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Hung LJ, Huang CY, Tung KC, Chen JS, Huang WK, Hsu CC, Fang YF, Wang CL, Liu PC, Yeh KY, Chang PH, Chang JWC, Lin YC, Huang SF, Chou WC. Comprehensive genomic profiling in multiple cancer types: A comparative analysis of the National Biobank Consortium of Taiwan and clinical practice cohorts. J Formos Med Assoc 2024:S0929-6646(24)00405-4. [PMID: 39244401 DOI: 10.1016/j.jfma.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/30/2024] [Accepted: 09/01/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND This retrospective study analyzed tumor tissue profiling data to assess the potential of comprehensive genomic profiling (CGP) for patient care across diverse solid tumors. MATERIAL AND METHODS Patients with newly diagnosed or recurrent stage IIIB or IV lung adenocarcinoma with a null immunophenotype and esophageal, gastric, pancreatic, or bile duct cancer between January 2020 and July 2023 at two medical centers in Taiwan were included. One cohort was a part of the National Biobank Consortium of Taiwan project, whereas the other consisted of patients undergoing routine clinical practice. Tumor samples were subjected to CGP using FoundationOne®CDx, with therapeutic implications determined using OncoKB classification. RESULTS FoundationOne®CDx testing of 574 patients was successful in 456 (79.4%) patients. Clinically actionable genomic alterations were detected in 21.1% (96/456) of the patients, including 17.5%, 2.9%, and 0.7% of patients with evidence levels 1, 2, and 3, respectively. Lung adenocarcinoma accounted for the largest proportion of samples with at least one actionable gene alteration (63.2%), followed by bile duct (26.9%), gastric (17.6%), esophageal (4.0%), and pancreatic (3.1%) cancers. Based on CGP results, 43 patients (9.4%) received matched targeted therapy. The median overall survival of patients who received matched therapy or not was 26.1 months (95% confidence interval (CI), 16.7-35.5 months) and 10.6 months (95% CI, 8.1-13.1 months; hazard ratio, 0.28, 95% CI, 0.14-0.55, p < 0.001), respectively. CONCLUSIONS This study provides comprehensive insights into the genomic profiles of diverse cancers in Taiwan, highlighting the crucial role of CGP in identifying actionable genomic alterations and guiding effective therapeutic strategies in real-world practice.
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Affiliation(s)
- Ling-Jen Hung
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan; Division of Hematology-Oncology, Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Chen-Yang Huang
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Kai-Che Tung
- Patient Journey Solution Division, Roche Products Ltd., Taipei, Taiwan; Department of Medical Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Jen-Shi Chen
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Wen-Kuan Huang
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Chih-Chung Hsu
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Yueh-Fu Fang
- Division of Thoracic Oncology, Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Chih-Liang Wang
- Division of Thoracic Oncology, Department of Thoracic Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Ping-Chi Liu
- Division of Thoracic Oncology, Department of Thoracic Medicine, Keelung Chang Gung Memorial Hospital and Chang Gung University, Keelung, Taiwan
| | - Kun-Yun Yeh
- Division of Hematology-Oncology, Department of Internal Medicine, Keelung Chang Gung Memorial Hospital and Chang Gung University, Keelung, Taiwan
| | - Pei-Hung Chang
- Division of Hematology-Oncology, Department of Internal Medicine, Keelung Chang Gung Memorial Hospital and Chang Gung University, Keelung, Taiwan
| | - John Wen-Cheng Chang
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Yung-Chang Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan
| | - Shiu-Feng Huang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Wen-Chi Chou
- Division of Hematology-Oncology, Department of Internal Medicine, Linkou Chang Gung Memorial Hospital and Chang Gung University, Taoyuan, Taiwan.
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Minne RL, Luo NY, Traynor AM, Huang M, DeTullio L, Godden J, Stoppler M, Kimple RJ, Baschnagel AM. Genomic and Immune Landscape Comparison of MET Exon 14 Skipping and MET-Amplified Non-small Cell Lung Cancer. Clin Lung Cancer 2024; 25:567-576.e1. [PMID: 38852006 DOI: 10.1016/j.cllc.2024.05.001] [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: 01/22/2024] [Revised: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Mutation or amplification of the mesenchymal-epithelial transition (MET) tyrosine kinase receptor causes dysregulation of receptor function and stimulates tumor growth in non-small cell lung cancer (NSCLC) with the most common mutation being MET exon 14 (METex14). We sought to compare the genomic and immune landscape of MET-altered NSCLC with MET wild-type NSCLC. METHODS 18,047 NSCLC tumors were sequenced with Tempus xT assay. Tumors were categorized based on MET exon 14 (METex14) mutations; low MET amplification defined as a copy number gain (CNG) 6-9, high MET amplification defined as CNG ≥ 10, and MET other type mutations. Immuno-oncology (IO) biomarkers and the frequency of other somatic gene alterations were compared across MET-altered and MET wild-type groups. RESULTS 276 (1.53%) METex14, 138 (0.76%) high METamp, 63 (0.35%) low METamp, 27 (0.15%) MET other, and 17,543 (97%) MET wild-type were identified. Patients with any MET mutation including METex14 were older, while patients with METex14 were more frequently female and nonsmokers. MET gene expression was highest in METamp tumors. PD-L1 positivity rates were higher in MET-altered groups than MET wild-type. METex14 exhibited the lowest tumor mutational burden (TMB) and lowest neoantigen tumor burden (NTB). METamp exhibited the lowest proportion of CD4 T cells and the highest proportion of NK cells. There were significant differences in co-alterations between METamp and METex14. CONCLUSIONS METex14 tumors exhibited differences in IO biomarkers and the somatic landscape compared to non-METex14 NSCLC tumors. Variations in immune profiles can affect immunotherapy selection in MET-altered NSCLC and require further exploration.
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Affiliation(s)
- Rachel L Minne
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Natalie Y Luo
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Anne M Traynor
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | | | | | | | | | - Randall J Kimple
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Andrew M Baschnagel
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin; University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
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3
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Simoni-Nieves A, Lindzen M, Giri S, Gupta N, Chatterjee R, Selvadurai BR, Van Daele M, Love D, Haga Y, Romaniello D, Salame TM, Zerbib M, Oren R, Tsutsumi Y, Lauriola M, Marrocco I, Yarden Y. A bispecific antibody targeting EGFR and AXL delays resistance to osimertinib. Cell Rep Med 2024:101703. [PMID: 39216477 DOI: 10.1016/j.xcrm.2024.101703] [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: 12/18/2023] [Revised: 06/19/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
Activating EGFR (epidermal growth factor receptor) mutations can be inhibited by specific tyrosine kinase inhibitors (TKIs), which have changed the landscape of lung cancer therapy. However, due to secondary mutations and bypass receptors, such as AXL (AXL receptor tyrosine kinase), drug resistance eventually emerges in most patients treated with the first-, second-, or third-generation TKIs (e.g., osimertinib). To inhibit AXL and resistance to osimertinib, we compare two anti-AXL drugs, an antibody (mAb654) and a TKI (bemcentinib). While no pair of osimertinib and an anti-AXL drug is able to prevent relapses, triplets combining osimertinib, cetuximab (an anti-EGFR antibody), and either anti-AXL drug are initially effective. However, longer monitoring uncovers superiority of the mAb654-containing triplet, possibly due to induction of receptor endocytosis, activation of immune mechanisms, or disabling intrinsic mutators. Hence, we constructed a bispecific antibody that engages both AXL and EGFR. When combined with osimertinib, the bispecific antibody consistently inhibits tumor relapses, which warrants clinical trials.
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Affiliation(s)
- Arturo Simoni-Nieves
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moshit Lindzen
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Suvendu Giri
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nitin Gupta
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rishita Chatterjee
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Boobash-Raj Selvadurai
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marieke Van Daele
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Danielle Love
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuya Haga
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Donatella Romaniello
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Tomer-Meir Salame
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mirie Zerbib
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan; Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Mattia Lauriola
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ilaria Marrocco
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.
| | - Yosef Yarden
- Departments of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
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Liang P, Peng M, Tao J, Wang B, Wei J, Lin L, Cheng B, Xiong S, Li J, Li C, Yu Z, Li C, Wang J, Li H, Chen Z, Fan J, Liang W, He J. Development of a genome atlas for discriminating benign, preinvasive, and invasive lung nodules. MedComm (Beijing) 2024; 5:e644. [PMID: 39036344 PMCID: PMC11258453 DOI: 10.1002/mco2.644] [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: 12/26/2023] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 07/23/2024] Open
Abstract
To tackle misdiagnosis in lung cancer screening with low-dose computed tomography (LDCT), we aimed to compile a genome atlas for differentiating benign, preinvasive, and invasive lung nodules and characterize their molecular pathogenesis. We collected 432 lung nodule tissue samples from Chinese patients, spanning benign, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (IA). We performed comprehensive sequencing, examining somatic variants, gene expressions, and methylation levels. Our findings uncovered EGFR and TP53 mutations as key drivers in - early lung cancer development, with EGFR mutation frequency increasing with disease progression. Both EGFR mutations and EGF/EGFR hypo-methylation activated the EGFR pathway, fueling cancer growth. Transcriptome analysis identified four lung nodule subtypes (G1-4) with distinct molecular features and immune cell infiltrations: EGFR-driven G1, EGFR/TP53 co-mutation G2, inflamed G3, stem-like G4. Estrogen/androgen response was associated with the EGFR pathway, proposing a new therapy combining tyrosine kinase inhibitors with antiestrogens. Preinvasive nodules exhibited stem cell pathway enrichment, potentially hindering invasion. Epigenetic regulation of various genes was essential for lung cancer initiation and development. This study provides insights into the molecular mechanism of neoplastic progression and identifies potential diagnostic biomarkers and therapeutic targets for lung cancer.
