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Yao Z, Yang H, Liu X, Jiang M, Deng W, Fu B. Preliminary study on the role of the CSMD2 gene in bladder cancer. Heliyon 2024; 10:e22593. [PMID: 38163223 PMCID: PMC10754709 DOI: 10.1016/j.heliyon.2023.e22593] [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: 07/06/2023] [Revised: 10/31/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
Background CSMD2 has been reported as a potential prognostic factor in several cancers. However, whether CSMD2 affects bladder cancer (BC) remains unclear. Methods Public data were obtained from the TCGA (https://cancergenome.nih.gov) databases. CSMD2expression and its prognostic value were analyzed using bioinformatics methods. CSMD2 mRNA level in patients with BC and BC cell lines was evaluated via quantitative reverse transcriptase polymerase chain reaction. CSMD2 protein level in patients with BC was evaluated via immunohistochemistry. BC cell lines T24 and UMUC-3 were selected for loss-of-function assays targeting CSMD2. Cell viability was determined by CCK8 and clone formation experiments. Cell migration and invasion were evaluated using Transwell assays. Furthermore, the transcriptome of UMUC-3 with CSMD2 knockdown was sequenced to analyze potential signaling network pathways. Finally, the TIMER2.0 database was employed to identify the correlation between CSMD2 and immune cells in the tumor microenvironment. Results CSMD2 expression was up-regulated in BC tissues compared to adjacent tissues. High CSMD2 expression was associated with poor survival and could serve as an independent predictor for survival in patients with BC. Furthermore, down-regulation of CSMD2 notably restrained the viability, migration, and invasion abilities of T24 and UMUC-3 cells. Moreover, transcriptomic sequencing after CSMD2 knockdown in UMUC-3 cells revealed its involvement in the regulation of the malignant phenotype in BC. Finally, public databases suggest a connection between CSMD2 and immune cell infiltration in BC. Conclusions These findings suggest that CSMD2 may promote proliferation and tumorigenicity, and could represent a potential target for improving the prognosis of BC.
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Affiliation(s)
- Zhijun Yao
- Department of Urology, The First Affiliated Hospital of Nanchang University, China
| | - Hailang Yang
- Department of Urology, The First Affiliated Hospital of Nanchang University, China
| | - Xiaoqiang Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, China
| | - Ming Jiang
- Department of Urology, The First Affiliated Hospital of Nanchang University, China
| | - Wen Deng
- Department of Urology, The First Affiliated Hospital of Nanchang University, China
| | - Bin Fu
- Department of Urology, The First Affiliated Hospital of Nanchang University, China
- Jiangxi Institute of Urology, China
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2
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Ouyang W, Yu J, Zeng Z, Gong J, Zhang J, Xie C. Genomic profiling of relapsed small cell lung cancer reveals potential pathways of therapeutic targets. J Thorac Dis 2023; 15:6796-6805. [PMID: 38249912 PMCID: PMC10797366 DOI: 10.21037/jtd-23-1657] [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: 10/30/2023] [Accepted: 12/05/2023] [Indexed: 01/23/2024]
Abstract
Background Almost all patients with small cell lung cancer (SCLC) relapse. The therapeutic options of relapsed SCLC are limited, and the clinical outcomes are poor. Thus, genomic profiling of relapsed SCLC patients may help to develop more effective therapeutic options. Methods We collected blood specimens and follow-up information from a consecutive cohort of 31 patients diagnosed with relapsed SCLC in Zhongnan Hospital, Wuhan University, between 2018 and 2019, to analyze the comprehensive genomic profiling, and to investigate the impact of genomic alterations on therapeutic options and survival. Results In our cohort of relapsed SCLC, the median number of genomic alterations was 5 (range, 1-11) per sample. The majority of patients were defined as low tumor mutation burden (TMB; 83.9%) and microsatellite stability (MSS; 87.1%). Immune checkpoint inhibitors (ICIs)-based treatment still brought considerable progression-free survival (PFS; 4.93-20.27 months) for patients with low TMB and MSS. Additionally, the most frequent genetic alterations observed in relapsed SCLC were TP53 (77%) and RB1 (52%). Other genomic alterations of high frequency were breast cancer 2 (BRCA2) (32%), ataxia telangiectasia mutated (ATM) (13%), epidermal growth factor receptor (EGFR) (10%), Notch receptor 1 (NOTCH1) (10%), and Fanconi anemia complementation group A (FANCA) (10%), in turn. Finally, based on the survival of therapeutic strategies targeting potential mutation genes, the role of genotyping in relapsed SCLC was confirmed. Conclusions Our studies first exhibited comprehensive genomic profiling of relapsed SCLC, identifying several candidate genes, and briefly analyzed the association of survival and genomic alterations. Our data from a small cohort of relapsed SCLC will benefit further exploration the potential targets or biomarkers.
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Affiliation(s)
- Wen Ouyang
- Department of Pulmonary Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Jing Yu
- Department of Pulmonary Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Pulmonary Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Jun Gong
- Department of Pulmonary Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Junhong Zhang
- Department of Pulmonary Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Conghua Xie
- Department of Pulmonary Oncology, Zhongnan Hospital, Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital, Wuhan University, Wuhan, China
- Hubei Clinical Cancer Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
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3
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Yurdakul E, Barlas Y, Ulgen KO. Circadian clock crosstalks with autism. Brain Behav 2023; 13:e3273. [PMID: 37807632 PMCID: PMC10726833 DOI: 10.1002/brb3.3273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/10/2023] [Accepted: 09/24/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND The mechanism underlying autism spectrum disorder (ASD) remains incompletely understood, but researchers have identified over a thousand genes involved in complex interactions within the brain, nervous, and immune systems, particularly during the mechanism of brain development. Various contributory environmental effects including circadian rhythm have also been studied in ASD. Thus, capturing the global picture of the ASD-clock network in combined form is critical. METHODS We reconstructed the protein-protein interaction network of ASD and circadian rhythm to understand the connection between autism and the circadian clock. A graph theoretical study is undertaken to evaluate whether the network attributes are biologically realistic. The gene ontology enrichment analyses provide information about the most important biological processes. RESULTS This study takes a fresh look at metabolic mechanisms and the identification of potential key proteins/pathways (ribosome biogenesis, oxidative stress, insulin/IGF pathway, Wnt pathway, and mTOR pathway), as well as the effects of specific conditions (such as maternal stress or disruption of circadian rhythm) on the development of ASD due to environmental factors. CONCLUSION Understanding the relationship between circadian rhythm and ASD provides insight into the involvement of these essential pathways in the pathogenesis/etiology of ASD, as well as potential early intervention options and chronotherapeutic strategies for treating or preventing the neurodevelopmental disorder.
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Affiliation(s)
- Ekin Yurdakul
- Department of Chemical EngineeringBogazici University, Biosystems Engineering LaboratoryIstanbulTurkey
| | - Yaman Barlas
- Department of Industrial EngineeringBogazici University, Socio‐Economic System Dynamics Research Group (SESDYN)IstanbulTurkey
| | - Kutlu O. Ulgen
- Department of Chemical EngineeringBogazici University, Biosystems Engineering LaboratoryIstanbulTurkey
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4
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Huang Y, Bao T, Zhang T, Ji G, Wang Y, Ling Z, Li W. Machine Learning Study of SNPs in Noncoding Regions to Predict Non-small Cell Lung Cancer Susceptibility. Clin Oncol (R Coll Radiol) 2023; 35:701-712. [PMID: 37689528 DOI: 10.1016/j.clon.2023.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/23/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common pathological subtype of lung cancer. Both environmental and genetic factors have been reported to impact the lung cancer susceptibility. We conducted a genome-wide association study (GWAS) of 287 NSCLC patients and 467 healthy controls in a Chinese population using the Illumina Genome-Wide Asian Screening Array Chip on 712,095 SNPs (single nucleotide polymorphisms). Using logistic regression modeling, GWAS identified 17 new noncoding region SNP loci associated with the NSCLC risk, and the top three (rs80040741, rs9568547, rs6010259) were under a stringent p-value (<3.02e-6). Notably, rs80040741 and rs6010259 were annotated from the intron regions of MUC3A and MLC1, respectively. Together with another five SNPs previously reported in Chinese NSCLC patients and another four covariates (e.g., smoking status, age, low dose CT screening, sex), a predictive model by machine learning methods can separate the NSCLC from healthy controls with an accuracy of 86%. This is the first time to apply machine learning method in predicting the NSCLC susceptibility using both genetic and clinical characteristics. Our findings will provide a promising method in NSCLC early diagnosis and improve our understanding of applying machine learning methods in precision medicine.
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Affiliation(s)
- Y Huang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - T Bao
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - T Zhang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - G Ji
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Y Wang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Z Ling
- Chengdu Genepre Technology Co., LTD, Chengdu, Sichuan, China
| | - W Li
- Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Respiratory and Critical Care Medicine, Institute of Respiratory Healthy, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, Sichuan 610041, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chengdu, Sichuan 610041, West China Hospital, China.
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5
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Sigin VO, Kalinkin AI, Nikolaeva AF, Ignatova EO, Kuznetsova EB, Chesnokova GG, Litviakov NV, Tsyganov MM, Ibragimova MK, Vinogradov II, Vinogradov MI, Vinogradov IY, Zaletaev DV, Nemtsova MV, Kutsev SI, Tanas AS, Strelnikov VV. DNA Methylation and Prospects for Predicting the Therapeutic Effect of Neoadjuvant Chemotherapy for Triple-Negative and Luminal B Breast Cancer. Cancers (Basel) 2023; 15:cancers15051630. [PMID: 36900421 PMCID: PMC10001080 DOI: 10.3390/cancers15051630] [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: 01/12/2023] [Revised: 02/24/2023] [Accepted: 03/05/2023] [Indexed: 03/09/2023] Open
Abstract
Despite advances in the diagnosis and treatment of breast cancer (BC), the main cause of deaths is resistance to existing therapies. An approach to improve the effectiveness of therapy in patients with aggressive BC subtypes is neoadjuvant chemotherapy (NACT). Yet, the response to NACT for aggressive subtypes is less than 65% according to large clinical trials. An obvious fact is the lack of biomarkers predicting the therapeutic effect of NACT. In a search for epigenetic markers, we performed genome-wide differential methylation screening by XmaI-RRBS in cohorts of NACT responders and nonresponders, for triple-negative (TN) and luminal B tumors. The predictive potential of the most discriminative loci was further assessed in independent cohorts by methylation-sensitive restriction enzyme quantitative PCR (MSRE-qPCR), a promising method for the implementation of DNA methylation markers in diagnostic laboratories. The selected most informative individual markers were combined into panels demonstrating cvAUC = 0.83 (TMEM132D and MYO15B markers panel) for TN tumors and cvAUC = 0.76 (TTC34, LTBR and CLEC14A) for luminal B tumors. The combination of methylation markers with clinical features that correlate with NACT effect (clinical stage for TN and lymph node status for luminal B tumors) produces better classifiers, with cvAUC = 0.87 for TN tumors and cvAUC = 0.83 for luminal B tumors. Thus, clinical characteristics predictive of NACT response are independently additive to the epigenetic classifier and in combination improve prediction.
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Affiliation(s)
- Vladimir O. Sigin
- Research Centre for Medical Genetics, 115522 Moscow, Russia
- Correspondence: ; Tel.: +7-916-279-5124
| | | | | | - Ekaterina O. Ignatova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
- N. N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia
| | - Ekaterina B. Kuznetsova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
- Laboratory of Medical Genetics, I. M. Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
| | | | - Nikolai V. Litviakov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Matvey M. Tsyganov
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Marina K. Ibragimova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 634009 Tomsk, Russia
| | - Ilya I. Vinogradov
- Regional Clinical Oncology Dispensary, 390011 Ryazan, Russia
- Department of Pathological Anatomy, Ryazan State Medical University, 390026 Ryazan, Russia
| | | | - Igor Y. Vinogradov
- Department of Pathological Anatomy, Ryazan State Medical University, 390026 Ryazan, Russia
| | | | - Marina V. Nemtsova
- Research Centre for Medical Genetics, 115522 Moscow, Russia
- Laboratory of Medical Genetics, I. M. Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
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Wildey G, Shay AM, McColl KS, Yoon S, Shatat MA, Perwez A, Spainhower KB, Kresak AM, Lipka M, Yang M, Behtaj M, Fu P, Alahmadi A, Mneimneh W, Abbas A, Dowlati A. Retinoblastoma Expression and Targeting by CDK4/6 Inhibitors in Small Cell Lung Cancer. Mol Cancer Ther 2023; 22:264-273. [PMID: 36399634 PMCID: PMC9898162 DOI: 10.1158/1535-7163.mct-22-0365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/02/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022]
Abstract
The canonical model of "small cell lung cancer" (SCLC) depicts tumors arising from dual inactivation of TP53 and RB1. However, many genomic studies have persistently identified tumors with no RB1 mutations. Here, we examined RB1 protein expression and function in SCLC. RB1 expression was examined by IHC analysis of 62 human SCLC tumors. These studies showed that ∼14% of SCLC tumors expressed abundant RB1 protein, which is associated with neuroendocrine gene expression and is enriched in YAP1 expression, but no other lineage proteins that stratify SCLC. SCLC cells and xenograft tumors with RB1 protein expression were sensitive to growth inhibition by the CDK4/6 inhibitor palbociclib, and this inhibition was shown to be dependent on RB1 expression by CRISPR knockout. Furthermore, a patient with biopsy-validated wild-type RB1 SCLC who received the CDK4/6 inhibitor abemaciclib demonstrated a dramatic decrease in mutant TP53 ctDNA allelic fraction from 62.1% to 0.4% and decreased tumor mass on CT scans. Importantly, IHC of the diagnostic biopsy specimen showed RB1 positivity. Finally, we identified a transcriptomics-based RB1 loss-of-function signature that discriminates between SCLC cells with or without RB1 protein expression and validated it in the patient who was responsive to abemaciclib, suggesting its potential use to predict CDK4/6 inhibitor response in patients with SCLC. Our study demonstrates that RB1 protein is an actionable target in a subgroup of SCLC, a cancer that exhibits no currently targetable mutations.
