathophysiology.
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Abstract
The three RAS genes - HRAS, NRAS and KRAS - are collectively mutated in one-third of human cancers, where they act as prototypic oncogenes. Interestingly, there are rather distinct patterns to RAS mutations; the isoform mutated as well as the position and type of substitution vary between different cancers. As RAS genes are among the earliest, if not the first, genes mutated in a variety of cancers, understanding how these mutation patterns arise could inform on not only how cancer begins but also the factors influencing this event, which has implications for cancer prevention. To this end, we suggest that there is a narrow window or 'sweet spot' by which oncogenic RAS signalling can promote tumour initiation in normal cells. As a consequence, RAS mutation patterns in each normal cell are a product of the specific RAS isoform mutated, as well as the position of the mutation and type of substitution to achieve an ideal level of signalling.
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Affiliation(s)
- Siqi Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center and Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Christopher M Counter
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA.
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Bielski CM, Donoghue MTA, Gadiya M, Hanrahan AJ, Won HH, Chang MT, Jonsson P, Penson AV, Gorelick A, Harris C, Schram AM, Syed A, Zehir A, Chapman PB, Hyman DM, Solit DB, Shannon K, Chandarlapaty S, Berger MF, Taylor BS. Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer. Cancer Cell 2018; 34:852-862.e4. [PMID: 30393068 PMCID: PMC6234065 DOI: 10.1016/j.ccell.2018.10.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/06/2018] [Accepted: 10/02/2018] [Indexed: 12/18/2022]
Abstract
Driver mutations in oncogenes encode proteins with gain-of-function properties that enhance fitness. Heterozygous mutations are thus viewed as sufficient for tumorigenesis. We describe widespread oncogenic mutant allele imbalance in 13,448 prospectively characterized cancers. Imbalance was selected for through modest dosage increases of gain-of-fitness mutations. Negative selection targeted haplo-essential effectors of the spliceosome. Loss of the normal allele comprised a distinct class of imbalance driven by competitive fitness, which correlated with enhanced response to targeted therapies. In many cancers, an antecedent oncogenic mutation drove evolutionarily dependent allele-specific imbalance. In other instances, oncogenic mutations co-opted independent copy-number changes via the evolutionary process of exaptation. Oncogenic allele imbalance is a pervasive evolutionary innovation that enhances fitness and modulates sensitivity to targeted therapy.
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Affiliation(s)
- Craig M Bielski
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mayur Gadiya
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aphrothiti J Hanrahan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Helen H Won
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew T Chang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Philip Jonsson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Gorelick
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher Harris
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Paul B Chapman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - Kevin Shannon
- Department of Pediatrics, University of California, San Francisco, CA 94158, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Ruiz-Patiño A, Castro CD, Ricaurte LM, Cardona AF, Rojas L, Zatarain-Barrón ZL, Wills B, Reguart N, Carranza H, Vargas C, Otero J, Corrales L, Martín C, Archila P, Rodriguez J, Avila J, Bravo M, Pino LE, Rosell R, Arrieta O. EGFR Amplification and Sensitizing Mutations Correlate with Survival in Lung Adenocarcinoma Patients Treated with Erlotinib (MutP-CLICaP). Target Oncol 2018; 13:621-629. [DOI: 10.1007/s11523-018-0594-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Optimization of Routine Testing for MET Exon 14 Splice Site Mutations in NSCLC Patients. J Thorac Oncol 2018; 13:1873-1883. [PMID: 30195702 DOI: 10.1016/j.jtho.2018.08.2023] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 01/20/2023]
Abstract
INTRODUCTION Genomic alterations affecting splice sites of MNNG HOS transforming gene (MET) exon 14 were recently identified in NSCLC patients. Objective responses to MET tyrosine kinase inhibitors have been reported in these patients. Thus, detection of MET exon 14 splice site mutations represents a major challenge. So far, most of these alterations were found by full-exome sequencing or large capture-based next-generation sequencing (NGS) panels, which are not suitable for routine diagnosis. METHODS Aiming to provide a molecular testing method applicable in routine practice, we first developed a fragment-length analysis for detecting deletions in introns flanking MET exon 14. Second, we designed an optimized targeted NGS panel called CLAPv1, covering the MET exon 14 and flanking regions in addition to the main molecular targets usually covered in genomic testing. In patients with MET exon 14 mutations, MET gene amplification, gene copy number and MET receptor expression were also determined. RESULTS Among 1514 formalin-fixed paraffin-embedded NSCLC samples, nonoptimized NGS allowed detection of MET exon 14 mutations in only 0.3% of the patients, and fragment length analysis detected deletions in 1.1% of the patients. Combined, the optimized CLAPv1 panel and fragment-length analysis implemented for routine molecular testing revealed MET exon 14 alterations in 2.2% of 365 additional NSCLC patients. MET gene amplification or high gene copy number was observed in 6 of 30 patients (20%) harboring MET exon 14 mutations. CONCLUSIONS These results show that optimized targeted NGS and fragment-length analysis improve detection of MET alterations in routine practice.
