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Akın D, Kahraman Çeti N N, Erdoğdu İH, Öztürk H, Meteoğlu İ. Clinicopathological significance of mutation profile detected by next generation sequencing in different metastatic organs of non-small cell lung cancers. Pathol Res Pract 2024; 260:155463. [PMID: 39013258 DOI: 10.1016/j.prp.2024.155463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/28/2024] [Accepted: 07/12/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND The primary tumor and it's metastases show heterogeneity in molecular studies for targeted therapies in Non-Small Cell Lung Cancer(NSCLC), the leading cause of cancer-related deaths worldwide. The study aimed to identify somatic mutations in biopsies from NSCLC patients' metastatic organs using Next-Generation Sequencing(NGS) and examine their association with clinicopathological parameters. MATERIALS AND METHODS The study included 128 NSCLC patients and, NGS was performed on tumor biopsies from different metastatic organs at Molecular Pathology laboratory of the Department of Medical Pathology in Aydın Adnan Menderes University Faculty of Medicine. The age, gender, histopathological diagnoses, metastatic organs, smoking and mutation status were all recorded, along with the analysis results of 72 genes and 4149 primers in the panel of the NGS system. RESULTS 53.9 % of the cases had a history of smoking and patients with brain metastases had a higher smoking rate(p=0.000). The most common occurrence(39.8 %) was lymph node metastasis, followed by brain(19.5 %). There was a strong correlation between mutation presence and metastasis in the liver(p=0.012), bone(p=0.002), and pleura(p=0.008). Smokers had a higher frequency of KRAS(p=0.000) and TP53(p=0.001) mutations. Brain metastases showed a statistically significant NF1 mutation(p=0.001), while the liver exhibited a significant BRAF mutation(p=0.000). NF1-TP53, PTEN-TP53 and NF1-PTEN were the most common concomitant mutations and, the brain was the most common metastatic organ in which they occurred. CONCLUSION Our results suggest prizing assessing detected mutations, in the prediction, follow-up and management of metastases, especially in patients with lung adenocarcinoma. The assessment also needs to consider the tumor's mutation status in metastatic organs. New therapeutic agents targeting NF1 mutations will be available in the future to treat NSCLC, especially in metastases.
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Affiliation(s)
- Dilara Akın
- Department of Pathology, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey
| | - Nesibe Kahraman Çeti N
- Department of Pathology, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey.
| | - İbrahim Halil Erdoğdu
- Department of Pathology, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey
| | - Hakan Öztürk
- Department of Biostatistics, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey
| | - İbrahim Meteoğlu
- Department of Pathology, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey
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2
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Sun J, Dong M, Xiang X, Zhang S, Wen D. Notch signaling and targeted therapy in non-small cell lung cancer. Cancer Lett 2024; 585:216647. [PMID: 38301911 DOI: 10.1016/j.canlet.2024.216647] [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: 08/02/2023] [Revised: 12/20/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024]
Abstract
The Notch signaling pathway plays pivotal roles in cell proliferation, stemness and invasion of non-small cell lung cancer (NSCLC). The human Notch family consists of four receptors, namely Notch1, Notch2, Notch3, and Notch4. These receptors are transmembrane proteins that play crucial roles in various cellular processes. Notch1 mostly acts as a pro-carcinogenic factor in NSCLC but sometimes acts as a suppressor. Notch2 has been demonstrated to inhibit the growth and progression of NSCLC, whereas Notch3 facilitates these biological behaviors of NSCLC. The role of Notch4 in NSCLC has not been fully elucidated, but it is evident that Notch4 promotes tumor progression. At present, drugs targeting the Notch pathway are being explored for NSCLC therapy, a majority of which are already in the stage of preclinical research and clinical trials, with bright prospects in the clinical treatment of NSCLC.
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Affiliation(s)
- Jiajun Sun
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, PR China
| | - Meichen Dong
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, PR China
| | - Xin Xiang
- Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, PR China
| | - Shubing Zhang
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, 410013, PR China.
| | - Doudou Wen
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, 410013, PR China.
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Smyth EN, John J, Tiu RV, Willard MD, Beyrer JK, Bowman L, Sheffield KM, Han Y, Brastianos PK. Clinicogenomic factors and treatment patterns among patients with advanced non-small cell lung cancer with or without brain metastases in the United States. Oncologist 2023; 28:e1075-e1091. [PMID: 37358877 PMCID: PMC10628559 DOI: 10.1093/oncolo/oyad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/19/2023] [Indexed: 06/27/2023] Open
Abstract
BACKGROUND This retrospective, real-world study evaluated the prevalence of brain metastases, clinicodemographic characteristics, systemic treatments, and factors associated with overall survival among patients with advanced non-small cell lung cancer (aNSCLC) in the US. We also described the genomic characterization of 180 brain metastatic specimens and frequency of clinically actionable genes. MATERIALS AND METHODS De-identified electronic health records-derived data of adult patients diagnosed with aNSCLC between 2011 and 2017 were analyzed from a US-nationwide clinicogenomic database. RESULTS Of 3257 adult patients with aNSCLC included in the study, approximately 31% (n = 1018) had brain metastases. Of these 1018 patients, 71% (n = 726) were diagnosed with brain metastases at initial NSCLC diagnosis; 57% (n = 583) of patients with brain metastases received systemic treatment. Platinum-based chemotherapy combinations were the most common first-line therapy; single-agent chemotherapies, epidermal growth factor receptor tyrosine kinase inhibitors, and platinum-based chemotherapy combinations were used in second line. Patients with brain metastases had a 1.56 times greater risk of death versus those with no brain metastases. In the brain metastatic specimens (n = 180), a high frequency of genomic alterations in the p53, MAPK, PI3K, mTOR, and cell-cycle associated pathways was observed. CONCLUSION The frequency of brain metastases at initial clinical presentation and associated poor prognosis for patients in this cohort underscores the importance of early screening for brain metastasis in NSCLC. Genomic alterations frequently identified in this study emphasize the continued need for genomic research and investigation of targeted therapies in patients with brain metastases.