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Affiliation(s)
- Peng Liang
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Minhua Peng
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Jinsheng Tao
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Bo Wang
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Jinwang Wei
- Department of Data ScienceGenomicare Biotechnology (Shanghai) Co., Ltd.ShanghaiChina
- Department of Data ScienceShanghai CreateCured Biotechnology Co., Ltd.ShanghaiChina
| | - Lixuan Lin
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Bo Cheng
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Shan Xiong
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jianfu Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Caichen Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Ziwen Yu
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Chunyan Li
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jun Wang
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Hui Li
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
| | - Zhiwei Chen
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
- AnchorDx Inc.FremontCaliforniaUSA
| | - Jian‐Bing Fan
- AnchorDx Medical Co., LtdGuangzhouGuangdongChina
- Department of PathologySouthern Medical UniversityGuangzhouGuangdongChina
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
| | - Jianxing He
- Department of Thoracic Surgery and Oncologythe First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory DiseaseGuangzhouGuangdongChina
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Marrocco I, Yarden Y. Resistance of Lung Cancer to EGFR-Specific Kinase Inhibitors: Activation of Bypass Pathways and Endogenous Mutators. Cancers (Basel) 2023; 15:5009. [PMID: 37894376 PMCID: PMC10605519 DOI: 10.3390/cancers15205009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Epidermal growth factor receptor (EGFR)-specific tyrosine kinase inhibitors (TKIs) have changed the landscape of lung cancer therapy. For patients who are treated with the new TKIs, the current median survival exceeds 3 years, substantially better than the average 20 month survival rate only a decade ago. Unfortunately, despite initial efficacy, nearly all treated patients evolve drug resistance due to the emergence of either new mutations or rewired signaling pathways that engage other receptor tyrosine kinases (RTKs), such as MET, HER3 and AXL. Apparently, the emergence of mutations is preceded by a phase of epigenetic alterations that finely regulate the cell cycle, bias a mesenchymal phenotype and activate antioxidants. Concomitantly, cells that evade TKI-induced apoptosis (i.e., drug-tolerant persister cells) activate an intrinsic mutagenic program reminiscent of the SOS system deployed when bacteria are exposed to antibiotics. This mammalian system imbalances the purine-to-pyrimidine ratio, inhibits DNA repair and boosts expression of mutation-prone DNA polymerases. Thus, the net outcome of the SOS response is a greater probability to evolve new mutations. Deeper understanding of the persister-to-resister transformation, along with the development of next-generation TKIs, EGFR-specific proteolysis targeting chimeras (PROTACs), as well as bispecific antibodies, will permit delaying the onset of relapses and prolonging survival of patients with EGFR+ lung cancer.
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Affiliation(s)
- Ilaria Marrocco
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy;
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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Luna HGC, Imasa MS, Juat N, Hernandez KV, Sayo TM, Cristal-Luna G, Asur-Galang SM, Bellengan M, Duga KJ, Buenaobra BB, De los Santos MI, Medina D, Samo J, Literal VM, Bascos NA, Sy-Naval S. The differential prognostic implications of PD-L1 expression in the outcomes of Filipinos with EGFR-mutant NSCLC treated with tyrosine kinase inhibitors. Transl Lung Cancer Res 2023; 12:1896-1911. [PMID: 37854154 PMCID: PMC10579834 DOI: 10.21037/tlcr-23-118] [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: 02/19/2023] [Accepted: 07/20/2023] [Indexed: 10/20/2023]
Abstract
Background The tumor immune microenvironment influences tumor evolution in non-small cell lung cancer (NSCLC). Yet, the prognostic value of programmed death-ligand 1 (PD-L1) in epidermal growth factor receptor (EGFR)-mutant NSCLC remains controversial. Additionally, prognostic studies in Filipinos with EGFR-mutant NSCLC remain unexplored to this day. Methods We prospectively studied the outcomes of EGFR-mutant NSCLC in Filipino cohort, and retrospectively verified the survival trend using The Cancer Genome Atlas (TCGA) cohort. Kaplan-Meier method and generalized linear regression were used to assess survival. Expression and DNA methylation of cluster of differentiation 274 (CD274, gene that codes for PD-L1) were examined from TCGA tumor profiles. Pearson's correlation was used to correlate PD-L1 expression with outcomes associated with occurrence of EGFR mutations, tyrosine kinase inhibitor (TKI) types, and programmed cell death protein 1 (PD-1) expression. Proteome network analysis was used to examine the correlation between drug resistance and PD-L1. Results PD-L1 positivity was associated with significantly longer progression-free survival (PFS; P=0.0096) but had a significantly contrasting influence in the overall survival (OS; P=0.0011). PD-L1 positivity (in both protein and RNA) was associated with longer median OS (mOS) in exon21 L858R, whereas, negativity was associated with longer mOS in exon19 deletion (exon19del). Stratification (high, low, negative) of PD-L1 expression lacked significant prognostic value (all P>0.05). PD-L1/CD274 expression (P<0.05) and DNA methylation (P<0.001) vary significantly among NSCLC subtypes and in different disease stages. Erlotinib treatment produced the longest median progression-free survival (mPFS; 874 days) relative to other EGFR-TKIs (137-311 days). PD-L1 lacked a significant correlation with EGFR-TKIs. Consistent with the immune-regulation activities of PD-1, higher expression leads to relatively shorter mOS. PD-1 correlated positively with PD-L1 expression and occurrence of exon21 L858R. Conclusions PD-L1 differentially influenced the outcomes of Filipinos with EGFR-mutant NSCLC. NSCLC subtypes, disease stage, and PD-1 expression may impact the collective outcomes associated with PD-L1 and EGFR-sensitizing mutations.
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Affiliation(s)
- Herdee Gloriane C. Luna
- Lung Center of the Philippines, Quezon City, Philippines
- National Kidney and Transplant Institute, Quezon City, Philippines
| | | | - Necy Juat
- National Kidney and Transplant Institute, Quezon City, Philippines
| | | | - Treah May Sayo
- Lung Center of the Philippines, Quezon City, Philippines
| | | | - Sheena Marie Asur-Galang
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Mirasol Bellengan
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Kent John Duga
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Bien Brian Buenaobra
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Marvin I. De los Santos
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Daniel Medina
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Jamirah Samo
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Venus Minerva Literal
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology-Philippine Council for Health Research and Development, Taguig City, Philippines
| | - Neil Andrew Bascos
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City, Philippines
- Protein, Proteomics and Metabolomics Facility, Philippine Genome Center, University of the Philippines System, Quezon City, Philippines
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7
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Gao Y, Stein MM, Kase M, Cummings AL, Bharanikumar R, Lau D, Garon EB, Patel SP. Comparison of the tumor immune microenvironment and checkpoint blockade biomarkers between stage III and IV non-small cell lung cancer. Cancer Immunol Immunother 2023; 72:339-350. [PMID: 35881197 PMCID: PMC9870967 DOI: 10.1007/s00262-022-03252-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/03/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Adjuvant immune checkpoint blockade (ICB) following chemoradiotherapy and adding ICB to chemotherapy have been key advances for stages III-IV non-small cell lung cancer (NSCLC) treatment. However, known biomarkers like PD-L1 are not consistently indicative of ICB response. Other markers within the tumor immune microenvironment (TIME) may better reflect ICB response and/or resistance mechanisms, but an understanding of how TIMEs differ between stage III and IV NSCLC has not been explored. METHODS Real-world data from unresectable, stage III-IV, non-squamous, pretreatment NSCLCs (stage III n = 106, stage IV n = 285) were retrospectively analyzed. PD-L1 immunohistochemistry (IHC) was compared to CD274 gene expression. Then, differential gene expression levels, pathway enrichment, and immune infiltrate between stages were calculated from whole-transcriptome RNA-seq. Analyses were stratified by EGFR status. RESULTS PD-L1 IHC and CD274 expression in tumor cells were highly correlated (n = 295, P < 2.2e-16, ⍴ = 0.74). CTLA4 expression was significantly increased in stage III tumors (P = 1.32e-04), while no differences were observed for other ICB-related genes. Metabolic pathway activity was significantly enriched in stage IV tumors (P = 0.004), whereas several immune-related KEGG pathways were enriched in stage III. Stage IV tumors had significantly increased macrophage infiltration (P = 0.0214), and stage III tumors had a significantly higher proportion of CD4 + T cells (P = 0.017). CD4 + T cells were also relatively more abundant in EGFR-mutant tumors vs. wild-type (P = 0.0081). CONCLUSION Directly comparing the TIMEs of stage III and IV NSCLC, these results carry implications for further studies of ICB response in non-resectable stage III NSCLC and guide further research of prognostic biomarkers and therapeutic targets.