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Riess JW, Gandara DR, Frampton GM, Madison R, Peled N, Bufill JA, Dy GK, Ou SHI, Stephens PJ, McPherson JD, Lara PN, Burich RA, Ross JS, Miller VA, Ali SM, Mack PC, Schrock AB. Diverse EGFR Exon 20 Insertions and Co-Occurring Molecular Alterations Identified by Comprehensive Genomic Profiling of NSCLC. J Thorac Oncol 2018; 13:1560-1568. [PMID: 29981927 DOI: 10.1016/j.jtho.2018.06.019] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/07/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022]
Abstract
INTRODUCTION EGFR exon 20 insertions (EGFRex20ins) comprise an uncommon subset of EGFR-activating alterations relatively insensitive to first- and second-generation EGFR tyrosine kinase inhibitors (TKIs). However, recent early clinical data suggests these patients may benefit from newer-generation EGFR-TKIs. Comprehensive genomic profiling (CGP) identifies a broad spectrum of EGFRex20ins and associated co-occurring genomic alterations (GAs) present in NSCLC. METHODS Hybrid capture-based CGP was performed prospectively on 14,483 clinically annotated consecutive NSCLC specimens to a mean coverage depth of greater than 650X for 236 or 315 cancer-related genes. RESULTS Of 14,483 NSCLC cases, CGP identified 263 (1.8%) cases with EGFRex20ins, representing 12% (263 of 2251) of cases with EGFR mutations. Sixty-four unique EGFRex20ins were identified, most commonly D770_N771>ASVDN (21%) and N771_P772>SVDNP (20%). EGFR amplification occurred in 22% (57 of 263). The most common co-occurring GAs effected tumor protein p53 (TP53) (56%), cyclin dependent kinase inhibitor 2A (CDKN2A) (22%), cyclin dependent kinase inhibitor 2B (CDKN2B) (16%), NK2 homeobox 1 (NKX2-1) (14%) and RB transcriptional corepressor 1 (RB1) (11%); co-occurring GAs in other known lung cancer drivers were rare (5%). Average tumor mutational burden was low (mean 4.3, range 0 to 40.3 mutations/Mb). Clinical outcomes to first- and second-generation EGFR TKIs were obtained for five patients and none responded. CONCLUSIONS In the largest series of EGFRex20ins NSCLC, diverse EGFRex20ins were detected in 12% of EGFR-mutant NSCLC, a higher frequency than previously reported in smaller single-institution studies. Clinical outcomes showed lack of response to EGFR TKIs. Tumor mutational burden was low, consistent with non-smoking associated NSCLC. Comprehensive sequencing revealed increased proportion and wide variety of EGFRex20ins, representing a population of patients significant enough for focused efforts on effective interventions.