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Affiliation(s)
- Emily Nash Smyth
- Eli Lilly and Company, Value Evidence Outcomes - Research, Indianapolis, IN 46225, USA
| | - Jincy John
- Eli Lilly and Company, Value Evidence Outcomes - Research, Indianapolis, IN 46225, USA
| | - Ramon V Tiu
- Eli Lilly and Company, Value Evidence Outcomes - Research, Indianapolis, IN 46225, USA
| | - Melinda Dale Willard
- Eli Lilly and Company, Lilly Global Clinical Development, Indianapolis, IN 46225, USA
| | - Julie Kay Beyrer
- Eli Lilly and Company, Value Evidence Outcomes - Research, Indianapolis, IN 46225, USA
| | - Lee Bowman
- Eli Lilly and Company, Value Evidence Outcomes - Research, Indianapolis, IN 46225, USA
| | - Kristin M Sheffield
- Eli Lilly and Company, Value Evidence Outcomes - Research, Indianapolis, IN 46225, USA
| | - Yimei Han
- Eli Lilly and Company, Statistics RWE, Indianapolis, IN 46225, USA
| | - Priscilla K Brastianos
- Divisions of Hematology/Oncology and Neuro-Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
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4
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Andrews LJ, Thornton ZA, Saleh R, Dawson S, Short SC, Daly R, Higgins JPT, Davies P, Kurian KM. Genomic landscape and actionable mutations of brain metastases derived from non-small cell lung cancer: A systematic review. Neurooncol Adv 2023; 5:vdad145. [PMID: 38130901 PMCID: PMC10734675 DOI: 10.1093/noajnl/vdad145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Background Brain metastases derived from non-small cell lung cancer (NSCLC) represent a significant clinical problem. We aim to characterize the genomic landscape of brain metastases derived from NSCLC and assess clinical actionability. Methods We searched Embase, MEDLINE, Web of Science, and BIOSIS from inception to 18/19 May 2022. We extracted information on patient demographics, smoking status, genomic data, matched primary NSCLC, and programmed cell death ligand 1 expression. Results We found 72 included papers and data on 2346 patients. The most frequently mutated genes from our data were EGFR (n = 559), TP53 (n = 331), KRAS (n = 328), CDKN2A (n = 97), and STK11 (n = 72). Common missense mutations included EGFR L858R (n = 80) and KRAS G12C (n = 17). Brain metastases of ever versus never smokers had differing missense mutations in TP53 and EGFR, except for L858R and T790M in EGFR, which were seen in both subgroups. Of the top 10 frequently mutated genes that had primary NSCLC data, we found 37% of the specific mutations assessed to be discordant between the primary NSCLC and brain metastases. Conclusions To our knowledge, this is the first systematic review to describe the genomic landscape of brain metastases derived from NSCLC. These results provide a comprehensive outline of frequently mutated genes and missense mutations that could be clinically actionable. These data also provide evidence of differing genomic landscapes between ever versus never smokers and primary NSCLC compared to the BM. This information could have important consequences for the selection and development of targeted drugs for these patients.
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Affiliation(s)
- Lily J Andrews
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Zak A Thornton
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Ruqiya Saleh
- Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan C Short
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Richard Daly
- Cellular Pathology Department, North Bristol NHS Trust, Bristol, UK
| | - Julian P T Higgins
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Philippa Davies
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
| | - Kathreena M Kurian
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, UK
- Brain Tumour Research Centre, Bristol Medical School, University of Bristol, Bristol, UK
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Ung TH, Meola A, Chang SD. Metastatic Lesions of the Brain and Spine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1405:545-564. [PMID: 37452953 DOI: 10.1007/978-3-031-23705-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Brain and spinal metastases are common in cancer patients and are associated with significant morbidity and mortality. Continued advancement in the systemic care of cancer has increased the life expectancy of patients, and consequently, the incidence of brain and spine metastasis has increased. There has been an increase in the understanding of oncogenic mutations, and research has also demonstrated spatial and temporal mutations in patients that may drive overall treatment resistance and failure. Combinatory treatments with radiation, surgery, and newer systemic therapies have continued to increase the life expectancy of patients with brain and spine metastases. Given the overall complexity of brain and spine metastases, this chapter aims to give a comprehensive overview and cover important topics concerning brain and spine metastases. This will include the molecular, genetic, radiographic, surgical, and non-surgical treatments of brain and spinal metastases.
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Affiliation(s)
- Timothy H Ung
- Center for Academic Medicine, Department of Neurosurgery, MC: 5327, Stanford University School of Medicine, 453 Quarry Road, Palo Alto, CA, 94304, USA
| | - Antonio Meola
- Center for Academic Medicine, Department of Neurosurgery, MC: 5327, Stanford University School of Medicine, 453 Quarry Road, Palo Alto, CA, 94304, USA.
| | - Steven D Chang
- Center for Academic Medicine, Department of Neurosurgery, MC: 5327, Stanford University School of Medicine, 453 Quarry Road, Palo Alto, CA, 94304, USA
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Matched Analyses of Brain Metastases versus Primary Non-Small Cell Lung Cancer Reveal a Unique microRNA Signature. Int J Mol Sci 2022; 24:ijms24010193. [PMID: 36613642 PMCID: PMC9820685 DOI: 10.3390/ijms24010193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Distant spreading of tumor cells to the central nervous system in non-small cell lung cancer (NSCLC) occurs frequently and poses major clinical issues due to limited treatment options. RNAs displaying differential expression in brain metastasis versus primary NSCLC may explain distant tumor growth and may potentially be used as therapeutic targets. In this study, we conducted systematic microRNA expression profiling from tissue biopsies of primary NSCLC and brain metastases from 25 patients. RNA analysis was performed using the nCounter Human v3 miRNA Expression Assay, NanoString technologies, followed by differential expression analysis and in silico target gene pathway analysis. We uncovered a panel of 11 microRNAs with differential expression and excellent diagnostic performance in brain metastasis versus primary NSCLC. Five microRNAs were upregulated in brain metastasis (miR-129-2-3p, miR-124-3p, miR-219a-2-3p, miR-219a-5p, and miR-9-5p) and six microRNAs were downregulated in brain metastasis (miR-142-3p, miR-150-5p, miR-199b-5p, miR-199a-3p, miR-199b-5p, and miR-199a-5p). The differentially expressed microRNAs were predicted to converge on distinct target gene networks originating from five to twelve core target genes. In conclusion, we uncovered a unique microRNA profile linked to two target gene networks. Our results highlight the potential of specific microRNAs as biomarkers for brain metastasis in NSCLC and indicate plausible mechanistic connections.
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Zhao W, Zhou W, Rong L, Sun M, Lin X, Wang L, Wang S, Wang Y, Hui Z. Epidermal growth factor receptor mutations and brain metastases in non-small cell lung cancer. Front Oncol 2022; 12:912505. [PMID: 36457515 PMCID: PMC9707620 DOI: 10.3389/fonc.2022.912505] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/20/2022] [Indexed: 10/07/2023] Open
Abstract
Studies have revealed that non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations has a high incidence of brain metastases (BMs). However, the association between EGFR mutations and BMs remains unknown. This review summarizes detailed information about the incidence of BMs, clinical and imaging characteristics of BMs, brain surveillance strategies, influence of treatments on BMs, prognosis after BMs, and differences in EGFR mutations between paired primary tumors and BMs in EGFR-mutated NSCLC. The prognostic results demonstrate that patients with mutated EGFR have a higher incidence of BMs, EGFR tyrosine kinase inhibitors (EGFR-TKIs) (afatinib and osimertinib) delay the development of BMs, and patients with mutated EGFR with synchronous or early BMs have better overall survival after BMs than those with wild-type EGFR. The EGFR mutation status of BM sites is not always in accordance with the primary tumors, which indicates that there is heterogeneity in EGFR gene status between paired primary tumors and BMs. However, the EGFR gene status of the primary site can largely represent that of BM sites. Among patients developing synchronous BMs, patients with mutated EGFR are less likely to have central nervous system (CNS) symptoms than patients with wild-type EGFR. However, the possibility of neuro-symptoms is high in patients with metachronous BMs. Patients with mutated EGFR tend to have multiple BMs as compared to patients with wild-type EGFR. Regarding very early-stage NSCLC patients without neuro-symptoms, regular neuroimaging follow-up is not recommended. Among advanced NSCLC patients with EGFR mutation, liberal brain imaging follow-up in the first several years showed more advantages in terms of cost.