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Affiliation(s)
- Gary Wildey
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Ashley M. Shay
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Karen S. McColl
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Suzy Yoon
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Mohammad A. Shatat
- Division of Pulmonary and Critical Care Medicine, Cleveland VA Medical Center; Cleveland, OH, USA, 44106
| | - Ahmad Perwez
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Kyle B. Spainhower
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Adam M. Kresak
- Division of Pathology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - MaryBeth Lipka
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Michael Yang
- Division of Pathology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Mohadese Behtaj
- Division of Pathology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Pingfu Fu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA, 44106
| | - Asrar Alahmadi
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Wadad Mneimneh
- Division of Pathology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Ata Abbas
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106
| | - Afshin Dowlati
- Division of Hematology and Oncology, Case Western Reserve University and University Hospitals Seidman Cancer Center; Cleveland, OH, USA, 44106.,Corresponding author: Dr. Afshin Dowlati, Division of Hematology and Oncology, University Hospitals Seidman Cancer Center, 11100 Euclid Avenue, Cleveland, Ohio 44016, 11-216-286-6741 (office), 11-216-844-5234 (FAX),
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Langthasa J, Mishra S, U M, Kalal R, Bhat R. Mutations in a set of ancient matrisomal glycoprotein genes across neoplasia predispose to disruption of morphogenetic transduction. COMPUTATIONAL AND SYSTEMS ONCOLOGY 2022. [DOI: 10.1002/cso2.1042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Jimpi Langthasa
- Department of Molecular Reproduction Development and Genetics Indian Institute of Science Bengaluru India
| | - Satyarthi Mishra
- Centre for Nano Science and Engineering Indian Institute of Science Bengaluru India
| | - Monica U
- Department of Molecular Reproduction Development and Genetics Indian Institute of Science Bengaluru India
| | - Ronak Kalal
- Department of Zoology University College of Science, Mohanlal Sukhadia University Udaipur India
| | - Ramray Bhat
- Department of Molecular Reproduction Development and Genetics Indian Institute of Science Bengaluru India
- Centre for BioSystems Science and Engineering Indian Institute of Science Bengaluru India
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8
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Guan X, Bao G, Liang J, Yao Y, Xiang Y, Zhong X. Evolution of small cell lung cancer tumor mutation: from molecular mechanisms to novel viewpoints. Semin Cancer Biol 2022; 86:346-355. [PMID: 35367118 DOI: 10.1016/j.semcancer.2022.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 01/27/2023]
Abstract
Small cell lung cancer (SCLC) is a clinically common malignant tumor originating from the lung neuroendocrine stem cells, which has a poor prognosis and accounts for approximately 15% of all lung cancer cases. However, research on its treatment has been slow, and the 5-year survival rate of patients with SCLC has been < 5% for many years. In recent years, the development and popularization of gene sequencing technology have facilitated the understanding of the gene mutation landscape and tumor evolution of SCLC, thereby leading to a more accurate prediction of the prognosis of SCLC and the development of individualized treatment. In this review, we aimed to discuss the mutation evolution of SCLC from the perspective of a tumor evolution theory and described the sequence of mutation evolution in the occurrence and development of SCLC. In addition, we summarized the existing whole-exome sequencing (WES) data of SCLC cases at our center along with relevant publications on sequencing. Thereafter, we discuss the role of different mutated pathways in the occurrence of SCLC to predict its prognosis more accurately and summarized individualized treatment strategies.
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Affiliation(s)
- Xiaojiao Guan
- Department of Pathology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Guangyao Bao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Jie Liang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yao Yao
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Yifan Xiang
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China
| | - Xinwen Zhong
- Department of Thoracic Surgery, First Affiliated Hospital, China Medical University, Shenyang, China.
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9
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Zhang C, Wang H. Accurate treatment of small cell lung cancer: Current progress, new challenges and expectations. Biochim Biophys Acta Rev Cancer 2022; 1877:188798. [PMID: 36096336 DOI: 10.1016/j.bbcan.2022.188798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/19/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022]
Abstract
Small cell lung cancer (SCLC) is a deadly disease with poor prognosis. Fast growing speed, inclination to metastasis, enrichment in cancer stem cells altogether constitute its aggressive nature. In stark contrast to non-small cell lung cancer (NSCLC) that strides vigorously on the road to precision oncology, SCLC has been on the embryonic path to achieve effective personalized treatments. The survival of patients with SCLC have not been improved greatly, which could be possibly due to our inadequate understanding of genetic alterations of SCLC. Recently, encouraging effects have been observed in patients with SCLC undergoing immunotherapy. However, exciting results have only been observed in a small fraction of patients with SCLC, warranting biomarkers predictive of responses as well as novel therapeutic strategies. In addition, SCLC has previously been viewed to be homogeneous. However, perspectives have been changed thanks to the advances in sequencing techniques and platforms, which unfolds the complex heterogeneity of SCLC both genetically and non-genetically, rendering the treatment of SCLC a further step forward into the precision era. To outline the road of SCLC towards precision oncology, we summarize the progresses and achievements made in precision treatment in SCLC in genomic, transcriptomic, epigenetic, proteomic and metabolic dimensions. Moreover, we conclude relevant therapeutic vulnerabilities in SCLC. Clinically tested drugs and clinical trials have also been demonstrated. Ultimately, we look into the opportunities and challenges ahead to advance the individualized treatment in pursuit of improved survival for patients with SCLC.
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Affiliation(s)
- Chenyue Zhang
- Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, 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.
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10
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Zhang J, Deng J, Feng X, Tan Y, Li X, Liu Y, Li M, Qi H, Tang L, Meng Q, Yan H, Qi L. Hierarchical identification of a transcriptional panel for the histological diagnosis of lung neuroendocrine tumors. Front Genet 2022; 13:944167. [PMID: 36105102 PMCID: PMC9465419 DOI: 10.3389/fgene.2022.944167] [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: 05/14/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Lung cancer is a complex disease composed of neuroendocrine (NE) and non-NE tumors. Accurate diagnosis of lung cancer is essential in guiding therapeutic management. Several transcriptional signatures have been reported to distinguish between adenocarcinoma (ADC) and squamous cell carcinoma (SCC) belonging to non-NE tumors. This study aims to identify a transcriptional panel that could distinguish the histological subtypes of NE tumors to complement the morphology-based classification of an individual.Methods: A public dataset with NE subtypes, including 21 small-cell lung cancer (SCLC), 56 large-cell NE carcinomas (LCNECs), and 24 carcinoids (CARCIs), and non-NE subtypes, including 85 ADC and 61 SCC, was used as a training set. In the training set, consensus clustering was first used to filter out the samples whose expression patterns disagreed with their histological subtypes. Then, a rank-based method was proposed to develop a panel of transcriptional signatures for determining the NE subtype for an individual, based on the within-sample relative gene expression orderings of gene pairs. Twenty-three public datasets with a total of 3,454 samples, which were derived from fresh-frozen, formalin-fixed paraffin-embedded, biopsies, and single cells, were used for validation. Clinical feasibility was tested in 10 SCLC biopsy specimens collected from cancer hospitals via bronchoscopy.Results: The NEsubtype-panel was composed of three signatures that could distinguish NE from non-NE, CARCI from non-CARCI, and SCLC from LCNEC step by step and ultimately determine the histological subtype for each NE sample. The three signatures achieved high average concordance rates with 97.31%, 98.11%, and 90.63%, respectively, in the 23 public validation datasets. It is worth noting that the 10 clinic-derived SCLC samples diagnosed via immunohistochemical staining were also accurately predicted by the NEsubtype-panel. Furthermore, the subtype-specific gene expression patterns and survival analyses provided evidence for the rationality of the reclassification by the NEsubtype-panel.Conclusion: The rank-based NEsubtype-panel could accurately distinguish lung NE from non-NE tumors and determine NE subtypes even in clinically challenging samples (such as biopsy). The panel together with our previously reported signature (KRT5-AGR2) for SCC and ADC would be an auxiliary test for the histological diagnosis of lung cancer.
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Affiliation(s)
- Juxuan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiaxing Deng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiao Feng
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yilong Tan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yixin Liu
- Basic Medicine College, Harbin Medical University, Harbin, China
| | - Mengyue Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haitao Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Lefan Tang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qingwei Meng
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Haidan Yan
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
- *Correspondence: Haidan Yan, ; Lishuang Qi,
| | - Lishuang Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- *Correspondence: Haidan Yan, ; Lishuang Qi,
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11
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Yu J, Zhao S, Su Z, Song C, Wu L, Wang J, Bi N, Wang L. Whole exome analysis reveals the genomic profiling related to chemo-resistance in Chinese population with limited-disease small cell lung cancer. Cancer Med 2022; 12:1035-1050. [PMID: 35735600 PMCID: PMC9883427 DOI: 10.1002/cam4.4950] [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: 03/11/2022] [Revised: 05/21/2022] [Accepted: 05/28/2022] [Indexed: 02/01/2023] Open
Abstract
PURPOSE The mechanism of chemo-resistance in small cell lung cancer (SCLC) is unclear. This study aims to explore the resistance-related genomic profiles of residual tumors after neo-adjuvant chemotherapy (NAC) in SCLC through the whole-exome sequencing (WES). EXPERIMENTAL DESIGN A total of 416 limited diseases (LD) SCLC patients underwent surgery were retrospectively analyzed, of which 40 patients received NAC. Then we selected 29 patients undergoing NAC (n = 19) and chemotherapy naïve (CTN, n = 10) to perform WES sequence with formalin-fixed paraffin-embedded samples including tumor and paired para-tumor. RESULTS In total, single nucleotide variation and mutation rate were similar between NAC and CTN groups. The mutation signatures were significantly discrepant between NAC and CTN groups, as well as among patients with partial response (PR), stable disease (SD), and progressive disease. There were more copy number variation deletions in NAC group compared with CTN group. The inactivation of TP53 and RB1 were the most significantly events in both NAC and CTN groups. RB1 nonsense mutations were recurrent in NAC group (9/19 vs. 0/9, 47.4% vs. 0%) with favorable survival, while the frame-shift deletions were frequent in CTN group (3/9 vs. 3/19, 33.3% vs.15.8%). Integrated function enrichment revealed that the frequently mutant genes were involved in cell cycle, metabolic reprogramming, and oncogenic signaling pathways in NAC group, such as BTG2 pathway, glycolysis in senescence and P53 pathway. A total of 27 genes presented frequently mutant in NAC group and might played a positive role in drug resistance. Multiple genes including BRINP3, MYH6, ST18, and PCHD15, which were associated with prognosis, occurred mutant frequently in PR and SD groups. CONCLUSION Residual tumors after neo-adjuvant therapy exhibited different mutation signature spectrum. Multiple genes including RB1 nonsense mutations, BRINP3, MYH6, ST18, and PCHD15 were with frequent mutation in residual tumors, which might participate chemo-resistance and influenced the prognosis in patients with limited disease SCLC.