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Wang S, Zhang X, Qiang G, Wang J. DelInsCaller: An Efficient Algorithm for Identifying Delins and Estimating Haplotypes from Long Reads with High Level of Sequencing Errors. Genes (Basel) 2022; 14:4. [PMID: 36672745 PMCID: PMC9858578 DOI: 10.3390/genes14010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 12/24/2022] Open
Abstract
Delins, as known as complex indel, is a combined genomic structural variation formed by deleting and inserting DNA fragments at a common genomic location. Recent studies emphasized the importance of delins in cancer diagnosis and treatment. Although the long reads from PacBio CLR sequencing significantly facilitate delins calling, the existing approaches still encounter computational challenges from the high level of sequencing errors, and often introduce errors in genotyping and phasing delins. In this paper, we propose an efficient algorithmic pipeline, named delInsCaller, to identify delins on haplotype resolution from the PacBio CLR sequencing data. delInsCaller design a fault-tolerant method by calculating a variation density score, which helps to locate the candidate mutational regions under a high-level of sequencing errors. It adopts a base association-based contig splicing method, which facilitates contig splicing in the presence of false-positive interference. We conducted a series of experiments on simulated datasets, and the results showed that delInsCaller outperformed several state-of-the-art approaches, e.g., SVseq3, across a wide range of parameter settings, such as read depth, sequencing error rates, etc. delInsCaller often obtained higher f-measures than other approaches; specifically, it was able to maintain advantages at ~15% sequencing errors. delInsCaller was able to significantly improve the N50 values with almost no loss of haplotype accuracy compared with the existing approach as well.
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Affiliation(s)
- Shenjie Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an 710049, China
| | - Xuanping Zhang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an 710049, China
| | - Geng Qiang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an 710049, China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an 710049, China
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Bubendorf L, Zoche M, Dafni U, Rüschoff JH, Prince SS, Marti N, Stavrou A, Kammler R, Finn SP, Moch H, Peters S, Stahel RA. Prognostic impact of tumour mutational burden in resected stage I and II lung adenocarcinomas from a European Thoracic Oncology Platform Lungscape cohort. Lung Cancer 2022; 174:27-35. [PMID: 36283211 DOI: 10.1016/j.lungcan.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The primary objective of this study is to evaluate tumor mutational burden (TMB), its associations with selected clinicopathological and molecular characteristics as well as its clinical significance, in a retrospective cohort of surgically resected stage I-II lung adenocarcinomas, subset of the ETOP Lungscape cohort. METHODS TMB was evaluated on tumor DNA extracted from resected primary lung adenocarcinomas, based on FoundationOne®CDx (F1CDx) genomic profiling, centrally performed at the University Hospital Zurich. The F1CDx test sequences the complete exons of 324 cancer-related genes and detects substitutions, insertions and deletions (indels), copy number alterations and gene rearrangements. In addition, the genomic biomarkers TMB and microsatellite instability (MSI) are analyzed. RESULTS In the Lungscape cohort, TMB was assessed in 78 surgically resected lung adenocarcinomas from two Swiss centers (62 % males, 55 %/45 % stage I/II). Median TMB was 7.6 Muts/Mb, with TMB high (≥10 Muts/Mb) in 40 % of cases (95 %CI:29 %-52 %). The most frequently mutated genes were TP53/KRAS/EGFR/MLL2 detected in 58 %/38 %/33 %/30 % of samples, respectively. TMB was significantly higher among males (TMB high: 50 % vs 23 % in females, p = 0.032), as well as among current/former smokers (TMB high: 44 % vs 8 % in never smokers, p = 0.023). Furthermore, TMB was significantly higher in TP53 mutated than in non-mutated patients (TMB high: 60 % vs 12 %, p < 0.001), while it was higher in EGFR non-mutated patients compared to EGFR mutated (TMB high: 48 % vs 23 %, p = 0.049). At a median follow-up time of 56.1 months (IQR:38.8-72.0), none of the three outcome variables (OS, RFS, TTR) differed significantly by TMB status (all p-values > 5 %). This was also true when adjusting for clinicopathological characteristics. CONCLUSIONS While presence of TP53 mutations and absence of EGFR mutations are associated with high TMB, increased TMB had no significant prognostic impact in patients with resected stage I/II lung adenocarcinoma beyond T and N classification, in both unadjusted and adjusted analyses.
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Affiliation(s)
- Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Martin Zoche
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Urania Dafni
- ETOP IBCSG Partners Foundation Statistical Center, Frontier Science Foundation-Hellas & National and Kapodistrian University of Athens, Athens, Greece
| | - Jan Hendrik Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Spasenija Savic Prince
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Nesa Marti
- Translational Research Coordination, ETOP IBCSG Partners Foundation, Coordinating Center Bern, Switzerland
| | - Androniki Stavrou
- ETOP IBCSG Partners Foundation Statistical Center, Frontier Science Foundation-Hellas, Athens, Greece
| | - Roswitha Kammler
- Translational Research Coordination, ETOP IBCSG Partners Foundation, Coordinating Center Bern, Switzerland
| | - Stephen P Finn
- Cancer Molecular Diagnostics and Histopathology, St. James's Hospital and Trinity College Dublin, Ireland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Rolf A Stahel
- ETOP IBCSG Partners Foundation, Coordinating Center, Bern, Switzerland.
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Saw SP, Ang MK, Tan DS. Adjuvant Immunotherapy in Patients with Early-Stage Non-small Cell Lung Cancer and Future Directions. Curr Treat Options Oncol 2022; 23:1721-1731. [PMID: 36451063 DOI: 10.1007/s11864-022-01034-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 12/03/2022]
Abstract
OPINION STATEMENT While cisplatin-based adjuvant chemotherapy has been the standard of care for the past two decades, the recent introduction of immunotherapy has heralded an important milestone in the adjuvant landscape of early-stage non-small cell lung cancer (NSCLC). The landmark approval of adjuvant atezolizumab based on disease-free survival (DFS) benefit in IMpower010 was swiftly followed by the recent data for use of adjuvant pembrolizumab in PEARLS/KEYNOTE-091, and similar trials involving other immune checkpoint inhibitors are eagerly anticipated. Although both atezolizumab and pembrolizumab demonstrated a significant DFS benefit in the intention-to-treat population, key subgroup analyses have raised questions about the role of predictive biomarkers such as PD-L1 expression and EGFR-mutation status. In this review, we examine the data from the two important trials (IMpower010 and PEARLS/KEYNOTE-091), discuss the controversies surrounding adjuvant immunotherapy including appropriate endpoints, biomarker selection and highlight key considerations in oncogene-driven NSCLC. Finally, we propose future directions including the impact of neoadjuvant therapy on developments in the adjuvant immunotherapy paradigm and role of minimal residual disease (MRD).
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Affiliation(s)
- Stephanie Pl Saw
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Mei-Kim Ang
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore
| | - Daniel Sw Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610, Singapore. .,SingHealth Duke-NUS Oncology Academic Clinical Programme, 11 Hospital Crescent, Singapore, 169610, Singapore.
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11
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High Tumor Mutation Burden Is Associated with Poor Clinical Outcome in EGFR-Mutated Lung Adenocarcinomas Treated with Targeted Therapy. Biomedicines 2022; 10:biomedicines10092109. [PMID: 36140210 PMCID: PMC9495802 DOI: 10.3390/biomedicines10092109] [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: 08/01/2022] [Revised: 08/19/2022] [Accepted: 08/26/2022] [Indexed: 11/22/2022] Open
Abstract
This study aimed to determine the association between TMB and treatment outcomes in patients with epidermal growth factor receptor (EGFR)-mutated lung cancer that were treated with tyrosine kinase inhibitors (TKIs). The TMB was assessed using a 409-gene targeted next-generation sequencing panel. We compared the response rate (RR), progression-free survival (PFS), overall survival (OS), and frequency of secondary T790M mutations among the different TMB groups. The median TMB of the study population (n = 88) was 3.36/megabases. We divided 52 (59%) and 36 (41%) patients into the low and high TMB groups, respectively. A high TMB level was significantly associated with liver metastasis and more advanced stage (all p < 0.05). RR was significantly lower in the high TMB group than that of the low TMB group (50.0% vs. 80.7%, all p = 0.0384). In multivariate analysis, high TMB was independently associated with a shorter PFS (hazard ratio [HR] = 1.80, p = 0.0427) and shorter OS (HR = 2.05, p = 0.0397) than that of the low TMB group. Further, high TMB was independently associated with decreased T790M mutation development. These results suggest that high TMB may be a predictive biomarker for adverse treatment outcomes and represent a patients’ subgroup warranting tailored therapeutic approaches.