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Affiliation(s)
- Wei Zhao
- Department of Radiation Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing, China
| | - Wei Zhou
- Department of Radiation Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing, China
| | - Li Rong
- Department of Gastroenterology, Bishan Hospital of Chongqing medical university/Bishan Hospital of Chongqing, Chongqing, China
| | - Mao Sun
- Department of Radiation Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing, China
| | - Xing Lin
- Department of Radiation Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing, China
| | - Lulu Wang
- Department of Radiation Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing, China
| | - Shiqiang Wang
- Department of Neurosurgery, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing, China
| | - Ying Wang
- Department of Radiation Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital, Chongqing, China
| | - Zhouguang Hui
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of VIP Medical Services, 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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Molecular Mechanisms Driving the Formation of Brain Metastases. Cancers (Basel) 2022; 14:cancers14194963. [PMID: 36230886 PMCID: PMC9563727 DOI: 10.3390/cancers14194963] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Brain metastases are the most common brain tumor in adults and are associated with poor prognosis. The propensity of different solid tumors to metastasize varies greatly, with lung, breast, and melanoma primary tumors commonly leading to brain metastases, while other primaries such as prostate rarely metastasize to the brain. The molecular mechanisms that predispose and facilitate brain metastasis development are poorly understood. In this review, we present the current data on the genomic landscape of brain metastases that arise from various primary cancers and also outline potential molecular mechanisms that drive the formation of distant metastases in the brain. Abstract Targeted therapies for cancers have improved primary tumor response rates, but concomitantly, brain metastases (BM) have become the most common brain tumors in adults and are associated with a dismal prognosis of generally less than 6 months, irrespective of the primary cancer type. They most commonly occur in patients with primary breast, lung, or melanoma histologies; however, they also appear in patients with other primary cancers including, but not limited to, prostate cancer, colorectal cancer, and renal cell carcinoma. Historically, molecular biomarkers have normally been identified from primary tumor resections. However, clinically informative genomic alterations can occur during BM development and these potentially actionable alterations are not always detected in the primary tumor leading to missed opportunities for effective targeted therapy. The molecular mechanisms that facilitate and drive metastasis to the brain are poorly understood. Identifying the differences between the brain and other extracranial sties of metastasis, and between primary tumors and BM, is essential to improving our understanding of BM development and ultimately patient management and survival. In this review, we present the current data on the genomic landscape of BM from various primary cancers which metastasize to the brain and outline potential mechanisms which may play a role in promoting the formation of the distant metastases in the brain.
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Feng A, Li Y, Li G, Wang Y, Wen Q, Yang Z, Tian K, Lv H, Guo L, Zhang S, Liu X, Jiang D. Genomic Features of Organ-Specific Metastases in Lung Adenocarcinoma. Front Oncol 2022; 12:908759. [PMID: 35912232 PMCID: PMC9331737 DOI: 10.3389/fonc.2022.908759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/09/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundThe genomic features of cancer cells may confer the metastatic ability of lung adenocarcinoma (LUAD) to metastasize to specific organs. We aimed to identify the differences in genomic alterations between patients with primary LUAD with and without metastases and to elucidate the metastatic biology that may help developing biomarker-directed therapies for advanced or metastatic disease.MethodsA retrospective cohort of 497 patients with LUAD including 388 primary tumors (PR), 53 bone metastases (MT-bone), 30 liver metastases (MT-liver), and 26 brain metastases (MT-brain) was tested for genomic alterations by a next-generation sequencing assay.ResultsThe EGFR, TP53, TERT, LRP1B, CDKN2A, ERBB2, ALK, and KMT2C genes had a high frequency of mutations, and the mutations were shared by PR and metastases groups. TP53 and EGFR were the most common mutated genes. In comparison with PR, KRAS, STK11, ATM, NPM1, and ROS1 were significantly mutated in MT-brain, and TP53, MYC, RSPO2, CDKN2a, and CDKN2B were significantly mutated in MT-liver. The frequencies of TP53, CDKN2A, MTAP, PRKCI, and APC mutations were higher in MT-bone than that in PR. The ERBB, phosphoinositide-3-kinase/protein kinase B (PI3K-AKT), cell cycle, Fibroblast growth factor (FGF), and homologous recombination deficiency signaling pathways were affected in both PR and metastases, and there is higher frequency of mutations in metastases. Moreover, the co-mutations in patients with PR and metastasis were respectively analyzed. In addition, the programmed death ligand 1 (PD-L1) level was obviously related to tumor stage and tumor metastases, and the tumor mutational burden was correlated to clinicopathological features including age, gender, pathological stages, and tumor metastases. FGFR1, KAT6A, MYC, RAD21, TP53, and DAXX were also dramatically correlated to the tumor mutational burden.ConclusionMetastases are the most devastating stage of tumors and the main cause of cancer-related deaths. Our results provided a clinically relevant view of the tumor-intrinsic mutational landscape of patients with metastatic LUAD.
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Affiliation(s)
- Alei Feng
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Shandong Qidu Pharmaceutical Co. Ltd., Shandong Provincial Key Laboratory of Neuroprotective Drugs, Zibo, China
| | - Yanjun Li
- Department of Thoracic Surgery, The Second People’s Hospital of Dezhou, Dezhou, China
| | - Guangxu Li
- Department of Thoracic Surgery, The Second People’s Hospital of Dezhou, Dezhou, China
| | - Yu Wang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qiang Wen
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Zhe Yang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Kaihua Tian
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongying Lv
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lijie Guo
- Shanghai OrigiMed Co., Ltd, Shanghai, China
| | | | | | - Da Jiang
- Medical Oncology, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
- *Correspondence: Da Jiang,
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Mekonnen N, Yang H, Shin YK. Homologous Recombination Deficiency in Ovarian, Breast, Colorectal, Pancreatic, Non-Small Cell Lung and Prostate Cancers, and the Mechanisms of Resistance to PARP Inhibitors. Front Oncol 2022; 12:880643. [PMID: 35785170 PMCID: PMC9247200 DOI: 10.3389/fonc.2022.880643] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022] Open
Abstract
Homologous recombination (HR) is a highly conserved DNA repair mechanism that protects cells from exogenous and endogenous DNA damage. Breast cancer 1 (BRCA1) and breast cancer 2 (BRCA2) play an important role in the HR repair pathway by interacting with other DNA repair proteins such as Fanconi anemia (FA) proteins, ATM, RAD51, PALB2, MRE11A, RAD50, and NBN. These pathways are frequently aberrant in cancer, leading to the accumulation of DNA damage and genomic instability known as homologous recombination deficiency (HRD). HRD can be caused by chromosomal and subchromosomal aberrations, as well as by epigenetic inactivation of tumor suppressor gene promoters. Deficiency in one or more HR genes increases the risk of many malignancies. Another conserved mechanism involved in the repair of DNA single-strand breaks (SSBs) is base excision repair, in which poly (ADP-ribose) polymerase (PARP) enzymes play an important role. PARP inhibitors (PARPIs) convert SSBs to more cytotoxic double-strand breaks, which are repaired in HR-proficient cells, but remain unrepaired in HRD. The blockade of both HR and base excision repair pathways is the basis of PARPI therapy. The use of PARPIs can be expanded to sporadic cancers displaying the “BRCAness” phenotype. Although PARPIs are effective in many cancers, their efficacy is limited by the development of resistance. In this review, we summarize the prevalence of HRD due to mutation, loss of heterozygosity, and promoter hypermethylation of 35 DNA repair genes in ovarian, breast, colorectal, pancreatic, non-small cell lung cancer, and prostate cancer. The underlying mechanisms and strategies to overcome PARPI resistance are also discussed.