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Affiliation(s)
- Jiangyong Yu
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Shuangtao Zhao
- Department of Thoracic Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest HospitalCapital Medical UniversityBeijingChina
| | - Zhe Su
- Peking‐Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina
| | | | | | - Jingbo Wang
- Department of Radiation Therapy, Cancer Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Nan Bi
- Department of Radiation Therapy, Cancer Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
| | - Lvhua Wang
- Department of Radiation Therapy, Cancer Hospital, Chinese Academy of Medical SciencesPeking Union Medical CollegeBeijingChina
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12
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Wang Y, Herzig G, Molano C, Liu A. Differential expression of the Tmem132 family genes in the developing mouse nervous system. Gene Expr Patterns 2022; 45:119257. [PMID: 35690356 DOI: 10.1016/j.gep.2022.119257] [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: 04/28/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/15/2022]
Abstract
The family of novel transmembrane proteins (TMEM) 132 have been associated with multiple neurological disorders and cancers in humans, but have hardly been studied in vivo. Here we report the expression patterns of the five Tmem132 genes (a, b, c, d and e) in developing mouse nervous system with RNA in situ hybridization in wholemount embryos and tissue sections. Our results reveal differential and partially overlapping expression of multiple Tmem132 family members in both the central and peripheral nervous system, suggesting potential partial redundancy among them.
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Affiliation(s)
- Yuan Wang
- Department of Occupational and Environmental Health, School of Public Health, China Medical University, Shenyang, PR China; Department of Biology, Eberly College of Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Graham Herzig
- Department of Biology, Eberly College of Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Cassandra Molano
- Department of Biology, Eberly College of Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Aimin Liu
- Department of Biology, Eberly College of Science and Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA.
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13
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Li S, Liu T, Li K, Bai X, Xi K, Chai X, Mi L, Li J. Spectrins and human diseases. Transl Res 2022; 243:78-88. [PMID: 34979321 DOI: 10.1016/j.trsl.2021.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022]
Abstract
Spectrin, as one of the major components of a plasma membrane-associated cytoskeleton, is a cytoskeletal protein composed of the modular structure of α and β subunits. The spectrin-based skeleton is essential for preserving the integrity and mechanical characteristics of the cell membrane. Moreover, spectrin regulates a variety of cell processes including cell apoptosis, cell adhesion, cell spreading, and cell cycle. Dysfunction of spectrins is implicated in various human diseases including hemolytic anemia, neurodegenerative diseases, ataxia, heart diseases, and cancers. Here, we briefly discuss spectrins function as well as the clinical manifestations and currently known molecular mechanisms of human diseases related to spectrins, highlighting that strategies for targeting regulation of spectrins function may provide new avenues for therapeutic intervention for these diseases.
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Affiliation(s)
- Shan Li
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Ting Liu
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Kejing Li
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Xinyi Bai
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Kewang Xi
- The First School of Clinical Medicine, Lanzhou University, Gansu, China
| | - Xiaojing Chai
- Central Laboratory, The First Hospital of Lanzhou University, Gansu, China
| | - Leyuan Mi
- The First School of Clinical Medicine, Lanzhou University, Gansu, China; Clinical Laboratory Center, Gansu Provincial Maternity and Child Care Hospital, Gansu, China
| | - Juan Li
- Gansu Key Laboratory of Genetic Study of Hematopathy, The First Hospital of Lanzhou University, Gansu, China; Central Laboratory, The First Hospital of Lanzhou University, Gansu, China.
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14
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Walia HK, Sharma P, Singh N, Sharma S. Immunotherapy in Small Cell Lung Cancer Treatment: a Promising Headway for Future Perspective. Curr Treat Options Oncol 2022; 23:268-294. [PMID: 35226309 DOI: 10.1007/s11864-022-00949-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2022] [Indexed: 12/24/2022]
Abstract
OPINION STATEMENT Despite advancements in clinical research, both prognosis and treatment for SCLC patients are still in the nascent stage. SCLC is a fatal disease with high tumor mutational burden and is strongly associated with exposure to tobacco. This leads to the development of potential neo-antigens, inhibition of immune responses, and development of paraneoplastic disorders. Surgery, radiation, and chemotherapy are widely accepted treatments for cancer globally, and most recently, immunotherapy has now become the "fourth pillar" of SCLC treatment. Various immune checkpoint pathways regulate the activation of T cells at multiple stages during an immune response. T cell checkpoint inhibitors such as anti-PD1 (pembrolizumab, nivolumab), anti-PDL1, and anti-CTLA-4 (tremelimumab, ipilimumab) have potential to show anti-cancer activity along with the promise to prolong survival in patients with SCLC. Treatment with the CTLA-4-specific antibodies can restore the immune response by increasing the accumulation and survival of T-cells whereas monoclonal antibodies block either PD-1 or its ligands that prevent downregulation of effector T-cell, which enables the T-cells to mediate the death of tumor cells. Furthermore, monoclonal antibody in combination with chemotherapy has attained quite a focus to enhance the survival of SCLC patients. Apart from this, various immunotherapeutic approaches have been evaluated in the clinical trials for SCLC patients such as TLR9 agonist, anti-CD47, anti-ganglioside therapy, and anti-Notch signaling. The current review focuses on the rationale as well as on the clinical studies of immunotherapy in SCLC along with the clinical end results of certain immunotherapeutic agents and novel therapeutic combinations in SCLC patients.
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Affiliation(s)
- Harleen Kaur Walia
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India
| | - Parul Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post-Graduate Institute of Medical Education & Research, Chandigarh, 160012, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India.
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15
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Trincado JL, Reixachs-Solé M, Pérez-Granado J, Fugmann T, Sanz F, Yokota J, Eyras E. ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer. PLoS Comput Biol 2021; 17:e1009411. [PMID: 34529669 PMCID: PMC8478223 DOI: 10.1371/journal.pcbi.1009411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 09/28/2021] [Accepted: 08/30/2021] [Indexed: 01/22/2023] Open
Abstract
Immunotherapies provide effective treatments for previously untreatable tumors and identifying tumor-specific epitopes can help elucidate the molecular determinants of therapy response. Here, we describe a pipeline, ISOTOPE (ISOform-guided prediction of epiTOPEs In Cancer), for the comprehensive identification of tumor-specific splicing-derived epitopes. Using RNA sequencing and mass spectrometry for MHC-I associated proteins, ISOTOPE identified neoepitopes from tumor-specific splicing events that are potentially presented by MHC-I complexes. Analysis of multiple samples indicates that splicing alterations may affect the production of self-epitopes and generate more candidate neoepitopes than somatic mutations. Although there was no difference in the number of splicing-derived neoepitopes between responders and non-responders to immune therapy, higher MHC-I binding affinity was associated with a positive response. Our analyses highlight the diversity of the immunogenic impacts of tumor-specific splicing alterations and the importance of studying splicing alterations to fully characterize tumors in the context of immunotherapies. ISOTOPE is available at https://github.com/comprna/ISOTOPE.
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Affiliation(s)
| | - Marina Reixachs-Solé
- Australian National University, Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
| | - Judith Pérez-Granado
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | | | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Dept. of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain
| | - Jun Yokota
- National Cancer Center Research Institute (NCCRI), Tokyo, Japan
| | - Eduardo Eyras
- Australian National University, Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- * E-mail:
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16
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Systematic integrated analyses of methylomic and transcriptomic impacts of early combined botanicals on estrogen receptor-negative mammary cancer. Sci Rep 2021; 11:9481. [PMID: 33947955 PMCID: PMC8096837 DOI: 10.1038/s41598-021-89131-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 04/21/2021] [Indexed: 11/09/2022] Open
Abstract
Dietary botanicals such as the cruciferous vegetable broccoli sprouts (BSp) as well as green tea polyphenols (GTPs) have shown exciting potential in preventing or delaying breast cancer (BC). However, little is known about their impact on epigenomic aberrations that are centrally involved in the initiation and progression of estrogen receptor-negative [ER(−)] BC. We have investigated the efficacy of combined BSp and GTPs diets on mammary tumor inhibition in transgenic Her2/neu mice that were administered the diets from prepubescence until adulthood. Herein, we present an integrated DNA methylome and transcriptome analyses for defining the early-life epigenetic impacts of combined BSp and GTPs on mammary tumors and our results indicate that a combinatorial administration of BSp and GTPs have a stronger impact at both transcriptome and methylome levels in comparison to BSp or GTPs administered alone. We also demonstrated a streamlined approach by performing an extensive preprocessing, quality assessment and downstream analyses on the genomic dataset. Our identification of differentially methylated regions in response to dietary botanicals administered during early-life will allow us to identify key genes and facilitate implementation of the subsequent downstream functional analyses on a genomic scale and various epigenetic modifications that are crucial in preventing ER(−) mammary cancer. Furthermore, our realtime PCR results were also found to be consistent with our genome-wide analysis results. These results could be exploited as a comprehensive resource for understanding understudied genes and their associated epigenetic modifications in response to these dietary botanicals.
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17
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Coll-SanMartin L, Davalos V, Piñeyro D, Rosselló-Tortella M, Bueno-Costa A, Setien F, Villanueva A, Granada I, Ruiz-Xiviller N, Kotter A, Helm M, Yokota J, Kawabata-Iwakawa R, Kohno T, Esteller M. Gene Amplification-Associated Overexpression of the Selenoprotein tRNA Enzyme TRIT1 Confers Sensitivity to Arsenic Trioxide in Small-Cell Lung Cancer. Cancers (Basel) 2021; 13:1869. [PMID: 33919717 PMCID: PMC8070726 DOI: 10.3390/cancers13081869] [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: 02/18/2021] [Revised: 04/06/2021] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
The alteration of RNA modification patterns is emerging as a common feature of human malignancies. If these changes affect key RNA molecules for mRNA translation, such as transfer RNA, they can have important consequences for cell transformation. TRIT1 is the enzyme responsible for the hypermodification of adenosine 37 in the anticodon region of human tRNAs containing serine and selenocysteine. Herein, we show that TRIT1 undergoes gene amplification-associated overexpression in cancer cell lines and primary samples of small-cell lung cancer. From growth and functional standpoints, the induced depletion of TRIT1 expression in amplified cells reduces their tumorigenic potential and downregulates the selenoprotein transcripts. We observed that TRIT1-amplified cells are sensitive to arsenic trioxide, a compound that regulates selenoproteins, whereas reduction of TRIT1 levels confers loss of sensitivity to the drug. Overall, our results indicate a role for TRIT1 as a small-cell lung cancer-relevant gene that, when undergoing gene amplification-associated activation, can be targeted with the differentiation agent arsenic trioxide.
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Affiliation(s)
- Laia Coll-SanMartin
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
| | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Margalida Rosselló-Tortella
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Germans Trias i Pujol Health Science Research Institute (IGTP), 08916 Barcelona, Spain
| | - Alberto Bueno-Costa
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
| | - Fernando Setien
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
| | - Alberto Villanueva
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance (ProCURE), Oncobell Program, IDIBELL, Institut Català d’Oncologia (ICO), L’Hospitalet del Llobregat, 08908 Barcelona, Spain;
| | - Isabel Granada
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Cytogenetics Platform, Hematology Laboratory Service, Institut Català d’Oncologia (ICO)-Hospital Germans Trias i Pujol (IGTP), 08916 Barcelona, Spain
| | - Neus Ruiz-Xiviller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Cytogenetics Platform, Hematology Laboratory Service, Institut Català d’Oncologia (ICO)-Hospital Germans Trias i Pujol (IGTP), 08916 Barcelona, Spain
| | - Annika Kotter
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; (A.K.); (M.H.)
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-Universität Mainz, 55128 Mainz, Germany; (A.K.); (M.H.)
| | - Jun Yokota
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.Y.); (R.K.-I.); (T.K.)
| | - Reika Kawabata-Iwakawa
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.Y.); (R.K.-I.); (T.K.)
- Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, Gunma 371-8511, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; (J.Y.); (R.K.-I.); (T.K.)
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo 104-0045, Japan
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain; (L.C.-S.); (V.D.); (D.P.); (M.R.-T.); (A.B.-C.); (F.S.); (I.G.); (N.R.-X.)