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12
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Comprehensive Analysis of Gene Signatures of m6ARNA Methylation Regulators in Lung Adenocarcinoma and Development of a Risk Scoring System. J Immunol Res 2022; 2022:7519838. [PMID: 36061307 PMCID: PMC9428682 DOI: 10.1155/2022/7519838] [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: 04/19/2022] [Accepted: 07/15/2022] [Indexed: 12/02/2022] Open
Abstract
The recent application of targeted immunotherapy has greatly improved the clinical outcomes of patients with lung adenocarcinoma (LUAD), but drug resistance continues to emerge, and to evaluate and to improve patient prognosis are arduous. The diagnostic and prognostic value of N6-methyladenosine (M6A) in LUAD has attracted increasing attention. We systematically studied correlations among important M6A methylation regulators, tumor mutational burden (TMB), and immune infiltration in clinical and sequencing data from the LUAD cohort of the cancer genome map (TCGA). The molecular subtype clusters 1 and 2 were identified by the consensus clustering of 16 M6A regulatory factors. Clinical prognosis, M6A regulatory factor expression, TMB, pathway enrichment, and immune cell infiltration significantly differed between clusters 1 and 2. Compared with other clinical traits, a prognostic risk score system constructed using the M6A regulatory factors HNRNPA2B1 and HNRNPC can serve as an independent prognostic method for LUAD, with higher predictive sensitivity and specificity. Risk scores were significantly higher for cluster 2 than 1, which was consistent with the trend towards a better prognosis in cluster 1. Overall, our findings revealed an important role of M6A methylation regulators in LUAD, and our risk scoring system involving these regulators might help to screen groups at high risk for LUAD and provide important theoretical bioinformatic support for evaluating the prognosis of such patients.
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13
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Scott SC, Shao XM, Niknafs N, Balan A, Pereira G, Marrone KA, Lam VK, Murray JC, Feliciano JL, Levy BP, Ettinger DS, Hann CL, Brahmer JR, Forde PM, Karchin R, Naidoo J, Anagnostou V. Sex-specific differences in immunogenomic features of response to immune checkpoint blockade. Front Oncol 2022; 12:945798. [PMID: 35992816 PMCID: PMC9382103 DOI: 10.3389/fonc.2022.945798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction The magnitude of response to immune checkpoint inhibitor (ICI) therapy may be sex-dependent, as females have lower response rates and decreased survival after ICI monotherapy. The mechanisms underlying this sex dimorphism in ICI response are unknown, and may be related to sex-driven differences in the immunogenomic landscape of tumors that shape anti-tumor immune responses in the context of therapy. Methods To investigate the association of immunogenic mutations with HLA haplotypes, we leveraged whole exome sequence data and HLA genotypes from 482 non-small cell lung cancer (NSCLC) tumors from The Cancer Genome Atlas (TCGA). To explore sex-specific genomic features linked with ICI response, we analyzed whole exome sequence data from patients with NSCLC treated with ICI. Tumor mutational burden (TMB), HLA class I and II restricted immunogenic missense mutation (IMM) load, and mutational smoking signature were defined for each tumor. IMM load was combined with HLA class I and II haplotypes and correlated with therapeutic response and survival following ICI treatment. We examined rates of durable clinical benefit (DCB) for at least six months from ICI treatment initiation. Findings were validated utilizing whole exome sequence data from an independent cohort of ICI treated NSCLC. Results Analysis of whole exome sequence data from NSCLC tumors of females and males revealed that germline HLA class II diversity (≥9 unique HLA alleles) was associated with higher tumor class II IMM load in females (p=0.01) and not in males (p=0.64). Similarly, in tumors of female patients, somatic HLA class II loss of heterozygosity was associated with increased IMM load (p=0.01) while this association was not observed in tumors in males (p=0.20). In females, TMB (p=0.005), class I IMM load (p=0.005), class II IMM load (p=0.004), and mutational smoking signature (p<0.001) were significantly higher in tumors responding to ICI as compared to non-responding tumors. In contrast, among males, there was no significant association between DCB and any of these features. When IMM was considered in the context of HLA zygosity, high MHC-II restricted IMM load and high HLA class II diversity was significantly associated with overall survival in males (p=0.017). Conclusions Inherent sex-driven differences in immune surveillance affect the immunogenomic determinants of response to ICI and likely mediate the dimorphic outcomes with ICI therapy. Deeper understanding of the selective pressures and mechanisms of immune escape in tumors in males and females can inform patient selection strategies and can be utilized to further hone immunotherapy approaches in cancer.
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Affiliation(s)
- Susan C. Scott
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Xiaoshan M. Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Archana Balan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Gavin Pereira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kristen A. Marrone
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Vincent K. Lam
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Joseph C. Murray
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Josephine L. Feliciano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Benjamin P. Levy
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David S. Ettinger
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Christine L. Hann
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Julie R. Brahmer
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Patrick M. Forde
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rachel Karchin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jarushka Naidoo
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Department of Oncology, Beaumont Hospital, Dublin, Ireland
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Valsamo Anagnostou,
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Yu D, Yuan C, Zhang H, Chu W. The association of efficacy with PD-1/PD-L1 inhibition and tumor mutational burden in advanced nonsmall cell lung cancer: A PRISMA-guided literature review and meta-analysis. Medicine (Baltimore) 2022; 101:e29676. [PMID: 35866790 PMCID: PMC9302280 DOI: 10.1097/md.0000000000029676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Tumor mutation burden (TMB) has been reported to emerge as an independent biomarker of response to identify patients who would achieve benefit from immune checkpoint inhibitors. However, it still remains controversy that whether TMB can be a robust biomarker of response to programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1) inhibition. We performed this meta-analysis to assess the relationship between TMB and the efficacy with PD-1/PD-L1 inhibition in advanced nonsmall cell lung cancer (NSCLC). METHODS Following the recommendations of the PRISMA statement, electronic databases literature search was done on the published articles till March 2021, including Pubmed, Embase, and Cochrane library databases. Studies were selected that focused on comparing the efficacy of TMB-high group and TMB-low group in NSCLC patients received with immune checkpoint inhibitors. Meta-analysis Revman 5.3 software was utilized to calculate the pooled outcomes. RESULTS A systematic literature search was conducted 8 articles, including 11 comparative articles. Findings of our studies shown that patients with TMB-high group was associated with better clinical outcomes than TMB-low group, including progression-free survival (odds ratio [OR], 0.38; 95% confidence interval [CI], 0.29-0.49; P < .00001), complete response (OR, 4.71; 95% CI, 2.32-9.57; P < .0001), durable clinical benefit (OR, 3.76; 95% CI, 2.38-5.96; P < .00001) and the objective response rate (OR, 3.14; 95% CI, 1.83-5.37; P < .0001). While, it failed to predict overall survival benefits (OR, 0.74; 95% CI, 0.45-1.20; P = .22). CONCLUSIONS Our study found that NSCLC with high TMB who benefit from immunotherapy. The findings suggest that TMB could associated with a greater predictive power of response. Possibly a more TMB-oriented prediction model might gain more benefits from PD-1/PD-L1 inhibitors.
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Affiliation(s)
- Dahui Yu
- Department of Cardiothoracic Surgery, Yuyao People's Hospital, Yuyao 315400, Zhejiang Province, China
| | - Chong Yuan
- Department of Cardiothoracic Surgery, Yuyao People's Hospital, Yuyao 315400, Zhejiang Province, China
| | - Hedan Zhang
- Department of Cardiothoracic Surgery, Yuyao People's Hospital, Yuyao 315400, Zhejiang Province, China
| | - Wenyan Chu
- Department of Cardiothoracic Surgery, Yuyao People's Hospital, Yuyao 315400, Zhejiang Province, China
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15
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Du X, Bai H, Wang Z, Daun J, Liu Z, Xu J, Chang G, Zhu Y, Wang J. Establishment of prognostic nomograms for predicting the progression free survival of EGFR-sensitizing mutation, advanced lung cancer patients treated with EGFR-TKIs. Thorac Cancer 2022; 13:1289-1298. [PMID: 35347870 PMCID: PMC9058307 DOI: 10.1111/1759-7714.14380] [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: 01/04/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/02/2022] Open
Abstract
Background There is a lack of clinically available predictive models for patients with epidermal growth factor receptor (EGFR) mutation positive, advanced non–small cell lung cancer (NSCLC) treated with EGFR‐tyrosine kinase inhibitors (TKIs). Methods The clinical data of patients at the Cancer Hospital, Chinese Academy of Medical Sciences between from January 2016 to January 2021 were retrospectively retrieved as training set. The patients from BENEFIT trial were for the validation cohort. The nomogram was built based on independent predictors identified by univariate and multivariate Cox regression analyses. The discrimination and calibration of the nomogram were evaluated by C‐index and calibration plots. Results A total of 502 patients with complete clinical data and follow‐up information were enrolled in this study. Five independent prognostic factors, including The Eastern Cooperative Oncology Group Performance Status scale (ECOG PS), EGFR mutation subtype, EGFR co‐mutation, liver metastasis and malignant pleural effusion (p < 0.05). The C‐indexes of the nomogram were 0.694 (95% confidence interval [CI], 0.663–0.725) for the training set and 0.653 (95% CI, 0.610–0.696) for the validation set. The calibration curves for the probabilities of 9‐, 12‐ and 18‐month progression‐free survival (PFS) revealed satisfactory consistency in both the internal and external validations. Additionally, the patients were divided into two groups according to risk (high‐risk, low‐risk), and significant differences in PFS were observed between the groups in the training and external validation cohorts (p < 0.001). Conclusions We constructed and validated a convenient nomogram that have the potential to become an accurate and reliable tool for patients with EGFR mutation positive, advanced NSCLC to individually predict their potential benefits from EGFR‐TKIs, and facilitate clinical decision‐making.