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Affiliation(s)
- Negesse Mekonnen
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Department of Veterinary Science, School of Animal Science and Veterinary Medicine, Bahir Dar University, Bahir Dar, Ethiopia
| | - Hobin Yang
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
| | - Young Kee Shin
- Department of Pharmacy, Research Institute of Pharmaceutical Science, Seoul National University College of Pharmacy, Seoul, South Korea
- Bio-MAX/N-Bio, Seoul National University, Seoul, South Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University Graduate School of Convergence Science and Technology, Seoul, South Korea
- LOGONE Bio Convergence Research Foundation, Center for Companion Diagnostics, Seoul, South Korea
- *Correspondence: Young Kee Shin,
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Tonse R, Rubens M, Appel H, Tom MC, Hall MD, Odia Y, McDermott MW, Ahluwalia MS, Mehta MP, Kotecha R. Systematic review and meta-analysis of lung cancer brain metastasis and primary tumor receptor expression discordance. Discov Oncol 2021; 12:48. [PMID: 35201504 PMCID: PMC8777541 DOI: 10.1007/s12672-021-00445-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Treatment paradigms for metastatic non-small cell lung cancer are increasingly based on biomarker-driven therapies, with the most common alteration being mutation in the epidermal growth factor receptor (EGFR). Change in expression of such biomarkers could have a profound impact on the choice and efficacy of a selected targeted therapeutic, and hence the objective of this study was to analyze discordance in EGFR status in patients with lung cancer brain metastasis (LCBM). METHODS Using PRISMA guidelines, a systematic review was performed of series in the Medline database of biopsied or resected LCBM published before May, 2020. Key words included "lung cancer" and "brain metastasis" combined with "epidermal growth factor receptor/EGFR," and "receptor conversion/discordance or concordance." Weighted random effects models were used to calculate pooled estimates. RESULTS We identified 501 patients from 19 full-text articles for inclusion in this study. All patients underwent biopsy or resection of at least one intracranial lesion to compare to the primary tumor. On primary/LCBM comparison, the weighted pooled estimate for overall EGFR receptor discordance was 10% (95% CI 5-17%). The weighted effects model estimated a gain of an EGFR mutation in a brain metastases in patients with negative primary tumors was 7% (95% CI 4-12%). Alternatively, the weighted effects model estimate of loss of an EGFR mutation in patients with detected mutations in the primary tumor was also 7% (95% CI 4-10%). KRAS testing was also performed on both primary tumors and LCBM in a subset of 148 patients. The weighted effects estimate of KRAS-mutation discordance among LCBM compared to primary tumors was 13% (95% CI 5-27%). The weighted effects estimated of KRAS gain and loss in LCBM was 10% (95% CI 6-18%) and 8% (95% CI 4-15%), respectively. Meta-regression analysis did not find any association with any factors that could be associated with discordances. CONCLUSIONS EGFR and KRAS mutation status discordance between primary tumor and LCBM occurs in approximately 10% and 13% of patients, respectively. Evaluation of LCBM receptor status is key to biomarker-driven targeted therapy for intracranial disease and awareness of subtype switching is critical for those patients treated with systemic therapy alone for intracranial disease.
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Affiliation(s)
- Raees Tonse
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Office 1R203, Miami, FL, 33176, USA
| | - Muni Rubens
- Office of Clinical Research, Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA
| | - Haley Appel
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Office 1R203, Miami, FL, 33176, USA
| | - Martin C Tom
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Office 1R203, Miami, FL, 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Matthew D Hall
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Office 1R203, Miami, FL, 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Yazmin Odia
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Division of Neuro-Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA
| | - Michael W McDermott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Department of Neurosurgery, Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL, USA
| | - Manmeet S Ahluwalia
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Department of Medical Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, FL, USA
| | - Minesh P Mehta
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Office 1R203, Miami, FL, 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Rupesh Kotecha
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Office 1R203, Miami, FL, 33176, USA.
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.
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12
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Karimpour M, Ravanbakhsh R, Maydanchi M, Rajabi A, Azizi F, Saber A. Cancer driver gene and non-coding RNA alterations as biomarkers of brain metastasis in lung cancer: A review of the literature. Biomed Pharmacother 2021; 143:112190. [PMID: 34560543 DOI: 10.1016/j.biopha.2021.112190] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 02/07/2023] Open
Abstract
Brain metastasis (BM) is the most common event in patients with lung cancer. Despite multimodal treatments and advances in systemic therapies, development of BM remains one of the main factors associated with poor prognosis and mortality in patients with lung cancer. Therefore, better understanding of mechanisms involved in lung cancer brain metastasis (LCBM) is of great importance to suppress cancer cells and to improve the overall survival of patients. Several cancer-related genes such as EGFR and KRAS have been proposed as potential predictors of LCBM. In addition, there is ample evidence supporting crucial roles of non-coding RNAs (ncRNAs) in mediating LCBM. In this review, we provide comprehensive information on risk assessment, predictive, and prognostic panels for early detection of BM in patients with lung cancer. Moreover, we present an overview of LCBM molecular mechanisms, cancer driver genes, and ncRNAs which may predict the risk of BM in lung cancer patients. Recent clinical studies have focused on determining mechanisms involved in LCBM and their association with diagnosis, prognosis, and treatment outcomes. These studies have shown that alterations in EGFR, KRAS, BRAF, and ALK, as the most frequent coding gene alterations, and dysregulation of ncRNAs such as miR-423, miR-330-3p, miR-145, piR-651, and MALAT1 can be considered as potential biomarkers of LCBM.
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Affiliation(s)
- Mina Karimpour
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reyhaneh Ravanbakhsh
- Department of Aquatic Biotechnology, Artemia and Aquaculture Research Institute, Urmia University, Urmia, Iran
| | - Melika Maydanchi
- Zimagene Medical Genetics Laboratory, Avicenna St., Hamedan, Iran
| | - Ali Rajabi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Faezeh Azizi
- Genetics Office, Non-Communicable Disease Control Department, Public Health Department, Ministry of Health and Medical Education, Tehran, Iran
| | - Ali Saber
- Zimagene Medical Genetics Laboratory, Avicenna St., Hamedan, Iran.