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08036 Barcelona, Spain
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18
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Xia C, Xu X, Ding Y, Yu C, Qiao J, Liu P. Abnormal spindle-like microcephaly-associated protein enhances cell invasion through Wnt/β-catenin-dependent regulation of epithelial-mesenchymal transition in non-small cell lung cancer cells. J Thorac Dis 2021; 13:2460-2474. [PMID: 34012593 PMCID: PMC8107535 DOI: 10.21037/jtd-21-566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background Lung cancer is one of the most common cancer worldwide, invasion and metastasis are still the bottleneck in the clinical setting. More diagnostic markers and drug targets need to be clarified. Therefore, we screened abnormal spindle-like microcephaly-associated protein (ASPM) as our candidate gene, which is associated with the poor prognosis. The aim of the present study was to understand the roles of ASPM in cell invasion in non-small cell lung cancer (NSCLC). Methods Gene Expression Omnibus (GEO) datamining was used to identify ASPM. Transwell invasion assay, quantitative reverse transcription polymerase chain reaction (qRT-PCR), and Western blot analysis were performed to discover the molecular functions of ASPM. Overexpression and small interfering mediated knockdown techniques have been used to study the cell invasion hallmarks of cancer. Results ASPM stood out among all the candidate genes from GEO datamining. ASPM in lung cancer tissues has been associated with poor overall survival rate. The protein levels of ASPM has been validated using lung cancer patients’ tissues, which upregulation of ASPM expression has been found in lung cancer patients. Silencing of ASPM decreased the cell invasion reflected by epithelial-mesenchymal transition (EMT) biomarkers: downregulation of vimentin and upregulation of E-cadherin. Matrix metalloproteinase (MMP) 2/9 protein levels were also affected upon transient knockdown of ASPM. Furthermore, the suppression of ASPM markedly inhibited the Wnt/β-catenin signaling pathway in vitro. The ectopic expression of ASPM had the opposite effect. The inhibition of β-catenin in ASPM-overexpressing lung cancer cells reduced the expression of EMT markers. The inhibitory effects on the Wnt/β-catenin signaling pathway were attenuated in cancer cells when ASPM was silenced. These findings demonstrated that the silencing of ASPM strongly reduced cell invasion in lung cancer. Conclusions ASPM promoted NSCLC invasion through EMT and by affecting the MMP family of proteins. The Wnt/β-catenin signaling pathway played an indispensable role in the ASPM-mediated NSCLC EMT-invasion cascade.
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Affiliation(s)
- Chunwei Xia
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Respiratory Medicine, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaofeng Xu
- Department of Respiratory Medicine, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Yiyan Ding
- Department of Respiratory Medicine, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Cunjun Yu
- Department of Respiratory Medicine, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Jianbing Qiao
- Department of Respiratory Medicine, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Ping Liu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Drapkin BJ, Rudin CM. Advances in Small-Cell Lung Cancer (SCLC) Translational Research. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038240. [PMID: 32513672 DOI: 10.1101/cshperspect.a038240] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past several years, we have witnessed a resurgence of interest in the biology and therapeutic vulnerabilities of small-cell lung cancer (SCLC). This has been driven in part through the development of a more extensive array of representative models of disease, including a diverse variety of genetically engineered mouse models and human tumor xenografts. Herein, we review recent progress in SCLC model development, and consider some of the particularly active avenues of translational research in SCLC, including interrogation of intratumoral heterogeneity, insights into the cell of origin and oncogenic drivers, mechanisms of chemoresistance, and new therapeutic opportunities including biomarker-directed targeted therapies and immunotherapies. Whereas SCLC remains a highly lethal disease, these new avenues of translational research, bringing together mechanism-based preclinical and clinical research, offer new hope for patients with SCLC.
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Affiliation(s)
- Benjamin J Drapkin
- University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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20
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Detection of Genetic Mutations by Next-Generation Sequencing for Predicting Prognosis of Extensive-Stage Small-Cell Lung Cancer. JOURNAL OF ONCOLOGY 2021; 2020:8811487. [PMID: 33643409 PMCID: PMC7901041 DOI: 10.1155/2020/8811487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/02/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023]
Abstract
Some studies have revealed that specific genetic mutations could be associated with chemotherapy response or even survival in small-cell lung cancer (SCLC). Our retrospective study aimed to identify the correlation between genetic mutations and progression-free survival (PFS) in extensive-stage SCLC after first-line chemotherapy. A total of 75 patients with extensive-stage SCLC confirmed by histopathology from February 2018 to February 2019 were retrospectively analyzed. The biopsy specimens of all patients were analyzed by Next-Generation Sequencing (NGS). All patients received first-line chemotherapy and follow-up at Shanghai Chest Hospital. Eleven genes were mutated in, at least, 10% of the 75 patients, including TP53 (96%), RB1 (77%), SMAD4 (32%), NOTCH1 (21%), PTEN (16%), FGFR1 (16%), KDR (15%), PIK3CA (15%), ROS1 (15%), BRCA2 (13%), and ERBB4 (10%). The median number of mutated genes among all patients was 5. Patients with more than 5 mutated genes (PFS = 6.7 months, P=0.004), mutant TP53 (PFS = 5.0 months, P=0.011), and mutant BRCA2 (PFS = 6.7 months, P=0.046) had better PFS after first-line chemotherapy than other patients. Multivariate Cox regression analysis showed that patients who achieved a PR (HR 3.729, 95% CI 2.038–6.822), had more than 5 mutated genes (HR 1.929, 95% CI 1.096–3.396), had BRCA2 mutations (HR 4.581, 95% CI 1.721–12.195), and had no liver metastasis (HR 0.415, 95% CI 0.181–0.951) showed improvements in PFS after first-line chemotherapy. In conclusion, the number of mutated genes and BRCA2 mutation status in extensive-stage SCLC were significantly related to PFS after first-line chemotherapy.
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21
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Saksis R, Silamikelis I, Laksa P, Megnis K, Peculis R, Mandrika I, Rogoza O, Petrovska R, Balcere I, Konrade I, Steina L, Stukens J, Breiksa A, Nazarovs J, Sokolovska J, Pirags V, Klovins J, Rovite V. Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue. Front Oncol 2021; 10:593760. [PMID: 33680922 PMCID: PMC7928352 DOI: 10.3389/fonc.2020.593760] [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: 08/18/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
Acromegaly is a disease mainly caused by pituitary neuroendocrine tumor (PitNET) overproducing growth hormone. First-line medication for this condition is the use of somatostatin analogs (SSAs), that decrease tumor mass and induce antiproliferative effects on PitNET cells. Dopamine agonists (DAs) can also be used if SSA treatment is not effective. This study aimed to determine differences in transcriptome signatures induced by SSA/DA therapy in PitNET tissue. We selected tumor tissue from twelve patients with somatotropinomas, with half of the patients receiving SSA/DA treatment before surgery and the other half treatment naive. Transcriptome sequencing was then carried out to identify differentially expressed genes (DEGs) and their protein–protein interactions, using pathway analyses. We found 34 upregulated and six downregulated DEGs in patients with SSA/DA treatment. Three tumor development promoting factors MUC16, MACC1, and GRHL2, were significantly downregulated in therapy administered PitNET tissue; this finding was supported by functional studies in GH3 cells. Protein–protein interactions and pathway analyses revealed extracellular matrix involvement in the antiproliferative effects of this type of the drug treatment, with pronounced alterations in collagen regulation. Here, we have demonstrated that somatotropinomas can be distinguished based on their transcriptional profiles following SSA/DA therapy, and SSA/DA treatment does indeed cause changes in gene expression. Treatment with SSA/DA significantly downregulated several factors involved in tumorigenesis, including MUC16, MACC1, and GRHL2. Genes that were upregulated, however, did not have a direct influence on antiproliferative function in the PitNET cells. These findings suggested that SSA/DA treatment acted in a tumor suppressive manner and furthermore, collagen related interactions and pathways were enriched, implicating extracellular matrix involvement in this anti-tumor effect of drug treatment.
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Affiliation(s)
- Rihards Saksis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Pola Laksa
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Kaspars Megnis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Raitis Peculis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ilona Mandrika
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Olesja Rogoza
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Inga Balcere
- Riga East Clinical University Hospital, Riga, Latvia.,Riga Stradins University, Riga, Latvia
| | - Ilze Konrade
- Riga East Clinical University Hospital, Riga, Latvia.,Riga Stradins University, Riga, Latvia
| | - Liva Steina
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Janis Stukens
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | - Austra Breiksa
- Pauls Stradins Clinical University Hospital, Riga, Latvia
| | | | | | - Valdis Pirags
- Pauls Stradins Clinical University Hospital, Riga, Latvia.,University of Latvia Faculty of Medicine, Riga, Latvia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Vita Rovite
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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22
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Wu J, Zhang A, Li L, Liu S, Yang F, Yang R. Meta-analysis of the Efficacy and Tolerability of Immune Checkpoint Inhibitors Combined With Chemotherapy in First-line Treatment of Small Cell Lung Cancer. Clin Ther 2021; 43:582-593.e2. [PMID: 33509647 DOI: 10.1016/j.clinthera.2020.12.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/25/2020] [Accepted: 12/25/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE The present study was conducted to evaluate the efficacy and tolerability of using an immune checkpoint inhibitor (ICI; programmed cell death protein 1/ligand 1 [PD-1/PD-L1] inhibitor or cytotoxic T-lymphocyte antigen [CTLA]-4 inhibitor) combined with chemotherapy in the first-line treatment of small cell lung cancer. METHODS Potential articles and studies were identified using Web of Science, Cochrane Library, and ClinicalTrials.gov. The end points included overall survival, progression-free survival, objective response rate, and adverse events. Significant heterogeneity was represented by a P value (Ph) of <0.05 or an I2 value of ≥50%, and the random-effects model was applied for pooled analysis. Otherwise, the fixed-effects model was used. Subgroup analysis was performed based on the type of ICI. Potential publication bias was evaluated via funnel plot and the Egger test. FINDINGS Five eligible articles were included. Both overall survival (hazard ratio [HR] = 0.83; 95% CI, 0.75-0.91; P < 0.001) and progression-free survival (HR = 0.80; 95% CI, 0.73-0.86; P < 0.001) were significantly prolonged by joint ICI + chemotherapy treatment. Additionally, the rates of tolerable grade ≥3 adverse events were similar between the ICI combination regimens and conventional chemotherapy (relative risk = 1.05; 95% CI, 0.98-1.12; P = 0.17). Subanalysis demonstrated that patient survival and objective response rate were more efficiently improved with a combination of anti-PD-1/PD-L1, but not anti-CTLA-4, + chemotherapy. IMPLICATIONS Based on data from the available literature, clinical efficacy (as measured by patient survival and objective response rate) was improved with a combination of anti-PD-1/PD-L1 + chemotherapy as first-line treatment compared with chemotherapy alone in patients with small cell lung cancer.
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Affiliation(s)
- Jiao Wu
- Department of the Second Medical Oncology, Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Aifen Zhang
- Department of Gastroenterology, The Second People's Hospital of Qujing, Qujing, China
| | - Lu Li
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Sicheng Liu
- Department of the Second Medical Oncology, Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fang Yang
- Department of the Second Medical Oncology, Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Runxiang Yang
- Department of the Second Medical Oncology, Third Affiliated Hospital of Kunming Medical University, Kunming, China.
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23
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Bonneville R, Paruchuri A, Wing MR, Krook MA, Reeser JW, Chen HZ, Dao T, Samorodnitsky E, Smith AM, Yu L, Nowacki N, Chen W, Roychowdhury S. Characterization of Clonal Evolution in Microsatellite Unstable Metastatic Cancers through Multiregional Tumor Sequencing. Mol Cancer Res 2020; 19:465-474. [PMID: 33229401 DOI: 10.1158/1541-7786.mcr-19-0955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 07/10/2020] [Accepted: 11/18/2020] [Indexed: 11/16/2022]
Abstract
Microsatellites are short, repetitive segments of DNA, which are dysregulated in mismatch repair-deficient (MMRd) tumors resulting in microsatellite instability (MSI). MSI has been identified in many human cancer types with varying incidence, and microsatellite instability-high (MSI-H) tumors often exhibit increased sensitivity to immune-enhancing therapies such as PD-1/PD-L1 inhibition. Next-generation sequencing (NGS) has permitted advancements in MSI detection, and recent computational advances have enabled characterization of tumor heterogeneity via NGS. However, the evolution and heterogeneity of microsatellite changes in MSI-positive tumors remains poorly described. We determined MSI status in 6 patients using our previously published algorithm, MANTIS, and inferred subclonal composition and phylogeny with Canopy and SuperFreq. We developed a simulated annealing-based method to characterize microsatellite length distributions in specific subclones and assessed the evolution of MSI in the context of tumor heterogeneity. We identified three to eight tumor subclones per patient, and each subclone exhibited MMRd-associated base substitution signatures. We noted that microsatellites tend to shorten over time, and that MMRd fosters heterogeneity by introducing novel mutations throughout the disease course. Some microsatellites are altered among all subclones in a patient, whereas other loci are only altered in particular subclones corresponding to subclonal phylogenetic relationships. Overall, our results indicate that MMRd is a substantial driver of heterogeneity, leading to both MSI and subclonal divergence. IMPLICATIONS: We leveraged subclonal inference to assess clonal evolution based on somatic mutations and microsatellites, which provides insight into MMRd as a dynamic mutagenic process in MSI-H malignancies.