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Affiliation(s)
- Xinyang Du
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianchun Daun
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Liu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiachen Xu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Geyun Chang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yixiang Zhu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Bayer P, Gatenby RA, McDonald PH, Duckett DR, Staňková K, Brown JS. Coordination games in cancer. PLoS One 2022; 17:e0261578. [PMID: 35061724 PMCID: PMC8782377 DOI: 10.1371/journal.pone.0261578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/03/2021] [Indexed: 11/19/2022] Open
Abstract
We propose a model of cancer initiation and progression where tumor growth is modulated by an evolutionary coordination game. Evolutionary games of cancer are widely used to model frequency-dependent cell interactions with the most studied games being the Prisoner's Dilemma and public goods games. Coordination games, by their more obscure and less evocative nature, are left understudied, despite the fact that, as we argue, they offer great potential in understanding and treating cancer. In this paper we present the conditions under which coordination games between cancer cells evolve, we propose aspects of cancer that can be modeled as results of coordination games, and explore the ways through which coordination games of cancer can be exploited for therapy.
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Affiliation(s)
- Péter Bayer
- Toulouse School of Economics, Toulouse, France
- Institute for Advanced Study in Toulouse, Toulouse, France
| | - Robert A. Gatenby
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Patricia H. McDonald
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, Florida United States of America
| | - Derek R. Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Kateřina Staňková
- Delft Institute of Applied Mathematics, Delft University, Delft, Netherlands
| | - Joel S. Brown
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
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17
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Katayama Y, Yamada T, Tokuda S, Okura N, Nishioka N, Morimoto K, Tanimura K, Morimoto Y, Iwasaku M, Horinaka M, Sakai T, Kita K, Yano S, Takayama K. Heterogeneity among tumors with acquired resistance to EGFR tyrosine kinase inhibitors harboring
EGFR
‐T790M mutation in non‐small cell lung cancer cells. Cancer Med 2022; 11:944-955. [PMID: 35029047 PMCID: PMC8855901 DOI: 10.1002/cam4.4504] [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: 07/29/2021] [Revised: 11/16/2021] [Accepted: 12/02/2021] [Indexed: 11/13/2022] Open
Abstract
EGFR‐T790M mutation is a major mechanism underlying acquired resistance to first‐ and second‐generation EGFR tyrosine kinase inhibitors (EGFR‐TKIs) in lung cancer with mutated EGFR. However, differences in the biological characteristics of T790M tumors based on treatment regimens with each generation of EGFR‐TKI are not fully understood. We established cell lines with acquired resistance harboring EGFR‐T790M mutation derived from xenograft tumors treated with each generation of EGFR‐TKI and examined their biological characteristics with respect to third‐generation EGFR‐TKI osimertinib sensitivity. Second‐generation EGFR‐TKI dacomitinib‐resistant cells with T790M‐exhibited higher sensitivity to osimertinib than first‐generation EGFR‐TKI gefitinib‐resistant cells with T790M via inhibition of AKT and ERK signaling and promotion of apoptosis. Furthermore, gefitinib‐resistant cells showed enhanced intratumor heterogeneity accompanied by genomic instability and activation of alternative resistance mechanisms compared with dacomitinib‐resistant cells; this suggests that the maintenance of EGFR dependency after acquiring resistance might depend on the type of EGFR‐TKI. Our results demonstrate that the progression of tumor heterogeneity via both genetic and non‐genetic mechanisms might affect osimertinib sensitivity in tumors with acquired resistance harboring EGFR‐T790M mutation.
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Affiliation(s)
- Yuki Katayama
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Tadaaki Yamada
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Shinsaku Tokuda
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Naoko Okura
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Naoya Nishioka
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Kenji Morimoto
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Keiko Tanimura
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Yoshie Morimoto
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Masahiro Iwasaku
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Mano Horinaka
- Department of Molecular‐Targeting Cancer Prevention Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Toshiyuki Sakai
- Department of Molecular‐Targeting Cancer Prevention Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
| | - Kenji Kita
- Division of Medical Oncology Cancer Research Institute Kanazawa University Kanazawa Japan
| | - Seiji Yano
- Division of Medical Oncology Cancer Research Institute Kanazawa University Kanazawa Japan
| | - Koichi Takayama
- Department of Pulmonary Medicine Graduate School of Medical Science Kyoto Prefectural University of Medicine Kyoto Japan
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Abstract
We propose a model of cancer initiation and progression where tumor growth is modulated by an evolutionary coordination game. Evolutionary games of cancer are widely used to model frequency-dependent cell interactions with the most studied games being the Prisoner's Dilemma and public goods games. Coordination games, by their more obscure and less evocative nature, are left understudied, despite the fact that, as we argue, they offer great potential in understanding and treating cancer. In this paper we present the conditions under which coordination games between cancer cells evolve, we propose aspects of cancer that can be modeled as results of coordination games, and explore the ways through which coordination games of cancer can be exploited for therapy.
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Affiliation(s)
- Péter Bayer
- Toulouse School of Economics, Toulouse, France
- Institute for Advanced Study in Toulouse, Toulouse, France
| | - Robert A Gatenby
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Patricia H McDonald
- Department of Cancer Physiology, Moffitt Cancer Center, Tampa, Florida United States of America
| | - Derek R Duckett
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Kateřina Staňková
- Delft Institute of Applied Mathematics, Delft University, Delft, Netherlands
| | - Joel S Brown
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Potential Prognostic Biomarkers of OSBPL Family Genes in Patients with Pancreatic Ductal Adenocarcinoma. Biomedicines 2021; 9:biomedicines9111601. [PMID: 34829830 PMCID: PMC8615799 DOI: 10.3390/biomedicines9111601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 12/24/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal malignancy with poor survival outcomes. In addition, oxysterol-binding protein-like (OSBPL) family members are reported to be involved in lipid binding and transport and play critical roles in tumorigenesis. However, relationships between PDAC and OSBPL family members have not comprehensively been elucidated. In this study, we used the Oncomine and GEPIA 2 databases to analyze OSBPL transcription expressions in PDAC. The Kaplan–Meier plotter and TIMER 2.0 were used to assess the relationships between overall survival (OS) and immune-infiltration with OSBPL family members. Co-expression data from cBioPortal were downloaded to assess the correlated pathways with OSBPL gene family members using DAVID. The expressions of OSBPL3, OSBPL8, OSBPL10, and OSBPL11 were found to be highly upregulated in PDAC. Low expressions of OSBPL3, OSBPL8, and OSBPL10 indicated longer OS. The functions of OSBPL family members were mainly associated with several potential signaling pathways in cancer cells, including ATP binding, integrin binding, receptor binding, and the renin-angiotensin system (RAS) signaling pathway. The transcription levels of OSBPL gene family members were connected with several immune infiltrates. Collectively, OSBPL family members are influential biomarkers for the early diagnosis of PDAC and have prognostic value, with the promise of precise treatment of PDAC in the future.
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20
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Li J, Li H, Zhang C, Zhang C, Jiang L, Wang H, Liu H. Identification of a Gene Signature Closely Related to Immunosuppressive Tumour Microenvironment Predicting Prognosis of Patients in EGFR Mutant Lung Adenocarcinoma. Front Oncol 2021; 11:732841. [PMID: 34631565 PMCID: PMC8498106 DOI: 10.3389/fonc.2021.732841] [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: 06/29/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
Lung adenocarcinomas (LUADs) harbouring epidermal growth factor receptor (EGFR) mutations are generally unable to benefit from immune checkpoint inhibitors (ICIs) due to an immunosuppressive tumour microenvironment (TME) and a lower tumour mutation burden. Currently, no gene signature can comprehensively evaluate the TME and predict the prognosis of patients with EGFR-mutant LUAD. Using the Cancer Genome Atlas database of EGFR-mutant LUAD based on the immune score derived from the ESTIMATE algorithm, we divided 80 patients with EGFR-mutant LUAD samples into high and low immune score groups with different immune microenvironments. Subsequently, we screened 396 differentially expressed immune-related genes with prognostic value. The top Gene Ontology terms were significantly enriched in biological functions related to T cell differentiation, immune response, cell cycle, and cell proliferation, which are closely related to the immune microenvironment of tumours. In addition, the KEGG pathway enrichment analysis mainly focused on cell cycle, cell adhesion molecules, and cytokine-cytokine receptor interaction, which also had a relationship with the immune response. Subsequently, we identified a three-gene signature including BTLA, BUB1B, and CENPE using the LASSO Cox regression model. The three-gene signature could accurately identify patients at risk of EGFR-mutant LUAD in the training and validation sets and high-risk patients from both the sets exhibited significantly shorter overall survival (p=0.0053 and p=0.035, respectively). CIBERSORT was used to evaluate the abundance of immune cell infiltration in the EGFR-mutant LUAD microenvironment. The immune activity of B cells and macrophages was higher in the low-risk group, while the immune activity of natural killer cells and T cells was higher in the high-risk group. Thus, the three-gene signature closely related to immunosuppressive TME could predict the risk and prognosis in patients with EGFR-mutant LUAD.