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13
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Biomarkers of Targeted Therapy and Immuno-Oncology in Cancers Metastatic to the Breast. Appl Immunohistochem Mol Morphol 2021; 28:661-668. [PMID: 31517642 PMCID: PMC7664953 DOI: 10.1097/pai.0000000000000808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The breast is a rare site for metastases, and their molecular characteristics have not been studied yet. Intrinsic molecular genetics, cancer characteristics, and breast tissue immune responses in diverse metastases to the breast have not been previously studied. We identified 64 patients with cancers metastatic to the breast: 51 carcinomas and 13 melanomas. Programmed death ligand 1 (PD-L1), steroid receptors, and HER2/neu expressions were evaluated using immunohistochemistry. Gene sequencing, copy number alterations, microsatellite instability, and tumor mutational burden were performed using next-generation sequencing platforms. The 3 most common primary sites for metastatic carcinomas were lung (37%), ovary (29%), and fallopian tubes/peritoneum (14%). TP53 mutations were commonly (50%) observed among the carcinoma cases, while other mutations were characteristic for the primary cancers (VHL in renal, BRCA1 in the fallopian tube, and BRAF in melanomas). High tumor mutational burden was detected in 5/14 carcinomas and 3/7 melanomas. Tumor cell PD-L1 expression was detected in 6 carcinomas, but not in any of the melanomas, whereas immune cells' expression of PD-L1 was seen in 17 carcinomas and 6 melanomas. Estrogen receptor status was positive in 13/49 carcinomas including 12 adenocarcinomas originating from the ovary and fallopian tube or peritoneum and 1 duodenal neuroendocrine carcinoma. No carcinoma was HER2/neu positive. Intrinsic genetic characteristics of the metastases to the breast followed the pattern commonly seen in primary tumors. Biomarkers of potential benefit to immune checkpoint inhibition therapy were limited to PD-L1-positive non-small cell lung cancer. No common characteristics of the heterogeneous group of tumor metastases to this organ were identified.
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14
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Zhao HY, Li Q, Tian Y, Chen YH, Alvi HAK, Yuan XG. CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing Data. BIOLOGY 2021; 10:biology10070584. [PMID: 34202028 PMCID: PMC8301091 DOI: 10.3390/biology10070584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary In this study, we propose a copy number variation (CNV) detection method called CIRCNV, which is based on a circular profile of the read depth from sequencing data. The proposed method is an extended version of our previously developed method CNV-LOF. The main difference of CIRCNV from CNV-LOF lies in its two new features: (1) it transfers the read depth profile from a line shape to a circular shape via a polar coordinate transformation to generate a meaningful two-dimensional dataset for CNV analysis and promote fairness between the ends and middle part of the genome, and (2) it performs two rounds of CNV declaration via estimating tumor purity and recovering the truth circular RD profile. We test and evaluate the performance of CIRCNV via conducting simulation studies and real sequencing tumor sample applications. The experimental results show that CIRCNV outperforms peer methods with respect to sensitivity, precision, and the F1-score. The experiments prove that the proposed method is a reliable and effective tool in the field of variation analysis of tumor genomes. Abstract Copy number variation (CNV) is a common type of structural variation in the human genome. Accurate detection of CNVs from tumor genomes can provide crucial information for the study of tumor genesis and cancer precision diagnosis. However, the contamination of normal genomes in tumor genomes and the crude profiles of the read depth make such a task difficult. In this paper, we propose an alternative approach, called CIRCNV, for the detection of CNVs from sequencing data. CIRCNV is an extension of our previously developed method CNV-LOF, which uses local outlier factors to predict CNVs. Comparatively, CIRCNV can be performed on individual tumor samples and has the following two new features: (1) it transfers the read depth profile from a line shape to a circular shape via a polar coordinate transformation, in order to improve the efficiency of the read depth (RD) profile for the detection of CNVs; and (2) it performs a second round of CNV declaration based on the truth circular RD profile, which is recovered by estimating tumor purity. We test and validate the performance of CIRCNV based on simulation and real sequencing data and perform comparisons with several peer methods. The results demonstrate that CIRCNV can obtain superior performance in terms of sensitivity and precision. We expect that our proposed method will be a supplement to existing methods and become a routine tool in the field of variation analysis of tumor genomes.
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Affiliation(s)
- Hai-Yong Zhao
- School of Computer Science and Technology, Liaocheng University, Liaocheng 252000, China;
| | - Qi Li
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Q.L.); (Y.T.); (H.A.K.A.)
| | - Ye Tian
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Q.L.); (Y.T.); (H.A.K.A.)
| | - Yue-Hui Chen
- Shandong Provincial Key Laboratory of Network Based Intelligent Computing, University of Jinan, Ji’nan 250022, China;
| | - Haque A. K. Alvi
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Q.L.); (Y.T.); (H.A.K.A.)
| | - Xi-Guo Yuan
- School of Computer Science and Technology, Xidian University, Xi’an 710071, China; (Q.L.); (Y.T.); (H.A.K.A.)
- Correspondence:
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15
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Niu L, Dang C, Li L, Guo N, Xu Y, Li X, Xu Q, Cheng L, Zhang L, Liu L. Next-generation sequencing-based identification of EGFR and NOTCH2 complementary mutations in non-small cell lung cancer. Oncol Lett 2021; 22:594. [PMID: 34149905 PMCID: PMC8200943 DOI: 10.3892/ol.2021.12855] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022] Open
Abstract
Although targeted therapy has emerged as an effective treatment strategy for non-small cell lung cancer (NSCLC), some patients cannot benefit from such therapy due to the limited number of therapeutic targets. The present study aimed to identify mutated genes associated with clinicopathological characteristics and prognosis and to screen for mutations that are not concurrent with applicable drug target sites in patients with NSCLC. Tumor tissue and blood samples were obtained from 97 patients with NSCLC. A lung cancer-specific panel of 55 genes was established and analyzed using next-generation sequencing (NGS). The results obtained from the clinical cohort were compared with the NSCLC dataset from The Cancer Genome Atlas (TCGA). Subsequently, 25 driver genes were identified by taking the intersection of the 55 lung-cancer-specific genes with three databases, namely, the Catalog of Somatic Mutations in Cancer database, the Network of Cancer Genes database and Vogelstein's list. Functional annotation and protein-protein interaction analysis were conducted on these 25 driver genes. The χ2 test and logistic regression were used to evaluate the association between mutations in the 25 driver genes and the clinicopathological characteristics of 97 patients, and phosphatase and tensin homolog (PTEN) and kirsten rat sarcoma viral oncogene homolog (KRAS) were associated with stage at diagnosis and sex, respectively, while epidermal growth factor receptor (EGFR) was associated with sex, stage at diagnosis, metastasis, CEA and CYFRA21-1. Moreover, the association between the 25 driver gene mutations and overall survival were examined using Cox regression analysis. Age and Notch homolog 2 (NOTCH2) mutations were independent prognostic factors in TCGA dataset. The correlations between statistically significant mutations in EGFR, KRAS, PTEN and NOTCH2 were further examined, both in the clinical data and TCGA dataset. There was a negative correlation between EGFR and NOTCH2 mutations (correlation coefficient, −0.078; P=0.027). Thus, the present study highlights the importance of NOTCH2 mutations and might provide novel therapeutic options for patients with NSCLC who do not harbor EGFR mutations.