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Affiliation(s)
- Russell Bonneville
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.,Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio
| | - Anoosha Paruchuri
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Michele R Wing
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Melanie A Krook
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Julie W Reeser
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Hui-Zi Chen
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Thuy Dao
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | | | - Amy M Smith
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
| | - Lianbo Yu
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Nicholas Nowacki
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Wei Chen
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Sameek Roychowdhury
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio. .,Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
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24
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Kwong A, Shin VY, Ho CYS, Au CH, Slavin TP, Weitzel JN, Chan TL, Ma ESK. Mutation screening of germline TP53 mutations in high-risk Chinese breast cancer patients. BMC Cancer 2020; 20:1053. [PMID: 33138793 PMCID: PMC7607817 DOI: 10.1186/s12885-020-07476-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/30/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Germline TP53 mutations are associated with Li-Fraumeni syndrome, a severe and rare hereditary cancer syndrome. Despite the rarity of germline TP53 mutations, the clinical implication for mutation carriers and their families is significant. The risk management of TP53 germline mutation carriers is more stringent than BRCA carriers, and radiotherapy should be avoided when possible. METHODS TP53 gene mutation screening was performed in 2538 Chinese breast cancer patients who tested negative for BRCA mutations. RESULTS Twenty TP53 mutations were identified with high next-generation sequencing concerning for germline mutations in Chinese breast cancer families. The majorities of the TP53 carriers had early-onset, hormone receptor-positive breast cancer, and had strong family history of cancer. Among all, 11 patients carried a germline mutation and 6 of which were likely de novo germline mutations. In addition, 1 case was suspected to be induced by chemotherapy or radiation, as this patient had no significant family history of cancer and aberrant clonal expansion can commonly include TP53 mutations. Furthermore, we have identified one mosaic LFS case. Two novel mutations (c.524_547dup and c.529_546del) were identified in patients with early-onset. CONCLUSIONS In view of the high lifetime risk of malignancy, identification of patients with germline TP53 mutations are important for clinicians to aid in accurate risk assessment and offer surveillance for patients and their families.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong and University of Hong Kong-Shenzhen Hospital, Hong Kong SAR, China.
- Department of Surgery, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China.
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China.
| | - Vivian Yvonne Shin
- Department of Surgery, The University of Hong Kong and University of Hong Kong-Shenzhen Hospital, Hong Kong SAR, China
| | - Cecilia Y S Ho
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Chun Hang Au
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Thomas P Slavin
- Department of Medical Oncology & Therapeutics Research, Division of Clinical Cancer Genetics, City of Hope, Duarte, CA, USA
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jeffrey N Weitzel
- Department of Medical Oncology & Therapeutics Research, Division of Clinical Cancer Genetics, City of Hope, Duarte, CA, USA
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Tsun-Leung Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong SAR, China
- Department of Pathology, Division of Molecular Pathology, Hong Kong Sanatorium & Hospital, Hong Kong SAR, China
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25
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Nishino K, Takasawa K, Okamura K, Arai Y, Sekiya A, Akutsu H, Umezawa A. Identification of an epigenetic signature in human induced pluripotent stem cells using a linear machine learning model. Hum Cell 2020; 34:99-110. [PMID: 33047283 PMCID: PMC7788050 DOI: 10.1007/s13577-020-00446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
The use of human induced pluripotent stem cells (iPSCs), used as an alternative to human embryonic stem cells (ESCs), is a potential solution to challenges, such as immune rejection, and does not involve the ethical issues concerning the use of ESCs in regenerative medicine, thereby enabling developments in biological research. However, comparative analyses from previous studies have not indicated any specific feature that distinguishes iPSCs from ESCs. Therefore, in this study, we established a linear classification-based learning model to distinguish among ESCs, iPSCs, embryonal carcinoma cells (ECCs), and somatic cells on the basis of their DNA methylation profiles. The highest accuracy achieved by the learned models in identifying the cell type was 94.23%. In addition, the epigenetic signature of iPSCs, which is distinct from that of ESCs, was identified by component analysis of the learned models. The iPSC-specific regions with methylation fluctuations were abundant on chromosomes 7, 8, 12, and 22. The method developed in this study can be utilized with comprehensive data and widely applied to many aspects of molecular biology research.
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Affiliation(s)
- Koichiro Nishino
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan. .,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan.
| | - Ken Takasawa
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoshikazu Arai
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Asato Sekiya
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Hidenori Akutsu
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
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26
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Wang Z, Kan G, Sheng C, Yao C, Mao Y, Chen S. ARHGEF19 regulates MAPK/ERK signaling and promotes the progression of small cell lung cancer. Biochem Biophys Res Commun 2020; 533:792-799. [PMID: 32993957 DOI: 10.1016/j.bbrc.2020.09.085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022]
Abstract
Small cell lung cancer (SCLC) is an aggressive lung tumor subtype with poor survival. To identify genes that differentially expressed in SCLC with tumor promotion activity as candidate therapeutic targets, we analyzed the expression of 50 RhoGEFs family genes in published microarray data of SCLC and normal tissues (Gene Expression Omnibus (GEO) dataset GSE43346). We identified ARHGEF19, a member of RhoGEFs family, as an overexpressed oncogene in SCLC. ARHGEF19 is up-regulated in SCLC tissues and ranks first in RhoGEFs family genes. Enforced ARHGEF19 expression promotes SCLC cell proliferation in vitro and its knockdown decreases cell proliferation in vitro and in vivo. ARHGEF19-DH and -PD domain interacts with HRAS and activates the MAPK/ERK pathway in SCLC cells and SCLC xenografts. Our study presents evidences that ARHGEF19 overexpression promotes SCLC cell growth and activates the MAPK/ERK pathway. These findings would shed light on the development of new therapeutics for SCLC management.
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Affiliation(s)
- Ziyang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, PR China
| | - Guangyan Kan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, PR China
| | - Chunjie Sheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, PR China
| | - Chen Yao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, PR China
| | - Yizhi Mao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, PR China
| | - Shuai Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, PR China.
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27
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Amanam I, Mambetsariev I, Gupta R, Achuthan S, Wang Y, Pharaon R, Massarelli E, Koczywas M, Reckamp K, Salgia R. Role of immunotherapy and co-mutations on KRAS-mutant non-small cell lung cancer survival. J Thorac Dis 2020; 12:5086-5095. [PMID: 33145085 PMCID: PMC7578487 DOI: 10.21037/jtd.2020.04.18] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background KRAS mutations reported in non-small cell lung cancer (NSCLC) represent a significant percentage of patients diagnosed with NSCLC. However, there still remains no therapeutic option designed to target KRAS. In an era with immunotherapy as a dominant treatment option in metastatic NSCLC, the role of immunotherapy in KRAS mutated patients is not clear. Methods Eligible patients diagnosed with NSCLC and found to have a KRAS mutation were identified in an institutional lung cancer database. Demographic, clinical, and molecular data was collected and analyzed. Results A total of 60 patients were identified for this retrospective analysis. Majority of patients were Caucasian (73%), diagnosed with stage IV (70%) adenocarcinoma (87%), and had a KRAS codon 12 mutation (78%). Twenty percent of patients were treated with immunotherapy. Median overall survival was 28 months in the cohort and patients who received immunotherapy were found to have better survival versus those who did not (33 vs. 22 months, P=0.31). Furthermore, there was an association between high survival and patients who received immunotherapy (P=0.007). Conclusions Patients with KRAS mutations have a unique co-mutation phenotype that requires further investigation. Immunotherapy seems to be an effective choice of treatment for KRAS positive patients in any treatment-line setting and yields better outcomes than conventional chemotherapy. The relationship between immunotherapy and KRAS mutations requires further studies to confirm survival advantage.
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Affiliation(s)
- Idoroenyi Amanam
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Isa Mambetsariev
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Rohan Gupta
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Srisairam Achuthan
- Center for Informatics, City of Hope National Medical Center, Duarte, CA, USA
| | - Yingyu Wang
- Center for Informatics, City of Hope National Medical Center, Duarte, CA, USA
| | - Rebecca Pharaon
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Erminia Massarelli
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Marianna Koczywas
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Karen Reckamp
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
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28
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Wu X, Zhang X, Tao L, Chen P. Risk of second primary malignancy in adults with pulmonary high-grade neuroendocrine carcinoma (HGNEC). BMC Cancer 2020; 20:719. [PMID: 32746796 PMCID: PMC7398247 DOI: 10.1186/s12885-020-07224-2] [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: 03/16/2020] [Accepted: 07/27/2020] [Indexed: 12/09/2022] Open
Abstract
Background Pulmonary high-grade neuroendocrine carcinoma (HGNEC) has a rising incidence of developing second primary malignancies (SPMs). This study is the first population-based analysis to quantify the SPM risks among survivors of lung HGNEC. Methods We used the Surveillance, Epidemiology, and End Results (SEER) database to calculate standardized incidence ratio (SIR) and absolute excess risk (AER) between 2000 and 2016 for patients with pulmonary HGNEC. Results The data of 1161 patients with SPMs were retrieved from the SEER database. The ratio of observed/expected number of SPMs in pulmonary HGNEC was 1.53. Solid tumours comprised 91% of all second malignancies in lung HGNEC patients, with the most common cancers reported in the oral cavity and pharynx, the urinary and respiratory systems Conclusions Our study observed an increased risk of SPMs among patients with pulmongnancies.
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Affiliation(s)
- Xiaomin Wu
- Department of Oncology, Yancheng No.1 People's Hospital, the Affiliated Hospital of Nanjing University, 166 Yulong West Road, Yancheng, 224200, People's Republic of China
| | - Xiaojing Zhang
- Department of Gynecologic Oncology, Zhejiang Cancer Hospital, Hangzhou, 310000, People's Republic of China
| | - Leilei Tao
- Department of Oncology, Yancheng No.1 People's Hospital, the Affiliated Hospital of Nanjing University, 166 Yulong West Road, Yancheng, 224200, People's Republic of China
| | - Ping Chen
- Department of Oncology, Yancheng No.1 People's Hospital, the Affiliated Hospital of Nanjing University, 166 Yulong West Road, Yancheng, 224200, People's Republic of China.
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29
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Chen QF, Shi F, Huang T, Huang C, Shen L, Wu P, Li W. ASTN1 is associated with immune infiltrates in hepatocellular carcinoma, and inhibits the migratory and invasive capacity of liver cancer via the Wnt/β‑catenin signaling pathway. Oncol Rep 2020; 44:1425-1440. [PMID: 32945491 PMCID: PMC7448461 DOI: 10.3892/or.2020.7704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022] Open
Abstract
Astrotactin 1 (ASTN1) is known to serve a physiological role in neuronal migration; however its role in liver cancer remains to be determined. In the present study, ASTN1 levels were lower in liver cancer tissues compared with those in matching normal tissue. ASTN1 levels were negatively associated with microscopic vascular invasion, advanced clinical stage and a less favorable prognosis in patients with hepatocellular carcinoma (HCC). Furthermore, ASTN1 overexpression in a liver cancer cell line reduced the migratory and invasive capacity of the cells. Based on bioinformatics analysis, ASTN1 levels were negatively associated with the Wnt signaling pathway. In addition, ASTN1 downregulated the protein expression levels of β-catenin, T-cell factor (TCF)1, TCF4, Jun proto-oncogene (C-jun), Myc proto-oncogene (C-myc), cyclooxygenase-2 (COX2), metalloproteinase (MMP)2, MMP9 and vascular endothelial growth factor (VEGF) protein levels, indicative of suppression of Wnt signaling. Furthermore, XAV939-induced Wnt signaling suppression reversed the ASTN1-mediated inhibition of invasion and migration in cells. Overexpression of ASTN1 in xenografts reduced cancer development as well as Wnt signaling. TIMER analysis showed that ASTN1 expression was negatively correlated with B cell, macrophage and neutrophil infiltrating levels in HCC. Together, the results of the present study showed that ASTN1 reduced the migratory and invasive capacity of liver cancer cells, potentially served as a candidate biomarker for diagnosis and prediction of the prognosis of HCC, and was associated with immune infiltration. Understanding the underlying mechanisms of action of ASTN1 may facilitate the development of novel strategies for prevention and treatment of liver cancer.