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Affiliation(s)
- Jia Li
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huahua Li
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Chenyue Zhang
- Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, China
| | - Chenxing Zhang
- Department of Nephrology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lifeng Jiang
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Haiyong Wang
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Huaimin Liu
- Department of Integrated Chinese and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
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21
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Xiao D, Deng Q, He D, Huang Y, Liang W, Wang F, Yang H. High Tumor Mutation Burden and DNA Repair Gene Mutations are Associated with Primary Resistance to Crizotinib in ALK-Rearranged Lung Cancer. Onco Targets Ther 2021; 14:4809-4817. [PMID: 34552337 PMCID: PMC8450189 DOI: 10.2147/ott.s325443] [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: 06/18/2021] [Accepted: 08/31/2021] [Indexed: 11/23/2022] Open
Abstract
Background About 20% of patients with ALK-rearranged non-small cell lung cancer (NSCLC) develop acquired resistance to tyrosine kinase inhibitor (TKI) during the first 6 months. This study aimed to examine the molecular mechanisms of early TKI resistance and prognosis in ALK-rearranged NSCLC. Methods Ten patients with ALK-rearranged NSCLC were included: five who developed rapid resistance to crizotinib (progression-free survival (PFS) ≤3 months) and five who exhibited a good response to crizotinib (PFS ≥36 months). The tumor specimens were subjected to whole-exome sequencing (WES). The validation cohort included 19 patients with ALK-rearranged NSCLC who received crizotinib; targeted sequencing of 43 selected genes was performed. The effect of the TP53 G245S mutation on crizotinib sensitivity was tested in H3122 cells. Results Mutations in DNA repair-associated genes were identified in primary resistance to crizotinib. Patients with a poor response to crizotinib harbored a greater burden of somatic mutations than those with a good response [median somatic mutations, 136 (range, 72-180) vs 31 (range, 10-48)]. Compared with the patients carrying wild-type TP53 or TP53 exon 3 deletion, 29 patients with TP53 G245S mutation showed a shorter survival time (P < 0.05), with a median PFS of 3 (95% CI: 1.9-4.1) months and a median overall survival of 7 (95% CI: 3.4-10.5) months. TP53 mutation promoted the proliferation of EML4-ALK-rearranged H3122 cells by approximately 3 folds (P < 0.001). H3122 cells with TP53 mutant were more sensitive to crizotinib compared with control cells. Conclusion A higher mutation burden and mutations in DNA repair gene, including TP53, were potentially associated with primary resistance to crizotinib in ALK-rearranged NSCLC. An immune-checkpoint inhibition strategy could be examined, which might overcome primary resistance to crizotinib in ALK-rearranged NSCLC.
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Affiliation(s)
- Dakai Xiao
- Research Center forTranslational Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
| | - Qiuhua Deng
- Research Center forTranslational Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
| | - Dongyun He
- Department of Thoracic Oncology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
| | - Ying Huang
- Department of Thoracic Oncology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
| | - Wenchi Liang
- Department of Thoracic Oncology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
| | - Fengnan Wang
- Department of Thoracic Oncology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
| | - Haihong Yang
- Department of Thoracic Oncology, State Key Laboratory of Respiratory Diseases, National Clinical Research Center of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China
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22
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Wang J, Yang F, Sun Q, Zeng Z, Liu M, Yu W, Zhang P, Yu J, Yang L, Zhang X, Ren X, Wei F. The prognostic landscape of genes and infiltrating immune cells in cytokine induced killer cell treated-lung squamous cell carcinoma and adenocarcinoma. Cancer Biol Med 2021; 18:j.issn.2095-3941.2021.0023. [PMID: 34459571 PMCID: PMC8610154 DOI: 10.20892/j.issn.2095-3941.2021.0023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/20/2021] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVE Patients with non-small cell lung cancer (NSCLC) respond differently to cytokine-induced killer cell (CIK) treatment. Therefore, potential prognostic markers to identify patients who would benefit from CIK treatment must be elucidated. The current research aimed at identifying predictive prognostic markers for efficient CIK treatment of patients with NSCLC. METHODS Patients histologically diagnosed with NSCLC were enrolled from the Tianjin Medical University Cancer Institute and Hospital. We performed whole-exome sequencing (WES) on the tumor tissues and paired adjacent benign tissues collected from 50 patients with NSCLC, and RNA-seq on tumor tissues of 17 patients with NSCLC before CIK immunotherapy treatment. Multivariate Cox proportional hazard regression analysis was used to analyze the association between clinical parameters and prognostic relevance. WES and RNA-seq data between lung squamous cell carcinoma (SCC) and adenocarcinoma (Aden) were analyzed and compared. RESULTS The pathology subtype of lung cancer was the most significantly relevant clinical parameter associated with DFS, as analyzed by multivariate Cox proportional hazard regression (P = 0.031). The patients with lung SCC showed better CIK treatment efficacy and extended DFS after CIK treatment. Relatively low expression of HLA class II genes and checkpoint molecules, and less immunosuppressive immune cell infiltration were identified in the patients with lung SCC. CONCLUSIONS Coordinated suppression of the expression of HLA class II genes and checkpoint molecules, as well as less immune suppressive cell infiltration together contributed to the better CIK treatment efficacy in lung SCC than lung Aden.
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Affiliation(s)
- Jian Wang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Fan Yang
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Qian Sun
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Ziqing Zeng
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Min Liu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Wenwen Yu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Peng Zhang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Lili Yang
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Xinwei Zhang
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Xiubao Ren
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Feng Wei
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
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23
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Al-Dherasi A, Liao Y, Al-Mosaib S, Hua R, Wang Y, Yu Y, Zhang Y, Zhang X, Jalayta R, Mousa H, Al-Danakh A, Alnadari F, Almoiliqy M, Baldi S, Shi L, Lv D, Li Z, Liu Q. Allele frequency deviation (AFD) as a new prognostic model to predict overall survival in lung adenocarcinoma (LUAD). Cancer Cell Int 2021; 21:451. [PMID: 34446004 PMCID: PMC8390239 DOI: 10.1186/s12935-021-02127-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) remains one of the world’s most known aggressive malignancies with a high mortality rate. Molecular biological analysis and bioinformatics are of great importance as they have recently occupied a large area in the studies related to the identification of various biomarkers to predict survival for LUAD patients. In our study, we attempted to identify a new prognostic model by developing a new algorithm to calculate the allele frequency deviation (AFD), which in turn may assist in the early diagnosis and prediction of clinical outcomes in LUAD. Method First, a new algorithm was developed to calculate AFD using the whole-exome sequencing (WES) dataset. Then, AFD was measured for 102 patients, and the predictive power of AFD was assessed using Kaplan–Meier analysis, receiver operating characteristic (ROC) curves, and area under the curve (AUC). Finally, multivariable cox regression analyses were conducted to evaluate the independence of AFD as an independent prognostic tool. Result The Kaplan–Meier analysis showed that AFD effectively segregated patients with LUAD into high-AFD-value and low-AFD-value risk groups (hazard ratio HR = 1.125, 95% confidence interval CI 1.001–1.26, p = 0.04) in the training group. Moreover, the overall survival (OS) of patients who belong to the high-AFD-value group was significantly shorter than that of patients who belong to the low-AFD-value group with 42.8% higher risk and 10% lower risk of death for both groups respectively (HR for death = 1.10; 95% CI 1.01–1.2, p = 0.03) in the training group. Similar results were obtained in the validation group (HR = 4.62, 95% CI 1.22–17.4, p = 0.02) with 41.6%, and 5.5% risk of death for patients who belong to the high and low-AFD-value groups respectively. Univariate and multivariable cox regression analyses demonstrated that AFD is an independent prognostic model for patients with LUAD. The AUC for 5-year survival were 0.712 and 0.86 in the training and validation groups, respectively. Conclusion AFD was identified as a new independent prognostic model that could provide a prognostic tool for physicians and contribute to treatment decisions. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02127-z.
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Affiliation(s)
- Aisha Al-Dherasi
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.,Department of Biochemistry, Faculty of Science, Ibb University, Ibb, Yemen
| | - Yuwei Liao
- Yangjiang Key Laboratory of Respiratory Diseases, Yangjiang Peoples Hospital, Yangjiang, Guangdong, People's Republic of China
| | - Sultan Al-Mosaib
- Department of Computer Science and Technology, Sahyadri Science Collage, Kuvempu University, Shimoga district, Karnataka, India
| | - Rulin Hua
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Yichen Wang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Yu Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Xuehong Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Raeda Jalayta
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Haithm Mousa
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Abdullah Al-Danakh
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Fawze Alnadari
- Department of Food Science and Engineering, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, People's Republic of China
| | - Marwan Almoiliqy
- Key Lab of Aromatic Plant Resources Exploitation and Utilization in Sichuan Higher Education, Yibin University, Yibin, 644000, Sichuan, China
| | - Salem Baldi
- Department of Clinical Biochemistry, College of Laboratory Diagnostic Medicine, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, 2005 Songhu Road, Shanghai, 200438, People's Republic of China
| | - Dekang Lv
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.
| | - Zhiguang Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.
| | - Quentin Liu
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, Liaoning, People's Republic of China.