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Affiliation(s)
- Lin Niu
- Department of Human Anatomy, Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Chunyan Dang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Lin Li
- Department of Human Anatomy, Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Na Guo
- Department of Immunology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Ying Xu
- Department of Immunology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Xiangling Li
- Department of Pathology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Qian Xu
- Basic Medical Institute, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Luyang Cheng
- Department of Immunology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Li Zhang
- Department of Oncology, Affiliated Hospital of Chengde Medical University, Chengde, Hebei 067000, P.R. China
| | - Lei Liu
- Department of Immunology, Chengde Medical University, Chengde, Hebei 067000, P.R. China
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16
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Molecular Profiles of Brain Metastases: A Focus on Heterogeneity. Cancers (Basel) 2021; 13:cancers13112645. [PMID: 34071176 PMCID: PMC8198739 DOI: 10.3390/cancers13112645] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Precision cancer medicine depends on the characterization of tumor samples, usually by a single-tumor biopsy, to administer an optimal therapeutic. However, primary tumors and their metastases are often heterogeneous. A metastatic lesion may harbor a completely different genetic makeup to that of its parent tumor, and a single tumor sampling may be ineffective in selecting the most efficient therapy. Brain metastases, due to their low availability and specific microenvironment, pose a particular challenge for precision medicine. In this review, we highlight the genetic landscape of brain metastases, with a particular focus on their heterogeneity. To illustrate this problem, we present phenotypic alterations in brain metastases originating from lung cancer, breast cancer, and melanoma. This article may help clinicians better understand alterations in brain metastases and the relevance of their heterogeneity. Abstract Brain metastasis is a common and devastating clinical entity. Intratumor heterogeneity in brain metastases poses a crucial challenge to precision medicine. However, advances in next-generation sequencing, new insight into the pathophysiology of driver mutations, and the creation of novel tumor models have allowed us to gain better insight into the genetic landscapes of brain metastases, their temporal evolution, and their response to various treatments. A plethora of genomic studies have identified the heterogeneous clonal landscape of tumors and, at the same time, introduced potential targets for precision medicine. As an example, we present phenotypic alterations in brain metastases originating from three malignancies with the highest brain metastasis frequency: lung cancer, breast cancer, and melanoma. We discuss the barriers to precision medicine, tumor heterogeneity, the significance of blood-based biomarkers in tracking clonal evolution, the phylogenetic relationship between primary and metastatic tumors, blood–brain barrier heterogeneity, and limitations to ongoing research.
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17
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Liu Z, Zheng M, Lei B, Zhou Z, Huang Y, Li W, Chen Q, Li P, Deng Y. Whole-exome sequencing identifies somatic mutations associated with lung cancer metastasis to the brain. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:694. [PMID: 33987392 PMCID: PMC8106079 DOI: 10.21037/atm-21-1555] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Lung cancer is the most aggressive cancer, resulting in one-quarter of all cancer-related deaths, and its metastatic spread accounts for >70% of these deaths, especially metastasis to the brain. Metastasis-associated mutations are important biomarkers for metastasis prediction and outcome improvement. Methods In this study, we applied whole-exome sequencing (WES) to identify potential metastasis-related mutations in 12 paired lung cancer and brain metastasis samples. Results We identified 1,702 single nucleotide variants (SNVs) and 6,131 mutation events among 1,220 genes. Furthermore, we identified several lung cancer metastases associated genes (KMT2C, AHNAK2). A mean of 3.1 driver gene mutation events per tumor with the dN/dS (non-synonymous substitution rate/synonymous substitution rate) of 2.13 indicating a significant enrichment for cancer driver gene mutations. Mutation spectrum analysis found lung-brain metastasis samples have a more similar Ti/Tv (transition/transversion) profile with brain cancer in which C to T transitions are more frequent while lung cancer has more C to A transversion. We also found the most important tumor onset and metastasis pathways, such as chronic myeloid leukemia, ErbB signaling pathway, and glioma pathway. Finally, we identified a significant survival associated mutation gene ERF in both The Cancer Genome Atlas (TCGA) (P=0.01) and our dataset (P=0.012). Conclusions In summary, we conducted a pairwise lung-brain metastasis based exome-wide sequencing and identified some novel metastasis-related mutations which provided potential biomarkers for prognosis and targeted therapeutics.
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Affiliation(s)
- Zhenghao Liu
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Meiguang Zheng
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bingxi Lei
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhiwei Zhou
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yutao Huang
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenpeng Li
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qinbiao Chen
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Pengcheng Li
- Department of Thoracic Oncology, Cancer Center of Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuefei Deng
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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18
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Zhang D, Wang X, Ma S, Li P, Xue F, Mao B, Guan X, Zhou W, Peng J, Su K, Zhang C, Jia W. Targeted exome sequencing for the identification of common mutational signatures and potential driver mutations for brain metastases and prognosis. Oncol Lett 2021; 21:179. [PMID: 33574918 DOI: 10.3892/ol.2021.12440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 09/28/2020] [Indexed: 11/06/2022] Open
Abstract
Brain metastases (BMs) are malignancies in the central nervous system with poor prognosis. Genetic landscapes of the primary tumor sites have been extensively profiled; however, mutations associated with BMs are poorly understood. In the present study, target exome sequencing of 560 cancer-associated genes in samples from 52 patients with brain metastasis from various primary sites was performed. Recurrent mutations for BMs from distinct origins were identified. There were both genetic homogeneity and heterogeneity between BMs and primary lung tumor tissues. The mutation rate of the major cancer driver gene, TP53, was consistently high in both the primary lung cancer sites and BMs, while some genetic alterations, associated with DNA damage response deficiency, were specifically enriched in BMs. The mutational signatures enriched in BMs could serve as actionable targets for treatment. The mutation in the primary site of the potential brain metastasis driver gene, nuclear mitotic apparatus protein 1 (NUMA1), affected the progression-free survival time of patients with lung cancer, and patients with the NUMA1 mutation in BMs had a good prognosis. This suggested that the occurrence and clinical outcome of brain metastases could be independent of each other.
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Affiliation(s)
- Dainan Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China.,Henan Key Laboratory of Neural Regeneration and Repairment, The First Affiliated Hospital of Xinxiang Medical University, Weihui, Henan 453000, P.R. China
| | - Xi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Shunchang Ma
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Peiliang Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Department of Neurosurgery, Ditan Hospital, Capital Medical University, Beijing 100070, P.R. China
| | - Fei Xue
- Novogene Co., Ltd., Beijing 100016, P.R. China
| | - Beibei Mao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Department of Neurosurgery, Beijing Shijitan Hospital, Capital Medical University, Beijing 100043, P.R. China
| | - Xiudong Guan
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Wenjianlong Zhou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Jiayi Peng
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Kun Su
- Novogene Co., Ltd., Beijing 100016, P.R. China
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
| | - Wang Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, P.R. China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, P.R. China
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Chen X, Bu Q, Yan X, Li Y, Yu Q, Zheng H, Zhao L, Zeng Y, Lu L, Lan D, Ma J. Genomic Mutations of Primary and Metastatic Lung Adenocarcinoma in Chinese Patients. JOURNAL OF ONCOLOGY 2020; 2020:6615575. [PMID: 33488709 PMCID: PMC7787720 DOI: 10.1155/2020/6615575] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022]
Abstract
Lung cancer is still the leading cause of cancer-related death worldwide. Of lung cancer, lung adenocarcinoma (LUAD) is the most common subtype. Most patients with LUAD would develop into metastasis, which limits the available treatment. Targeted therapy and immunotherapy provided options for those advanced patients. But they also broached up challenges to identify the appropriate patients. This study aims to reveal the landscapes of genomic mutations in primary and metastatic LUAD and their actionability. This study enrolled 636 patients with LUAD, of whom 85 and 551 were from patients with and without metastasis, respectively. Next-generation sequencing technology was used to retrieve their genomic information. Genomic mutations including short nucleotide variation, long variation, copy number variations, and fusions were called. The corresponding actionability was revealed. A comparison of genomic mutations and actionability between primary and metastatic LUAD was performed. In primary tumors, BRCA2 and FAT3 were significantly mutated in older patients; while in metastases, ALK and NOTCH2 were significantly mutated in younger patients. Primary tumors in male patients were significantly mutated in LRP1B and KRAS. Compared to primary tumors, metastases harbored less short nucleotide variations but more copy number variations and fusions. In metastases, chromosome 1 and chromosome 9 had less short nucleotide variations and more CNV than in primary tumors. Genomic variations of activated dendritic cells were more frequently mutated in metastases. EGFR genomic variations were negatively associated with PD-L1 and TMB. Patients with EGFR inhibitor treatment tend to have lower PD-L1 expression. The revealed discrepancy between primary and metastatic lung cancer could help guide the treatment strategies and the development of novel drugs.