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Affiliation(s)
- Qi-Feng Chen
- Department of Medical Imaging and Interventional Radiology, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Feng Shi
- Department of Interventional Radiology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, P.R. China
| | - Tao Huang
- Department of Medical Imaging and Interventional Radiology, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Chaoyun Huang
- State Key Laboratory of Oncology in South China, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Lujun Shen
- Department of Medical Imaging and Interventional Radiology, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Peihong Wu
- Department of Medical Imaging and Interventional Radiology, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
| | - Wang Li
- Department of Medical Imaging and Interventional Radiology, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong 510060, P.R. China
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30
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Wang J, He Z, Duan R. [Expression of ASPM in Lung Adenocarcinoma and Its Relationship with Development and Prognosis]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:29-35. [PMID: 31948535 PMCID: PMC7007395 DOI: 10.3779/j.issn.1009-3419.2020.01.05] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Previous studies have shown that ASPM is a tumorigenesis associated protein, mutations in ASPM can lead to MCPH. This study mainly explores the relationship between the ASPM expression of lung adenocarcinoma and the development and prognosis of lung cancer. The aim of this study was to investigate the relationship between the expression of abnormal spindle-like microcephaly-associated protein (ASPM) in lung adenocarcinoma and the development and prognosis in lung cancer. METHODS A total of 90 cases of lung adenocarcinoma tissue specimens and 90 cases of benign pulmonary lesions were collected, the expression of ASPM was detected by immunohistochemical technique, and the expression of ASPM in 12 pairs of tissues was detected by real-time quantity polymerase chain reaction and western blot. RESULTS (1) The expression of ASPM in the tissue specimens of benign pulmonary lesions was negative while the expression level of ASPM in lung adenocarcinoma was significantly higher than lung tissue of benign pulmonary lesions (P<0.05). (2) The expression level of ASPM has no remarkable difference in lung adenocarcinoma with lymph node development and the lung cancer without lymph node development, there was no statistically significant (P<0.05). (3) The ASPM expression level in the tumor's size ≥4 cm was significantly higher than than of the size<4 cm (P<0.05). (4) Hierarchical analysis results show that T stage is related to ASPM expression level (P<0.05). (5) The high expression level of ASPM in lung adenocarcinoma was significantly positively correlated with the poor prognosis (P<0.05). CONCLUSIONS (1) The expression level of ASPM in lung cancer is obviously increased and closely related to the progress of lung adenocarcinoma. (2) The expression level of ASPM in lung adenocarcinoma was significantly positively correlated with poor prognosis (P<0.05). (3) Detection of the expression level of ASPM in lung adenocarcinoma help to predict the prognosis of lung adenocarcinoma in advance.
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Affiliation(s)
- Junjie Wang
- Department of Oncology, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Zhenyu He
- Department of Radiotherapy, Cancer Hospital, Sun Yat-Sen University, Guangzhou 510060, China
| | - Renhui Duan
- Department of Oncology, Xinxiang Central Hospital, Xinxiang 453000, China
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Sun X, Shang J, Wu A, Xia J, Xu F. Identification of dynamic signatures associated with smoking-related squamous cell lung cancer and chronic obstructive pulmonary disease. J Cell Mol Med 2019; 24:1614-1625. [PMID: 31829519 PMCID: PMC6991676 DOI: 10.1111/jcmm.14852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 01/09/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a risk factor for the development of lung cancer. The aim of this study was to identify early diagnosis biomarkers for lung squamous cell carcinoma (SQCC) in COPD patients and to determine the potential pathogenetic mechanisms. The GSE12472 data set was downloaded from the Gene Expression Omnibus database. Differentially co‐expressed links (DLs) and differentially expressed genes (DEGs) in both COPD and normal tissues, or in both SQCC + COPD and COPD samples were used to construct a dynamic network associated with high‐risk genes for the SQCC pathogenetic process. Enrichment analysis was performed based on Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We used the gene expression data and the clinical information to identify the co‐expression modules based on weighted gene co‐expression network analysis (WGCNA). In total, 205 dynamic DEGs, 5034 DLs and one pathway including CDKN1A, TP53, RB1 and MYC were found to have correlations with the pathogenetic progress. The pathogenetic mechanisms shared by both SQCC and COPD are closely related to oxidative stress, the immune response and infection. WGCNA identified 11 co‐expression modules, where magenta and black were correlated with the “time to distant metastasis.” And the “surgery due to” was closely related to the brown and blue modules. In conclusion, a pathway that includes TP53, CDKN1A, RB1 and MYC may play a vital role in driving COPD towards SQCC. Inflammatory processes and the immune response participate in COPD‐related carcinogenesis.
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Affiliation(s)
- Xiaoru Sun
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingzhe Shang
- Center of Systems Medicine, Chinese Academy of Medical Science (CAMS), Suzhou Institute of System Medicine, Suzhou, China
| | - Aiping Wu
- Center of Systems Medicine, Chinese Academy of Medical Science (CAMS), Suzhou Institute of System Medicine, Suzhou, China
| | - Jingyan Xia
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Feng Xu
- Department of Infectious Diseases, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Identifying Mutually Exclusive Gene Sets with Prognostic Value and Novel Potential Driver Genes in Patients with Glioblastoma. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4860367. [PMID: 31815141 PMCID: PMC6878817 DOI: 10.1155/2019/4860367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/15/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022]
Abstract
The pathogenesis and prognosis of glioblastoma (GBM) remain poorly understood. Mutual exclusivity analysis can distinguish driver genes and pathways from passenger ones. The purpose of this study was to identify mutually exclusive gene sets (MEGSs) that have prognostic value and to detect novel driver genes in GBM. The genomic alteration profile and clinical information were derived from The Cancer Genome Atlas, and the MEGSA method was used to identify the MEGS. Next, we performed survival analysis and constructed a risk prediction model for prognostic stratification. Leave-one-out cross-validation and permutation test were used to evaluate its performance. Finally, we identified 21 statistically significant MEGSs. We found that the MEGS in the RB pathway was significantly associated with poor prognosis, after adjusting for age and gender (HR = 1.837, 95% CI: 1.192-2.831). Based on the risk prediction model, 208 (80.9%) and 49 (19.1%) patients were assigned to high- and low-risk groups, respectively (log-rank: p < 0.001, adjusted p=0.001). Additionally, we found that SPTA1, a novel gene involved in the MEGS, was mutually exclusive with members of cell cycle, P53, and RB pathways. In conclusion, the MEGS in the RB pathway had considerable clinical value for GBM prognostic stratification. Mutated SPTA1 may be involved in GBM development.
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Tarsani E, Kranis A, Maniatis G, Avendano S, Hager-Theodorides AL, Kominakis A. Discovery and characterization of functional modules associated with body weight in broilers. Sci Rep 2019; 9:9125. [PMID: 31235723 PMCID: PMC6591351 DOI: 10.1038/s41598-019-45520-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Aim of the present study was to investigate whether body weight (BW) in broilers is associated with functional modular genes. To this end, first a GWAS for BW was conducted using 6,598 broilers and the high density SNP array. The next step was to search for positional candidate genes and QTLs within strong LD genomic regions around the significant SNPs. Using all positional candidate genes, a network was then constructed and community structure analysis was performed. Finally, functional enrichment analysis was applied to infer the functional relevance of modular genes. A total number of 645 positional candidate genes were identified in strong LD genomic regions around 11 genome-wide significant markers. 428 of the positional candidate genes were located within growth related QTLs. Community structure analysis detected 5 modules while functional enrichment analysis showed that 52 modular genes participated in developmental processes such as skeletal system development. An additional number of 14 modular genes (GABRG1, NGF, APOBEC2, STAT5B, STAT3, SMAD4, MED1, CACNB1, SLAIN2, LEMD2, ZC3H18, TMEM132D, FRYL and SGCB) were also identified as related to body weight. Taken together, current results suggested a total number of 66 genes as most plausible functional candidates for the trait examined.
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Affiliation(s)
- Eirini Tarsani
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece.
| | - Andreas Kranis
- Aviagen Ltd., Newbridge, Midlothian, EH28 8SZ, UK.,The Roslin Institute, University of Edinburgh, EH25 9RG, Midlothian, United Kingdom
| | | | | | - Ariadne L Hager-Theodorides
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Antonios Kominakis
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
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Shigemura T, Matsuda K, Kurata T, Sakashita K, Okuno Y, Muramatsu H, Yue F, Ebihara Y, Tsuji K, Sasaki K, Nakahata T, Nakazawa Y, Koike K. Essential role of PTPN11 mutation in enhanced haematopoietic differentiation potential of induced pluripotent stem cells of juvenile myelomonocytic leukaemia. Br J Haematol 2019; 187:163-173. [PMID: 31222725 DOI: 10.1111/bjh.16060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
We established mutated and non-mutated induced pluripotent stem cell (iPSC) clones from a patient with PTPN11 (c.226G>A)-mutated juvenile myelomonocytic leukaemia (JMML). Both types of iPSCs fulfilled the quality criteria. Mutated iPSC colonies generated significantly more CD34+ and CD34+ CD45+ cells compared to non-mutated iPSC colonies in a culture coated with irradiated AGM-S3 cells to which four growth factors were added sequentially or simultaneously. The haematopoietic differentiation potential of non-mutated JMML iPSC colonies was similar to or lower than that of iPSC colonies from a healthy individual. The PTPN11 mutation coexisted with the OSBP2 c.389C>T mutation. Zinc-finger nuclease-mediated homologous recombination revealed that correction of PTPN11 mutation in iPSCs with PTPN11 and OSBP2 mutations resulted in reduced CD34+ cell generation to a level similar to that obtained with JMML iPSC colonies with the wild-type of both genes, and interestingly, to that obtained with normal iPSC colonies. Transduction of the PTPN11 mutation into JMML iPSCs with the wild-type of both genes increased CD34+ cell production to a level comparable to that obtained with JMML iPSC colonies harbouring the two genetic mutations. Thus, PTPN11 mutation may be the most essential abnormality to confer an aberrant haematopoietic differentiation potential in this disorder.
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Affiliation(s)
- Tomonari Shigemura
- Department of Paediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kazuyuki Matsuda
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Matsumoto, Japan
| | - Takashi Kurata
- Department of Paediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kazuo Sakashita
- Department of Haematology/Oncology, Nagano Children's Hospital, Azumino, Japan
| | - Yusuke Okuno
- Department of Paediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Paediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fengming Yue
- Department of Anatomy and Organ Technology, Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Yasuhiro Ebihara
- Department of Laboratory Medicine, International Medical Centre, Saitama Medical University, Hidaka, Japan
| | - Kohichiro Tsuji
- Department of Paediatrics, Komoro Kogen Hospital, Komoro, Japan
| | - Katsunori Sasaki
- Department of Anatomy and Organ Technology, Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Tatsutoshi Nakahata
- Department of Clinical Application, Centre for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yozo Nakazawa
- Department of Paediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kenichi Koike
- Department of Paediatrics, Shinshu University School of Medicine, Matsumoto, Japan.,Minami Nagano Medical Centre, Shinonoi General Hospital, Nagano, Japan
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de Almeida BP, Apolónio JD, Binnie A, Castelo-Branco P. Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers. BMC Cancer 2019; 19:219. [PMID: 30866861 PMCID: PMC6416975 DOI: 10.1186/s12885-019-5403-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Breast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The aim of this study is to characterize the relationship between DNA methylation and aberrant gene expression in breast cancer. METHODS We analysed DNA methylation and gene expression profiles from breast cancer tissue and matched normal tissue in The Cancer Genome Atlas (TCGA). Genome-wide differential methylation analysis and methylation-gene expression correlation was performed. Gene expression changes were subsequently validated in the METABRIC dataset. The Oncoscore tool was used to identify genes that had previously been associated with cancer in the literature. A subset of genes that had not previously been studied in cancer was chosen for further analysis. RESULTS We identified 368 CpGs that were differentially methylated between tumor and normal breast tissue (∆β > 0.4). Hypermethylated CpGs were overrepresented in tumor tissue and were found predominantly (56%) in upstream promoter regions. Conversely, hypomethylated CpG sites were found primarily in the gene body (66%). Expression analysis revealed that 209 of the differentially-methylated CpGs were located in 169 genes that were differently expressed between normal and breast tumor tissue. Methylation-expression correlations were predominantly negative (70%) for promoter CpG sites and positive (74%) for gene body CpG sites. Among these differentially-methylated and differentially-expressed genes, we identified 7 that had not previously been studied in any form of cancer. Three of these, TDRD10, PRAC2 and TMEM132C, contained CpG sites that showed diagnostic and prognostic value in breast cancer, particularly in estrogen-receptor (ER)-positive samples. A pan-cancer analysis confirmed differential expression of these genes together with diagnostic and prognostic value of their respective CpG sites in multiple cancer types. CONCLUSION We have identified 368 DNA methylation changes that characterize breast cancer tumor tissue, of which 209 are associated with genes that are differentially-expressed in the same samples. Novel DNA methylation markers were identified, of which cg12374721 (PRAC2), cg18081940 (TDRD10) and cg04475027 (TMEM132C) show promise as diagnostic and prognostic markers in breast cancer as well as other cancer types.
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Affiliation(s)
- Bernardo P. de Almeida
- Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Present address: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Joana Dias Apolónio
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
| | - Alexandra Binnie
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
- William Osler Health System, Brampton, ON Canada
| | - Pedro Castelo-Branco
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
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Pezzuto F, Fortarezza F, Lunardi F, Calabrese F. Are there any theranostic biomarkers in small cell lung carcinoma? J Thorac Dis 2019; 11:S102-S112. [PMID: 30775033 DOI: 10.21037/jtd.2018.12.14] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Small cell lung cancer (SCLC), an aggressive lung tumour with a poor prognosis, has a high load of somatic mutations, mainly induced by tobacco carcinogens given the strong association with smoking. Advances in genomic, epigenetic and proteomic profiling have significantly improved our understanding of the molecular and cellular biology of SCLC. Given the high mutational burden of SCLC the immune microenvironment is another exciting area under investigation even if it seems to be quite distinct from that of other solid tumours. In this review we will outline the current progress in molecular etiology of SCLC mentioning some key markers considered promising theranostic biomarkers.