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Affiliation(s)
| | - David R Gandara
- UC Davis Comprehensive Cancer Center, Sacramento, California
| | | | | | - Nir Peled
- The Legacy Heritage Oncology Center and Dr. Larry Norton Institute, Soroka Medical Center and Ben-Gurion University, Beer-Sheva, Israel
| | - Jose A Bufill
- Michiana Hematology-Oncology, PC, Mishawaka, Indiana
| | - Grace K Dy
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Sai-Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, University of California at Irvine, Orange, California
| | | | | | - Primo N Lara
- UC Davis Comprehensive Cancer Center, Sacramento, California
| | | | | | | | - Siraj M Ali
- Foundation Medicine, Cambridge, Massachusetts
| | - Philip C Mack
- UC Davis Comprehensive Cancer Center, Sacramento, California
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PHIP as a therapeutic target for driver-negative subtypes of melanoma, breast, and lung cancer. Proc Natl Acad Sci U S A 2018; 115:E5766-E5775. [PMID: 29866840 DOI: 10.1073/pnas.1804779115] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The identification and targeting of key molecular drivers of melanoma and breast and lung cancer have substantially improved their therapy. However, subtypes of each of these three common, lethal solid tumors lack identified molecular drivers, and are thus not amenable to targeted therapies. Here we show that pleckstrin homology domain-interacting protein (PHIP) promotes the progression of these "driver-negative" tumors. Suppression of PHIP expression significantly inhibited both tumor cell proliferation and invasion, coordinately suppressing phosphorylated AKT, cyclin D1, and talin1 expression in all three tumor types. Furthermore, PHIP's targetable bromodomain is functional, as it specifically binds the histone modification H4K91ac. Analysis of TCGA profiling efforts revealed PHIP overexpression in triple-negative and basal-like breast cancer, as well as in the bronchioid subtype of nonsmall cell lung cancer. These results identify a role for PHIP in the progression of melanoma and breast and lung cancer subtypes lacking identified targeted therapies. The use of selective, anti-PHIP bromodomain inhibitors may thus yield a broad-based, molecularly targeted therapy against currently nontargetable tumors.
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Zhang S, Zhu L, Xia B, Chen E, Zhao Q, Zhang X, Chen X, Chen X, Ma S. Epidermal growth factor receptor (EGFR) T790M mutation identified in plasma indicates failure sites and predicts clinical prognosis in non-small cell lung cancer progression during first-generation tyrosine kinase inhibitor therapy: a prospective observational study. Cancer Commun (Lond) 2018; 38:28. [PMID: 29789021 PMCID: PMC5993134 DOI: 10.1186/s40880-018-0303-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/26/2017] [Indexed: 12/21/2022] Open
Abstract
Introduction Plasma circulating tumor DNA (ctDNA) is an ideal approach to detecting the epidermal growth factor receptor (EGFR) T790M mutation, which is a major mechanism of resistance to first-generation EGFR-tyrosine kinase inhibitor (TKI) therapy. The present study aimed to explore the association of ctDNA-identified T790M mutation with disease failure sites and clinical prognosis in non-small cell lung cancer (NSCLC) patients. Methods Patients who progressed on first-generation TKIs were categorized into failure site groups of chest limited (CF), brain limited (BF) and other (OF). Amplification refractory mutation system (ARMS) and droplet digital PCR (ddPCR) were used to identify the T790M mutation in ctDNA. Prognosis was analyzed with Kaplan–Meier methods. Results Overall concordance between the two methods was 78.3%. According to both ARMS and ddPCR, patients in the OF group had a significantly higher rate of T790M mutation than did patients in the BF and CF groups (P < 0.001), and a significantly higher T790M mutation rate was also observed in OF-group patients than in those in the CF and BF groups (P < 0.001). AZD9291 was found to be an excellent treatment option and yielded the longest survival for T790M+ patients in all groups who had progressed on EGFR-TKIs; for other treatments, the prognosis of T790M− patient subgroups varied. Conclusions The present study demonstrates that T790M mutation in ctDNA is associated with failure sites for NSCLC patients after EGFR-TKI therapy and indicates that both failure site and T790M mutational status greatly influence treatment selection and prognosis. Electronic supplementary material The online version of this article (10.1186/s40880-018-0303-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shirong Zhang
- Center for Translational Medicine, Hangzhou First People's Hospital, Nanjing Medical University, No. 261 Huansha Road, Shangcheng District, Hangzhou, 310006, Zhejiang, China.,Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou, 310006, Zhejiang, China
| | - Lucheng Zhu
- Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou, 310006, Zhejiang, China.,Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, 310000, Zhejiang, China
| | - Bing Xia
- Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, 310000, Zhejiang, China
| | - Enguo Chen
- Department of Respiratory, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, Zhejiang, China
| | - Qiong Zhao
- Department of Oncology, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Xiaochen Zhang
- Department of Oncology, the First Affiliated Hospital, Zhejiang University, Hangzhou, 310006, Zhejiang, China
| | - Xueqin Chen
- Department of Oncology, Hangzhou Cancer Hospital, Hangzhou, 310000, Zhejiang, China
| | - Xufeng Chen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Shenglin Ma
- Center for Translational Medicine, Hangzhou First People's Hospital, Nanjing Medical University, No. 261 Huansha Road, Shangcheng District, Hangzhou, 310006, Zhejiang, China. .,Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Hangzhou, 310006, Zhejiang, China.
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