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Affiliation(s)
- Xinyu Chen
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qing Bu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xuexin Yan
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ye Li
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qian Yu
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Haiping Zheng
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liang Zhao
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | | | | | - Dong Lan
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jie Ma
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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20
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Lee WC, Reuben A, Hu X, McGranahan N, Chen R, Jalali A, Negrao MV, Hubert SM, Tang C, Wu CC, Lucas AS, Roh W, Suda K, Kim J, Tan AC, Peng DH, Lu W, Tang X, Chow CW, Fujimoto J, Behrens C, Kalhor N, Fukumura K, Coyle M, Thornton R, Gumbs C, Li J, Wu CJ, Little L, Roarty E, Song X, Lee JJ, Sulman EP, Rao G, Swisher S, Diao L, Wang J, Heymach JV, Huse JT, Scheet P, Wistuba II, Gibbons DL, Futreal PA, Zhang J, Gomez D, Zhang J. Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity. Genome Biol 2020; 21:271. [PMID: 33148332 PMCID: PMC7640699 DOI: 10.1186/s13059-020-02175-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary. RESULTS We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases. Furthermore, we analyze published WES data from 35 primary NSCLC and metastasis pairs, and transcriptomic data from 4 autopsy cases with metastatic NSCLC and one metastatic lung cancer mouse model. The majority of somatic mutations are shared between primary tumors and paired distant metastases although mutational signatures suggest different mutagenesis processes in play before and after metastatic spread. Subclonal analysis reveals evidence of monoclonal seeding in 41 of 42 patients. Pathway analysis of transcriptomic data reveals that downregulated pathways in metastases are mainly immune-related. Further deconvolution analysis reveals significantly lower infiltration of various immune cell types in metastases with the exception of CD4+ T cells and M2 macrophages. These results are in line with lower densities of immune cells and higher CD4/CD8 ratios in metastases shown by IHC. Analysis of transcriptomic data from autopsy cases and animal models confirms that immunosuppression is also present in extracranial metastases. Significantly higher somatic copy number aberration and allelic imbalance burdens are identified in metastases. CONCLUSIONS Metastasis is a molecularly late event, and immunosuppression driven by different molecular events, including somatic copy number aberration, may be a common characteristic of tumors with metastatic plasticity.
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Affiliation(s)
- Won-Chul Lee
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Runzhe Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shawna M Hubert
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad Tang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Whijae Roh
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kenichi Suda
- Department of Thoracic Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Jihye Kim
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Aik-Choon Tan
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kazutaka Fukumura
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcus Coyle
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rebecca Thornton
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik P Sulman
- New York University Langone School of Medicine, New York, NY, USA
| | - Ganesh Rao
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen Swisher
- Department of Thoracic Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason T Huse
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel Gomez
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Current Address: Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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21
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Liang H, Li C, Zhao Y, Zhao S, Huang J, Cai X, Cheng B, Xiong S, Li J, Wang W, Zhu C, Li W, He J, Liang W. Concomitant Mutations in EGFR 19Del/L858R Mutation and Their Association with Response to EGFR-TKIs in NSCLC Patients. Cancer Manag Res 2020; 12:8653-8662. [PMID: 32982456 PMCID: PMC7509478 DOI: 10.2147/cmar.s255967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/08/2020] [Indexed: 11/23/2022] Open
Abstract
Objective Differences in efficacy of epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKI) have been observed between non-small cell lung cancer (NSCLC) patients with 19 exon deletion (19Del) and L858R mutation. We explored whether the total number or pattern of concomitant mutations of 19Del and L858R may explain their different sensitivities. Patients and Methods This study contained the mutational profiles of EGFR-mutated NSCLC patients from two cohorts: Guangzhou (G1) and database (G2). Concomitant mutation status and EGFR-TKI response information were retrieved. Results A total of 403 patients covered 283 genes in the G1 and 803 patients with a different gene set in the G2 were included. Similar prevalence of total concomitant mutation number was observed in both G1 (19Del 32.48% vs L858R 30.45%; P=0.68) and G2 (19Del 74.9% vs L858R 73.2%; P=0.65) cohorts. Only HGF/c-Met pathway same more related to L858R mutation. EGFR-TKI response information was recorded for 134 patients in the G2 cohort. 19Del showed a higher objective response (OR) rate compared with L858R, regardless of concomitant mutations. Compared to patients with OR, non-OR patients had more concomitant mutations, both in 19Del (53.8% vs 83.3%; P=0.021) and L858R (51.4% vs 77.8%; P=0.029). In particular, total concomitant mutations (OR=0.27; P=0.03), sensitive EGFR mutations (OR=2.21; P=0.04), and T790M (OR=0.244; P=0.02) significantly affected the TKI response. Conclusion Concomitant mutations were widespread in 19Del and L858R and were associated with poorer OR to EGFR-TKIs. However, 19Del and L858R had similar numbers and patterns of concomitant mutations, which might not explain the different sensitivity to EGFR-TKI.
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Affiliation(s)
- Hengrui Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Caichen Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Yi Zhao
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Shen Zhao
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Jun Huang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Xiuyu Cai
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China.,Department of General Internal Medicine, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, People's Republic of China
| | - Bo Cheng
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Shan Xiong
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Jianfu Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Wei Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Changbin Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, People's Republic of China
| | - Weiwei Li
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou 510006, People's Republic of China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou, People's Republic of China
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22
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Li L, Liu Z, Han R, Li L, Wang M, Huang D, He Y. Genetic Heterogeneity Between Paired Primary and Brain Metastases in Lung Adenocarcinoma. CLINICAL MEDICINE INSIGHTS-ONCOLOGY 2020; 14:1179554920947335. [PMID: 32922114 PMCID: PMC7450461 DOI: 10.1177/1179554920947335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
Abstract
Purpose: About one-third of nonsmall cell lung cancer (NSCLC) patients develop brain
metastases (BM). However, there is an unmet need for early diagnosis and
treatment of BM. The precise mechanism for BM is still unknown. However, the
genetic heterogeneity between primary tumor and paired BM indicates that
sampling from the primary tumor may not be able to fully represent the
mutational status in metastases. In this study, the genetic heterogeneity of
primary lung adenocarcinoma and paired BM was analyzed. Patients and methods: A total of 11 paired samples of primary tumors and BM from lung cancer
patients were included, in which 7 paired samples of patients were finally
analyzed. Samples were sequenced by whole-exome sequencing (WES) to
investigate the common and unique mutations in the primary tumors and BM,
and the similarities and differences in copy number variation (CNV). Results: The consistency of gene mutation between primary lung adenocarcinoma and
paired BM was 33% to 86%. FAM129C and ADAMTSs specifically mutated in BM,
along with NKX2-1 high amplification and SAMD2/4 copy number deletion. Conclusion: The consistency of gene mutation between primary lung adenocarcinoma and
corresponding BM is relatively high, while the individual differences were
significant. FAM129C and ADAMTSs mutations and high amplification of NKX2-1
may be related to BM of lung cancer. The loss of copy number of SAMD2/4 may
be a potential therapeutic target for BM from lung adenocarcinoma.