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Affiliation(s)
- Federica Pezzuto
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, Padova, Italy
| | - Francesco Fortarezza
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, Padova, Italy
| | - Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, Padova, Italy
| | - Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, Padova, Italy
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Lallo A, Frese KK, Morrow CJ, Sloane R, Gulati S, Schenk MW, Trapani F, Simms N, Galvin M, Brown S, Hodgkinson CL, Priest L, Hughes A, Lai Z, Cadogan E, Khandelwal G, Simpson KL, Miller C, Blackhall F, O'Connor MJ, Dive C. The Combination of the PARP Inhibitor Olaparib and the WEE1 Inhibitor AZD1775 as a New Therapeutic Option for Small Cell Lung Cancer. Clin Cancer Res 2018; 24:5153-5164. [PMID: 29941481 DOI: 10.1158/1078-0432.ccr-17-2805] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 04/05/2018] [Accepted: 06/20/2018] [Indexed: 12/12/2022]
Abstract
Purpose: Introduced in 1987, platinum-based chemotherapy remains standard of care for small cell lung cancer (SCLC), a most aggressive, recalcitrant tumor. Prominent barriers to progress are paucity of tumor tissue to identify drug targets and patient-relevant models to interrogate novel therapies. Following our development of circulating tumor cell patient-derived explants (CDX) as models that faithfully mirror patient disease, here we exploit CDX to examine new therapeutic options for SCLC.Experimental Design: We investigated the efficacy of the PARP inhibitor olaparib alone or in combination with the WEE1 kinase inhibitor AZD1775 in 10 phenotypically distinct SCLC CDX in vivo and/or ex vivo These CDX represent chemosensitive and chemorefractory disease including the first reported paired CDX generated longitudinally before treatment and upon disease progression.Results: There was a heterogeneous depth and duration of response to olaparib/AZD1775 that diminished when tested at disease progression. However, efficacy of this combination consistently exceeded that of cisplatin/etoposide, with cures in one CDX model. Genomic and protein analyses revealed defects in homologous recombination repair genes and oncogenes that induce replication stress (such as MYC family members), predisposed CDX to combined olaparib/AZD1775 sensitivity, although universal predictors of response were not noted.Conclusions: These preclinical data provide a strong rationale to trial this combination in the clinic informed by prevalent, readily accessed circulating tumor cell-based biomarkers. New therapies will be evaluated in SCLC patients after first-line chemotherapy, and our data suggest that the combination of olaparib/AZD1775 should be used as early as possible and before disease relapse. Clin Cancer Res; 24(20); 5153-64. ©2018 AACR.
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Affiliation(s)
- Alice Lallo
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Kristopher K Frese
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Christopher J Morrow
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Robert Sloane
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Sakshi Gulati
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Maximillian W Schenk
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Francesca Trapani
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Nicole Simms
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Melanie Galvin
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Stewart Brown
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Cassandra L Hodgkinson
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Lynsey Priest
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Adina Hughes
- Oncology Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Zhongwu Lai
- Oncology Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Waltham, Massachusetts
| | - Elaine Cadogan
- Oncology Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Garima Khandelwal
- RNA Biology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Kathryn L Simpson
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Crispin Miller
- RNA Biology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Fiona Blackhall
- Institute of Cancer Sciences, University of Manchester, and Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Mark J O'Connor
- Oncology Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Cambridge, United Kingdom.
| | - Caroline Dive
- Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, United Kingdom.
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Wagner AH, Devarakonda S, Skidmore ZL, Krysiak K, Ramu A, Trani L, Kunisaki J, Masood A, Waqar SN, Spies NC, Morgensztern D, Waligorski J, Ponce J, Fulton RS, Maggi LB, Weber JD, Watson MA, O'Conor CJ, Ritter JH, Olsen RR, Cheng H, Mukhopadhyay A, Can I, Cessna MH, Oliver TG, Mardis ER, Wilson RK, Griffith M, Griffith OL, Govindan R. Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer. Nat Commun 2018; 9:3787. [PMID: 30224629 PMCID: PMC6141466 DOI: 10.1038/s41467-018-06162-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/13/2018] [Indexed: 12/27/2022] Open
Abstract
Nearly all patients with small cell lung cancer (SCLC) eventually relapse with chemoresistant disease. The molecular mechanisms driving chemoresistance in SCLC remain un-characterized. Here, we describe whole-exome sequencing of paired SCLC tumor samples procured at diagnosis and relapse from 12 patients, and unpaired relapse samples from 18 additional patients. Multiple somatic copy number alterations, including gains in ABCC1 and deletions in MYCL, MSH2, and MSH6, are identifiable in relapsed samples. Relapse samples also exhibit recurrent mutations and loss of heterozygosity in regulators of WNT signaling, including CHD8 and APC. Analysis of RNA-sequencing data shows enrichment for an ASCL1-low expression subtype and WNT activation in relapse samples. Activation of WNT signaling in chemosensitive human SCLC cell lines through APC knockdown induces chemoresistance. Additionally, in vitro-derived chemoresistant cell lines demonstrate increased WNT activity. Overall, our results suggest WNT signaling activation as a mechanism of chemoresistance in relapsed SCLC.
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Affiliation(s)
- Alex H Wagner
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Siddhartha Devarakonda
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Zachary L Skidmore
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Kilannin Krysiak
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Avinash Ramu
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Lee Trani
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Jason Kunisaki
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Ashiq Masood
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- Saint Luke's Health System, Kansas City, MO, USA
| | - Saiama N Waqar
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Nicholas C Spies
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Daniel Morgensztern
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Jason Waligorski
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Jennifer Ponce
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Leonard B Maggi
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jason D Weber
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- ICCE Institute, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Mark A Watson
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
| | - Christopher J O'Conor
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jon H Ritter
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rachelle R Olsen
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Haixia Cheng
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Anandaroop Mukhopadhyay
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Ismail Can
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Melissa H Cessna
- Intermountain Healthcare BioRepository and Department of Pathology, Intermountain Healthcare, Salt Lake City, UT, 84103, USA
| | - Trudy G Oliver
- Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, UT, 84112, USA
| | - Elaine R Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Nationwide Children's Hospital, Columbus, OH, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Ramaswamy Govindan
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Alvin J Siteman Cancer Center, Washington University, St. Louis, MO, 63110, USA.
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39
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Saito M, Shiraishi K, Goto A, Suzuki H, Kohno T, Kono K. Development of targeted therapy and immunotherapy for treatment of small cell lung cancer. Jpn J Clin Oncol 2018; 48:603-608. [PMID: 29762727 DOI: 10.1093/jjco/hyy068] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/25/2018] [Indexed: 01/20/2023] Open
Abstract
Targeted therapy against druggable genetic aberrations has shown a significantly positive response rate and longer survival in various cancers, including lung cancer. In lung adenocarcinoma (LADC), specific thyroxin kinase inhibitors against EGFR mutations and ALK fusions are used as a standard treatment regimen and show significant positive efficacy. On the other hand, targeted therapy against driver gene aberrations has not been adapted yet in small cell lung cancer (SCLC). This is because driver genes and druggable aberrations are rarely identified by next generation sequencing in SCLC. Recent advances in the understanding of molecular biology have revealed several candidate therapeutic targets. To date, poly [ADP-ribose] polymerase (PARP), enhancer of zeste homologue 2 (EZH2) or delta-like canonical Notch ligand 3 (DLL3) are considered to be druggable targets in SCLC. In addition, another candidate of personalized therapy for SCLC is immune blockade therapy of programmed death-1 (PD-1) and its ligand, PD-L1. PD-1/PD-L1 blockade therapy is not a standard therapy for SCLC, so many clinical trials have been performed to investigate its efficacy. Herein, we review gene aberrations exploring the utility of targeted therapy and discuss blockade of immune checkpoints therapy in SCLC.
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Affiliation(s)
- Motonobu Saito
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo.,Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine.,Department of Chest Surgery, Fukushima Medical University School of Medicine, Fukushima
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Hiroyuki Suzuki
- Department of Chest Surgery, Fukushima Medical University School of Medicine, Fukushima
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine
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40
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Šlekienė L, Stakišaitis D, Balnytė I, Valančiūtė A. Sodium Valproate Inhibits Small Cell Lung Cancer Tumor Growth on the Chicken Embryo Chorioallantoic Membrane and Reduces the p53 and EZH2 Expression. Dose Response 2018; 16:1559325818772486. [PMID: 29760602 PMCID: PMC5944146 DOI: 10.1177/1559325818772486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 12/30/2022] Open
Abstract
The study aims to test the effect of different sodium valproate (NaVP) doses on small cell lung cancer NCI-H146 cells tumor in chicken embryo chorioallantoic membrane (CAM) model. Xenografts were investigated in the following groups: nontreated control and 5 groups treated with different NaVP doses (2, 3, 4, 6, and 8 mmol/L). Invasion of tumors into CAM in the nontreated group reached 76%. Tumors treated with 8 mmol/L NaVP doses significantly differed in tumor invasion frequency from the control and those treated with 2 mmol/L (P < .01). The calculated probability of 50% tumor noninvasion into CAM was when tumors were treated with 4 mmol/L of NaVP. Number of p53-positive cells in tumors was significantly reduced when treated with NaVP doses from 3 to 8 mmol/L as compared with control; number of EZH2-positive cells in control significantly differed from all NaVP-treated groups. No differences in p53- and EZH2-positive cell numbers were found among 4, 6, and 8 mmol/L NaVP-treated groups. Invaded tumors had an increased N-cadherin and reduced E-cadherin expression. The results indicate the increasing NaVP dose to be able to inhibit tumors progression. Expression of p53 and EZH2 may be promising target markers of therapeutic efficacy evaluation.
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Affiliation(s)
- Lina Šlekienė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Donatas Stakišaitis
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.,Laboratory of Molecular Oncology, National Cancer Institute, Vilnius, Lithuania
| | - Ingrida Balnytė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Angelija Valančiūtė
- Department of Histology and Embryology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
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41
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Sanchez-Pulido L, Ponting CP. TMEM132: an ancient architecture of cohesin and immunoglobulin domains define a new family of neural adhesion molecules. Bioinformatics 2018; 34:721-724. [PMID: 29088312 PMCID: PMC6030884 DOI: 10.1093/bioinformatics/btx689] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 09/29/2017] [Accepted: 10/26/2017] [Indexed: 11/26/2022] Open
Abstract
Summary The molecular functions of TMEM132 genes remain poorly understood and under-investigated despite their mutations associated with non-syndromic hearing loss, panic disorder and cancer. Here we show the full domain architecture of human TMEM132 family proteins solved using in-depth sequence and structural analysis. We reveal them to be five previously unappreciated cell adhesion molecules whose domain architecture has an early holozoan origin prior to the emergence of choanoflagellates and metazoa. The extra-cellular portions of TMEM132 proteins contain five conserved domains including three tandem immunoglobulin domains, and a cohesin domain homologue, the first such domain found in animals. These findings strongly predict a cellular adhesion function for TMEM132 family, connecting the extracellular medium with the intracellular actin cytoskeleton. Contact luis.sanchez-pulido@igmm.ed.ac.uk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Luis Sanchez-Pulido
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Chris P Ponting
- Medical Research Council Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
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42
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MYCL is a target of a BET bromodomain inhibitor, JQ1, on growth suppression efficacy in small cell lung cancer cells. Oncotarget 2018; 7:77378-77388. [PMID: 27764802 PMCID: PMC5363592 DOI: 10.18632/oncotarget.12671] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022] Open
Abstract
We aimed to elucidate the effect of JQ1, a BET inhibitor, on small cell lung cancers (SCLCs) with MYCL amplification and/or expression. Fourteen SCLC cell lines, including four with MYCL amplification, were examined for the effects of JQ1 on protein and gene expression by Western blot and mRNA microarray analyses. The sensitivity of SCLC cells to JQ1 was assessed by cell growth and apoptosis assays. MYCL was expressed in all the 14 cell lines, whereas MYC/MYCN expression was restricted mostly to cell lines with gene amplification. ASCL1, a transcription factor shown to play a role in SCLC, was also expressed in 11/14 cell lines. All SCLC cell lines were sensitive to JQ1 with GI50 values ≤1.23 μM, with six of them showing GI50 values <0.1 μM. Expression of MYCL as well as MYCN, ASCL1 and other driver oncogenes including CDK6 was reduced by JQ1 treatment, in particular in the cell lines with high expression of the respective genes; however, no association was observed between the sensitivity to JQ1 and the levels of MYCL, MYCN and ASCL1 expression. In contrast, levels of CDK6 expression and its reduction rates by JQ1 were associated with JQ1 sensitivity. Therefore, we concluded that CDK6 is a novel target of JQ1 and predictive marker for JQ1 sensitivity in SCLC cells.