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Wang M, Herbst RS, Boshoff C. Toward personalized treatment approaches for non-small-cell lung cancer. Nat Med 2021; 27:1345-1356. [PMID: 34385702 DOI: 10.1038/s41591-021-01450-2] [Citation(s) in RCA: 376] [Impact Index Per Article: 125.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/24/2021] [Indexed: 12/25/2022]
Abstract
Worldwide, lung cancer is the most common cause of cancer-related deaths. Molecular targeted therapies and immunotherapies for non-small-cell lung cancer (NSCLC) have improved outcomes markedly over the past two decades. However, the vast majority of advanced NSCLCs become resistant to current treatments and eventually progress. In this Perspective, we discuss some of the recent breakthrough therapies developed for NSCLC, focusing on immunotherapies and targeted therapies. We highlight our current understanding of mechanisms of resistance and the importance of incorporating genomic analyses into clinical studies to decipher these further. We underscore the future role of neoadjuvant and maintenance combination therapy approaches to potentially cure early disease. A major challenge to successful development of rational combination therapies will be the application of robust predictive biomarkers for clear-cut patient stratification, and we provide our views on clinical research areas that could influence how NSCLC will be managed over the coming decade.
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Affiliation(s)
- Meina Wang
- Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Roy S Herbst
- Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT, USA.
| | - Chris Boshoff
- Yale Comprehensive Cancer Center, Yale School of Medicine, New Haven, CT, USA. .,Pfizer Inc., New York City, NY, USA.
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25
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Huang YH, Hsu KH, Chin CS, Tseng JS, Yang TY, Chen KC, Su KY, Yu SL, Chen JJW, Chang GC. The Clinical Outcomes of Different First-Line EGFR-TKIs plus Bevacizumab in Advanced EGFR-mutant Lung Adenocarcinoma. Cancer Res Treat 2021; 54:434-444. [PMID: 34352999 PMCID: PMC9016311 DOI: 10.4143/crt.2021.671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 11/30/2022] Open
Abstract
Purpose The aim of this study was to investigate the efficacy of various epidermal growth factor receptor (EGFR)–tyrosine kinase inhibitors (TKIs) plus bevacizumab in advanced EGFR-mutant lung adenocarcinoma patients. Materials and Methods From August 2016 to October 2020, we enrolled advanced lung adenocarcinoma patients harboring exon 19 deletion or L858R receiving gefitinib, erlotinib and afatinib plus bevacizumab as the first-line treatment for the purposes of analysis. Results A total of 36 patients were included in the final analysis. Three patients received gefitinib, 17 received erlotinib, and 16 received afatinib combined with bevacizumab as the first-line treatment. The objective response rate was 77.8%, and disease control rate was 94.4%. The overall median progression-free survival (PFS) was 16.4 months, while the median PFS was 17.1 months in patients with exon 19 deletion, and 16.2 months in patients with L858R mutation (p=0.311). Regarding the use of different EGFR-TKIs, the median PFS was 17.1 months in the erlotinib group and 21.6 months in the afatinib group (p=0.617). In patients with brain metastasis at baseline, the median PFS was 18.9 months in the erlotinib group and 16.4 months in the afatinib group (p=0.747). Amongst patients harboring exon 19 deletion, the median PFS was 16.2 months in the erlotinib group and not-reached in the afatinib group (p=0.141). In patients with L858R mutation, the median PFS was 18.9 months in the erlotinib group and 16.2 months in the afatinib group (p=0.481). Conclusion Our research demonstrates that not only erlotinib combined with bevacizumab, but also afatinib plus bevacizumab as first-line treatment, provides solid clinical efficacy in advanced EGFR-mutant lung adenocarcinoma patients.
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Affiliation(s)
- Yen-Hsiang Huang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kuo-Hsuan Hsu
- Division of Critical Care and Respiratory Therapy, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chun-Shih Chin
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jeng-Sen Tseng
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Tsung-Ying Yang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Kun-Chieh Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan.,Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Center of Genomic and Precision Medicine, National Taiwan University, Taipei,Taiwan.,Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jeremy J W Chen
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Gee-Chen Chang
- Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Division of Pulmonary Medicine, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan.,Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan
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26
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Wang H, Chen S, Meng D, Wu C, Zhu J, Jiang M, Ning J, Wu S, Wu L, Li J, Chen B, Zhao S, Li W, Yu J, Fang Q, Zhu J, Zhao W, He Y, Zhou C. Tumor Mutation Burden and Differentially Mutated Genes Among Immune Phenotypes in Patients with Lung Adenocarcinoma. Onco Targets Ther 2021; 14:2953-2965. [PMID: 33976553 PMCID: PMC8106479 DOI: 10.2147/ott.s294993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
Introduction Nowadays, immune checkpoint blockades (ICBs) have been extensively applied in non-small cell lung cancer (NSCLC) treatment. However, the outcome of anti-program death-1/program death ligand-1 (anti-PD-1/PD-L1) therapy is not satisfying in EGFR-mutant lung adenocarcinoma (LUAD) patients and its exact mechanisms have not been fully understood. Since tumor mutation burden (TMB) and tumor immune phenotype had been thought as potential predictors for efficacy of ICBs, we further studied the TMB and immune phenotype in LUAD patients to explore potential mechanisms for poor efficacy of ICBs in EGFR positive mutated patients and to find possible factors that could impact the tumor immune phenotype which might uncover some new therapeutic strategies or combination therapies. Methods We enrolled 223 LUAD patients who underwent surgery in our hospital. We evaluated TMB through targeted panel sequencing. The tumor immune phenotype, which could be divided into non-inflamed, intermediate and inflamed, was determined through immunohistochemistry using formalin-fixed paraffin-embedded samples. Enumeration data were analyzed by Chi-square test or Fisher exact test and shown as number (proportion). Logistic regression model was employed for univariate and multivariate analysis of the association between TMB levels and clinical characteristics. Results The median TMB level was 4.0445 mutations/Mb. Multivariate analysis showed the TMB level was significantly associated with age (P=0.026), gender (P=0.041) and EGFR mutation status (P=0.015), and in EGFR-mutant patients we found a lower proportion of patients with mutated KRAS and BRCA2. Furthermore, we found patients with or without metastatic lesions would have different immune phenotype (P=0.007). And the mutational frequencies of ALK, CDKN2A, MAP2K1, IDH2 and PTEN were significantly different among three immune phenotypes. Conclusion Low TMB level could be the reason for the poor efficacy of ICBs in patients having EGFR mutation. And mutational frequencies of KRAS and BRCA2 were lower in EGFR-mutant patients. Furthermore, ALK, CDKN2A, MAP2K1, IDH2 and PTEN might involve in the formation of immune phenotypes.
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Affiliation(s)
- Hao Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Shanhao Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China
| | - Die Meng
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Chunyan Wu
- Pathology Department, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China
| | - Junjie Zhu
- Surgery Department, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China
| | - Minlin Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Jing Ning
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Shengyu Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Lijia Wu
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, 214104, People's Republic of China
| | - Jingjie Li
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, 214104, People's Republic of China
| | - Bin Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China
| | - Sha Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China
| | - Jia Yu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Qiyu Fang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Jun Zhu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Wencheng Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China.,Medical School, Tongji University, Shanghai, 200433, People's Republic of China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Shanghai, 200433, People's Republic of China
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27
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Yang DP, Lu HP, Chen G, Yang J, Gao L, Song JH, Chen SW, Mo JX, Kong JL, Tang ZQ, Li CB, Zhou HF, Yang LJ. Integrated expression analysis revealed RUNX2 upregulation in lung squamous cell carcinoma tissues. IET Syst Biol 2020; 14:252-260. [PMID: 33095746 PMCID: PMC8687175 DOI: 10.1049/iet-syb.2020.0063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/01/2020] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
This study aimed to investigate the clinicopathological significance and prospective molecular mechanism of RUNX family transcription factor 2 (RUNX2) in lung squamous cell carcinoma (LUSC). The authors used immunohistochemistry (IHC), RNA-seq, and microarray data from multi-platforms to conduct a comprehensive analysis of the clinicopathological significance and molecular mechanism of RUNX2 in the occurrence and development of LUSC. RUNX2 expression was significantly higher in 16 LUSC tissues than in paired non-cancerous tissues detected by IHC (P < 0.05). RNA-seq data from the combination of TCGA and genotype-tissue expression (GTEx) revealed significantly higher expression of RUNX2 in 502 LUSC samples than in 476 non-cancer samples. The expression of RUNX2 protein was also significantly higher in pathologic T3-T4 than in T1-T2 samples (P = 0.031). The pooled standardised mean difference (SMD) for RUNX2 was 0.87 (95% CI, 0.58-1.16), including 29 microarrays from GEO and one from ArrayExpress. The co-expression network of RUNX2 revealed complicated connections between RUNX2 and 45 co-expressed genes, which were significantly clustered in pathways including ECM-receptor interaction, focal adhesion, protein digestion and absorption, human papillomavirus infection and PI3K-Akt signalling pathway. Overexpression of RUNX2 plays an essential role in the clinical progression of LUSC.