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Affiliation(s)
- Li Li
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Zhulin Liu
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Rui Han
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Lin Li
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Mengyao Wang
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, P.R. China
| | - Depei Huang
- The Medical Department, 3D Medicines Inc., Shanghai, P.R. China
| | - Yong He
- Department of Respiratory Disease, Daping Hospital, Army Medical University, Chongqing, P.R. China
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23
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Deshpande K, Buchanan I, Martirosian V, Neman J. Clinical Perspectives in Brain Metastasis. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a037051. [PMID: 31615863 DOI: 10.1101/cshperspect.a037051] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Brain metastases (BMs) are responsible for decline in neurological function, reduction in overall quality of life, and mortality from recurrent or untreatable lesions. Advances in diagnostics and imaging have led to increased detection of central nervous system (CNS) metastases in patients with progressive cancers. Improved control of extracranial systemic disease, and the limited ability of current therapeutics to cross the blood-brain barrier (BBB) also contribute to the increase in incidence of brain metastases, as tumor cells seek refuge in the brain. Surgery, chemotherapy, and/or radiation (whole-brain radiation therapy and stereotactic radiation surgery [WBRT/SRS]) are a clinically established treatment paradigm for patients with brain metastases. With the advent of genetic and molecular characterization of tumors and their immune microenvironment, clinical trials seek to include targeted drugs into the therapeutic regimen for eligible patients. Several challenges, like treatment of multiple CNS lesions, superior uptake of chemotherapy into the brain, and trials with multidisciplinary approaches, are now being clinically addressed.
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Affiliation(s)
- Krutika Deshpande
- Department of Neurological Surgery, University of Southern California, Los Angeles, California 90033, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Ian Buchanan
- Department of Neurological Surgery, University of Southern California, Los Angeles, California 90033, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Vahan Martirosian
- Department of Neurological Surgery, University of Southern California, Los Angeles, California 90033, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
| | - Josh Neman
- Department of Neurological Surgery, University of Southern California, Los Angeles, California 90033, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
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24
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Characterizations of Gene Alterations in Melanoma Patients from Chinese Population. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6096814. [PMID: 32083130 PMCID: PMC7011309 DOI: 10.1155/2020/6096814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/23/2019] [Accepted: 09/01/2019] [Indexed: 12/29/2022]
Abstract
Melanoma is a human skin malignant tumor with high invasion and poor prognosis. The limited understanding of genomic alterations in melanomas in China impedes the diagnosis and therapeutic strategy selection. We conducted comprehensive genomic profiling of melanomas from 39 primary and metastatic formalin-fixed paraffin-embedded (FFPE) samples from 27 patients in China based on an NGS panel of 223 genes. No significant difference in gene alterations was found between primary and metastasis melanomas. The status of germline mutation, CNV, and somatic mutation in our cohort was quite different from that reported in Western populations. We further delineated the mutation patterns of 4 molecular subgroups (BRAF, RAS, NF1, and Triple-WT) of melanoma in our cohort. BRAF mutations were more frequently identified in melanomas without chromic sun-induced damage (non-CSD), while RAS mutations were more likely observed in acral melanomas. NF1 and Triple-WT subgroups were unbiased between melanomas arising in non-CSD and acral skin. BRAF, RAS, and NF1 mutations were significantly associated with lymph node metastasis or presence of ulceration, implying that these cancer driver genes were independent prognostic factors. In summary, our results suggest that mutational profiles of malignant melanomas in China are significantly different from Western countries, and both gene mutation and amplification play an important role in the development and progression of melanomas.
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25
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Suda K. For a better adjuvant strategy for resected lung cancer-lessons from treatment failure patterns of the ADJUVANT trial (CTONG 1104). Transl Lung Cancer Res 2019; 8:S395-S399. [PMID: 32038923 PMCID: PMC6987354 DOI: 10.21037/tlcr.2019.08.24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 08/27/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Kenichi Suda
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
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26
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Liao L, Yu H, Ge M, Zhan Q, Huang R, Ji X, Liang X, Zhou X. Upregulation of phosphoserine phosphatase contributes to tumor progression and predicts poor prognosis in non-small cell lung cancer patients. Thorac Cancer 2019; 10:1203-1212. [PMID: 30977310 PMCID: PMC6500996 DOI: 10.1111/1759-7714.13064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 01/07/2023] Open
Abstract
Background Growing evidence indicates that high phosphoserine phosphatase (PSPH) expression is associated with tumor prognosis in many types of cancers. However, the role of PSPH in non‐small cell lung cancer (NSCLC) is unclear. The purpose of this study was to investigate the clinical significance of PSPH in NSCLC. Methods One hundred forty‐three patients with histologically confirmed NSCLC who underwent surgery were included. Quantitative real‐time PCR and Western blot were used to assess PSPH expression in paired tumor and corresponding adjacent non‐tumorous tissues. The role of PSPH in invasion and cell growth was investigated in vitro. Results Compared to adjacent normal lung tissues, PSPH messenger RNA and protein levels were significantly higher in NSCLC tissues, and the PSPH expression level was positively related to clinical stage, metastasis, and recurrence. High PSPH expression was predictive of poor overall survival. A549 cells transfected with small interfering‐PSPH showed inhibited cell migration, invasion, and proliferation. We further demonstrated that PSPH might promote the invasive capabilities of NSCLC cells through the AKT/AMPK signaling pathway. Conclusion Our results indicate that PSPH may act as a putative oncogene in NSCLC, and may be a vital molecular marker for the metastasis and proliferation of NSCLC cells by regulating the AKT/AMPK signaling pathway.
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Affiliation(s)
- Li Liao
- Department of Oncology, Huashan Hospital Fudan University, Shanghai, China
| | - Huajian Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengxi Ge
- Department of Oncology, Huashan Hospital Fudan University, Shanghai, China
| | - Qiong Zhan
- Department of Oncology, Huashan Hospital Fudan University, Shanghai, China
| | - Ruofan Huang
- Department of Oncology, Huashan Hospital Fudan University, Shanghai, China
| | - Xiaoyu Ji
- Department of Oncology, Huashan Hospital Fudan University, Shanghai, China
| | - Xiaohua Liang
- Department of Oncology, Huashan Hospital Fudan University, Shanghai, China
| | - Xinli Zhou
- Department of Oncology, Huashan Hospital Fudan University, Shanghai, China
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