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Affiliation(s)
- Da-Ping Yang
- Department of Pathology, The Eighth Affiliated Hospital of Guangxi Medical University/Guigang People's Hospital, Guigang, Guangxi, People's Republic of China
| | - Hui-Ping Lu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Jie Yang
- Department of Pharmacology, School of Pharmacy, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Li Gao
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Jian-Hua Song
- Department of Pathology, The Eighth Affiliated Hospital of Guangxi Medical University/Guigang People's Hospital, Guigang, Guangxi, People's Republic of China
| | - Shang-Wei Chen
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Jun-Xian Mo
- Department of Cardio-Thoracic Surgery, The Seventh Affiliated Hospital of Guangxi Medical University/Wuzhou Gongren Hospital, Wuzhou, Guangxi, People's Republic of China
| | - Jin-Liang Kong
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Zhong-Qing Tang
- Department of Pathology, The Seventh Affiliated Hospital of Guangxi Medical University/Wuzhou Gongren Hospital, Wuzhou, Guangxi, People's Republic of China
| | - Chang-Bo Li
- Department of Cardio-Thoracic Surgery, The Seventh Affiliated Hospital of Guangxi Medical University/Wuzhou Gongren Hospital, Wuzhou, Guangxi, People's Republic of China
| | - Hua-Fu Zhou
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China.
| | - Lin-Jie Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People's Republic of China
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28
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Zhu YJ, Qu X, Zhan DD, Chen HH, Li HP, Liu LR, Chen X, Liu YH, Li Y, Bai JP, Ye S, Zhang HB. Specific Gene Co-variation Acts Better Than Number of Concomitant Altered Genes in Predicting EGFR-TKI Efficacy in Non-small-cell Lung Cancer. Clin Lung Cancer 2020; 22:e98-e111. [PMID: 33067127 DOI: 10.1016/j.cllc.2020.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 08/01/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND There occurs huge heterogeneity in clinical outcomes for patients with epidermal growth factor receptor (EGFR)-mutated non-small-cell lung cancer (NSCLC) treated with EGFR tyrosine kinase inhibitors (EGFR-TKIs). The purpose of this study was to indicate genetic biomarkers predicting primary resistance of EGFR-TKIs in these patients. PATIENTS AND METHODS Using a next-generation sequencing panel with 168 cancer-related genes, matched tumor biopsy and plasma samples before treatments from patients with NSCLC were analyzed. Patients taking EGFR-TKIs were followed-up with imaging examination. Correlation of co-alterative genes with progression-free survival (PFS) was analyzed. RESULTS Of the 48 patients treated with EGFR-TKIs, 46 (95.83%) had at least 1 genetic co-variant beyond EGFR mutation. Multivariate analysis indicated that RB1, PIK3CA, and ERBB2 co-alterations, rather than number of co-alterative genes, were independently associated with poorer PFS. Grouping patients by specific gene status showed best likelihood ratio χ2, Akaike information criterion, and Harrell concordance index. The median PFS for patients in group A (less genetic co-variations and wild specific genes), group B (more genetic co-variations and wild specific genes), group C (less genetic co-variations and altered specific genes), and group D (more genetic co-variations and altered specific genes) were 10.4, 9.13 (vs. group A; P = .3112), 6.33 (vs. group B; P = .0465), and 3.90 (vs. group C; P = .0309) months, respectively. CONCLUSIONS This study revealed a high concomitant genetic alteration rate in patients with EGFR-mutated NSCLC. Specific gene variants were more important than number of altered genes in predicting poor PFS, and may help select patients needing new treatment strategies.
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Affiliation(s)
- Yan-Juan Zhu
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xin Qu
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Dan-Dan Zhan
- Department of Oncology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hui-Hui Chen
- Department of Oncology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Gynecology, Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, Zhuhai, China
| | - Hai-Peng Li
- Department of Oncology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China; Area 7 of Tumor Chemotherapy Department, Central Hospital of Guangdong Nongken, Zhanjiang, China
| | - Li-Rong Liu
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xian Chen
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yi-Hong Liu
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yong Li
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Jian-Ping Bai
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Sheng Ye
- Department of Oncology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hai-Bo Zhang
- Department of Oncology, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Oncology, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou, China.
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29
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Li WQ, Cui JW. Non-small cell lung cancer patients with ex19del or exon 21 L858R mutation: distinct mechanisms, different efficacies to treatments. J Cancer Res Clin Oncol 2020; 146:2329-2338. [PMID: 32596787 DOI: 10.1007/s00432-020-03296-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022]
Abstract
With the development of antitumor therapies, different treatment methods including monotherapy and combined therapy have achieved clinical efficacy in advanced epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer (NSCLC) patients. Exon 19 deletion (ex19del) and exon 21 L858R mutation are common sensitive subtypes of EGFR mutation. However, potential distinct mechanisms are found from several dimensions including molecular structures, biological behaviors, concomitant mutations, resistance mechanisms and tumor mutation burdens. More evidence indicates the prognostic difference of EGFR subgroups. This review focused on the progress of potential distinct mechanisms and outcomes in clinical trials of advanced NSCLC patients with ex19del or exon 21 L858R mutation.
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Affiliation(s)
- W-Q Li
- Department of Cancer Center, The First Hospital of Jilin University, Changchun, 130021, Jilin, China
| | - J-W Cui
- Department of Cancer Center, The First Hospital of Jilin University, Changchun, 130021, Jilin, China.
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30
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Yu YY, Chiou HL, Tsao SM, Huang CC, Lin CY, Lee CY, Tsao TCY, Yang SF, Huang YW. Association of Carbonic Anhydrase 9 Polymorphism and the Epithelial Growth Factor Receptor Mutations in Lung Adenocarcinoma Patients. Diagnostics (Basel) 2020; 10:diagnostics10050266. [PMID: 32365566 PMCID: PMC7277165 DOI: 10.3390/diagnostics10050266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
Carbonic anhydrase 9 (CA9) plays a vital role in lung cancer progression. The current study explored the effect of CA9 gene polymorphisms and the epidermal growth factor receptor (EGFR) mutations on the clinicopathological characters of lung adenocarcinoma. In this study, three loci of CA9 single nucleotide polymorphism (SNP) (rs2071676 A>G, rs3829078 A>G, and rs1048638 C>A) were genotyped using the TaqMan allelic discrimination method in 193 EGFR wild type individuals and 281 EGFR mutation subjects. After adjusting for age, gender, and cigarette smoking status in logistic regression, all three CA9 SNPs illustrated a non-significant difference for the distribution between the EGFR wild type group and EGFR mutation group. Nevertheless, a significantly lower rate of CA9 SNP rs2071676 AG (adjusted odds ratio (AOR): 0.40, 95% confidence interval (CI): 0.16-0.95, p = 0.039) and AG+GG (AOR: 0.43, 95% CI: 0.18-0.98, p = 0.046) were found in the male population with L858R EGFR mutation compared to men with EGFR wild type. In addition, the CA9 SNP rs2071676 AG+GG genotype were significantly correlated to the lower tumor stage of lung adenocarcinoma in the whole study population (p = 0.044) and EGFR wild type individuals (p = 0.033). For the male population, the presence of CA9 SNP rs2071676 AG+GG genotype was also correlated to a lower tumor stage (p = 0.037) and fewer lymph node invasion (p = 0.003) in those with EGFR wild type. In conclusion, the existence of CA9 SNP rs2071676 is associated with the rate of EGFR L858R mutation in males. Furthermore, the CA9 SNP rs2071676 is correlated to lower tumor stage and lower risk for developing lymph node metastasis in lung adenocarcinoma, mainly in the EGFR wild type.
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Affiliation(s)
- Ya-Yen Yu
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Clinical Laboratory, Changhua Hospital, Changhua 513, Taiwan
| | - Hui-Ling Chiou
- School of Medical Laboratory and Biotechnology, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Clinical Laboratory, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Shih-Ming Tsao
- Division of Chest, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan; (S.-M.T.); (T.C.-Y.T.)
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
- Institute of Biochemistry, Microbiology and Immunology, Chung Shan Medical University, Taichung 402, Taiwan
| | - Chen-Cheng Huang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Hospital, Ministry of Health and Welfare, Taichung 403, Taiwan;
| | - Chih-Yun Lin
- Department of Health, Pulmonary and Critical Care Unit, Changhua Hospital, Changhua 500, Taiwan;
| | - Chia-Yi Lee
- Department of Ophthalmology, Show Chwan Memorial Hospital, Changhua 500, Taiwan;
| | - Thomas Chang-Yao Tsao
- Division of Chest, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan; (S.-M.T.); (T.C.-Y.T.)
- School of Medicine, Chung Shan Medical University, Taichung 402, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung 402, Taiwan
- Correspondence: (S.-F.Y.); (Y.-W.H.)
| | - Yi-Wen Huang
- Institute of Medicine, Chung Shan Medical University, Taichung 402, Taiwan;
- Department of Health, Pulmonary and Critical Care Unit, Changhua Hospital, Changhua 500, Taiwan;
- Correspondence: (S.-F.Y.); (Y.-W.H.)
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