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43
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Bennett CW, Berchem G, Kim YJ, El-Khoury V. Cell-free DNA and next-generation sequencing in the service of personalized medicine for lung cancer. Oncotarget 2018; 7:71013-71035. [PMID: 27589834 PMCID: PMC5342606 DOI: 10.18632/oncotarget.11717] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/11/2016] [Indexed: 12/13/2022] Open
Abstract
Personalized medicine has emerged as the future of cancer care to ensure that patients receive individualized treatment specific to their needs. In order to provide such care, molecular techniques that enable oncologists to diagnose, treat, and monitor tumors are necessary. In the field of lung cancer, cell free DNA (cfDNA) shows great potential as a less invasive liquid biopsy technique, and next-generation sequencing (NGS) is a promising tool for analysis of tumor mutations. In this review, we outline the evolution of cfDNA and NGS and discuss the progress of using them in a clinical setting for patients with lung cancer. We also present an analysis of the role of cfDNA as a liquid biopsy technique and NGS as an analytical tool in studying EGFR and MET, two frequently mutated genes in lung cancer. Ultimately, we hope that using cfDNA and NGS for cancer diagnosis and treatment will become standard for patients with lung cancer and across the field of oncology.
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Affiliation(s)
- Catherine W Bennett
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Guy Berchem
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg.,Centre Hospitalier de Luxembourg, L-1210 Luxembourg, Luxembourg
| | - Yeoun Jin Kim
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Victoria El-Khoury
- Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
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44
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Fiorentino FP, Tokgün E, Solé-Sánchez S, Giampaolo S, Tokgün O, Jauset T, Kohno T, Perucho M, Soucek L, Yokota J. Growth suppression by MYC inhibition in small cell lung cancer cells with TP53 and RB1 inactivation. Oncotarget 2018; 7:31014-28. [PMID: 27105536 PMCID: PMC5058735 DOI: 10.18632/oncotarget.8826] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/31/2016] [Indexed: 12/20/2022] Open
Abstract
Small cell lung cancer (SCLC) is the most aggressive type of lung cancer with high mortality. One of the MYC family genes, MYC, MYCL or MYCN, is amplified in ~20% of the SCLCs; therefore, MYC proteins are potential therapeutic targets in SCLC patients. We investigated the therapeutic impact of Omomyc, a MYC dominant negative, in a panel of SCLC cell lines. Strikingly, Omomyc suppressed the growth of all tested cell lines by inducing cell cycle arrest and/or apoptosis. Induction of G1 arrest by Omomyc was found to be dependent on the activation of CDKN1A, in part, through the TP73 pathway. Our results strongly indicate that SCLC cells carrying amplification of MYC, MYCL or MYCN are addicted to MYC function, suggesting that MYC targeting would be an efficient therapeutic option for SCLC patients.
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Affiliation(s)
- Francesco Paolo Fiorentino
- Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Barcelona, Spain
| | - Elvan Tokgün
- Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Barcelona, Spain
| | - Sònia Solé-Sánchez
- Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Barcelona, Spain
| | - Sabrina Giampaolo
- Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Barcelona, Spain
| | - Onur Tokgün
- Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Barcelona, Spain
| | - Toni Jauset
- Vall d'Hebron Institute of Oncology (VHIO) Hospital Vall d'Hebron, Barcelona, Spain
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Manuel Perucho
- Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Laura Soucek
- Vall d'Hebron Institute of Oncology (VHIO) Hospital Vall d'Hebron, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jun Yokota
- Genomics and Epigenomics of Cancer Prediction Program, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Barcelona, Spain.,Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
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45
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Saito M, Saito K, Shiraishi K, Maeda D, Suzuki H, Minamiya Y, Kono K, Kohno T, Goto A. Identification of candidate responders for anti-PD-L1/PD-1 immunotherapy, Rova-T therapy, or EZH2 inhibitory therapy in small-cell lung cancer. Mol Clin Oncol 2017; 8:310-314. [PMID: 29435295 DOI: 10.3892/mco.2017.1536] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/01/2017] [Indexed: 11/06/2022] Open
Abstract
A useful candidate for small-cell lung cancer (SCLC) therapy is immune checkpoint blockade therapy targeting programmed death-1 (PD-1) and its ligand, PD-L1. Furthermore, rovalpituzumab tesirine (Rova-T), a delta-like protein 3 (DLL3)-targeted antibody-drug conjugate, and enhancer of zeste homologue 2 (EZH2) inhibitor are expected to be the first targeted therapy for SCLC. The aim of the present study was to evaluate PD-L1, DLL3 and EZH2 expression in SCLCs to find a candidate responder to those therapies. Immunohistochemical (IHC) staining for PD-L1, DLL3 and EZH2 was performed in 20 patients with SCLC and the clinicopathological characteristics and IHC staining intensity were compared. It was demonstrated that 1/20 patients (5.0%) exhibited positive PD-L1 expression in the metastatic lesions, as well as in the primary lung tumor. DLL3 was highly expressed in 14/20 patients (70%) and EZH2 was positive in 17/20 patients (85%). None of these cases exhibited any correlation with age, sex, smoking, stage or treatment, whereas IHC staining was able to identify candidate responders to anti-PD-L1/PD-1 immunotherapy, Rova-T therapy, or EZH2 inhibitor therapy.
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Affiliation(s)
- Motonobu Saito
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Fukushima 960-1295, Japan
| | - Katsuharu Saito
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Fukushima 960-1295, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Daichi Maeda
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita, Akita 010-8543, Japan
| | - Hiroyuki Suzuki
- Department of Chest Surgery, Fukushima Medical University School of Medicine, Fukushima, Fukushima 960-1295, Japan
| | - Yoshihiro Minamiya
- Department of Thoracic Surgery, Graduate School of Medicine, Akita University, Akita, Akita 010-8543, Japan
| | - Koji Kono
- Department of Gastrointestinal Tract Surgery, Fukushima Medical University School of Medicine, Fukushima, Fukushima 960-1295, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Akiteru Goto
- Department of Cellular and Organ Pathology, Graduate School of Medicine, Akita University, Akita, Akita 010-8543, Japan
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46
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Zamò A, Pischimarov J, Horn H, Ott G, Rosenwald A, Leich E. The exomic landscape of t(14;18)-negative diffuse follicular lymphoma with 1p36 deletion. Br J Haematol 2017; 180:391-394. [PMID: 29193015 DOI: 10.1111/bjh.15041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022]
Abstract
Predominantly diffuse t(14;18) negative follicular lymphoma (FL) with 1p36 deletion shows distinctive clinical, morphological and molecular features that distinguish it from classical FL. In order to investigate whether it possesses a unique mutation profile, we performed whole exome sequencing of six well-characterised cases. Our analysis showed that the mutational landscape of this subtype is largely distinct from classical FL. It appears to harbour several recurrent mutations, affecting STAT6, CREBBP and basal membrane protein genes with high frequency. Our data support the view that this FL subtype should be considered a separate entity from classical FL.
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Affiliation(s)
- Alberto Zamò
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy.,Alexander von Humboldt Fellow, Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Jordan Pischimarov
- Institute of Pathology and Comprehensive Cancer Center Mainfranken (CCC MF), University of Würzburg, Würzburg, Germany
| | - Heike Horn
- Dr Margarete Fischer-Bosch-Institute for Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - Andreas Rosenwald
- Institute of Pathology and Comprehensive Cancer Center Mainfranken (CCC MF), University of Würzburg, Würzburg, Germany
| | - Ellen Leich
- Institute of Pathology and Comprehensive Cancer Center Mainfranken (CCC MF), University of Würzburg, Würzburg, Germany
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47
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Kargapolova Y, Levin M, Lackner K, Danckwardt S. sCLIP-an integrated platform to study RNA-protein interactomes in biomedical research: identification of CSTF2tau in alternative processing of small nuclear RNAs. Nucleic Acids Res 2017; 45:6074-6086. [PMID: 28334977 PMCID: PMC5449641 DOI: 10.1093/nar/gkx152] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/23/2017] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) are central for gene expression by controlling the RNA fate from birth to decay. Various disorders arising from perturbations of RNA-protein interactions document their critical function. However, deciphering their function is complex, limiting the general functional elucidation of this growing class of proteins and their contribution to (patho)physiology. Here, we present sCLIP, a simplified and robust platform for genome-wide interrogation of RNA-protein interactomes based on crosslinking-immunoprecipitation and high-throughput sequencing. sCLIP exploits linear amplification of the immunoprecipitated RNA improving the complexity of the sequencing-library despite significantly reducing the amount of input material and omitting several purification steps. Additionally, it permits a radiolabel-free visualization of immunoprecipitated RNA. In a proof of concept, we identify that CSTF2tau binds many previously not recognized RNAs including histone, snoRNA and snRNAs. CSTF2tau-binding is associated with internal oligoadenylation resulting in shortened snRNA isoforms subjected to rapid degradation. We provide evidence for a new mechanism whereby CSTF2tau controls the abundance of snRNAs resulting in alternative splicing of several RNAs including ANK2 with critical roles in tumorigenesis and cardiac function. Combined with a bioinformatic pipeline sCLIP thus uncovers new functions for established RBPs and fosters the illumination of RBP-protein interaction landscapes in health and disease.
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Affiliation(s)
- Yulia Kargapolova
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Germany.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Germany
| | - Michal Levin
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Germany.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Germany
| | - Karl Lackner
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Germany.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Germany
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48
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McColl K, Wildey G, Sakre N, Lipka MB, Behtaj M, Kresak A, Chen Y, Yang M, Velcheti V, Fu P, Dowlati A. Reciprocal expression of INSM1 and YAP1 defines subgroups in small cell lung cancer. Oncotarget 2017; 8:73745-73756. [PMID: 29088741 PMCID: PMC5650296 DOI: 10.18632/oncotarget.20572] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/03/2017] [Indexed: 12/14/2022] Open
Abstract
The majority of small cell lung cancer (SCLC) patients demonstrate initial chemo-sensitivity, whereas a distinct subgroup of SCLC patients, termed chemo-refractory, do not respond to treatment. There is little understanding of how to distinguish these patients prior to disease treatment. Here we used gene expression profiling to stratify SCLC into subgroups and characterized a molecular phenotype that may identify, in part, chemo-refractive SCLC patients. Two subgroups of SCLC were identified in both cell lines and tumors by the reciprocal expression of two genes; INSM1, a neuroendocrine transcription factor, and YAP1, a key mediator of the Hippo pathway. The great majority of tumors expressed INSM1, which was prognostic for increased progression-free survival and associated with chemo-sensitivity in cell lines. YAP1 is expressed in a minority of SCLC tumors and was shown in cell lines to be downstream of the retinoblastoma protein (RB1) and associated with decreased drug sensitivity. RB1 expression in SCLC cell lines sensitizes them to CDK4/6 inhibitors. Wild-type RB1 mutation status, used as a surrogate marker of YAP1 expression, was prognostic for decreased patient survival and increased chemo-refractory tumor response. Thus, the reciprocal expression of INSM1 and YAP1 appears to stratify SCLC into distinct subgroups and may be useful, along with RB1 mutation status, to identify chemo-refractory SCLC patients.
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Affiliation(s)
- Karen McColl
- Division of Hematology and Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - Gary Wildey
- Division of Hematology and Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - Nneha Sakre
- Division of Hematology and Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - Mary Beth Lipka
- Division of Hematology and Oncology, Case Western Reserve University, Cleveland, OH, USA
| | - Mohadese Behtaj
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Adam Kresak
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Yanwen Chen
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Michael Yang
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Vamsidhar Velcheti
- Division of Hematology and Oncology, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Pingfu Fu
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Afshin Dowlati
- Division of Hematology and Oncology, Case Western Reserve University, University Hospitals Seidman Cancer Center, Cleveland, OH, USA
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49
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Zamò A, Pischimarov J, Schlesner M, Rosenstiel P, Bomben R, Horn H, Grieb T, Nedeva T, López C, Haake A, Richter J, Trümper L, Lawerenz C, Klapper W, Möller P, Hummel M, Lenze D, Szczepanowski M, Flossbach L, Schreder M, Gattei V, Ott G, Siebert R, Rosenwald A, Leich E. Differences between BCL2-break positive and negative follicular lymphoma unraveled by whole-exome sequencing. Leukemia 2017; 32:685-693. [PMID: 28824170 DOI: 10.1038/leu.2017.270] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 08/08/2017] [Indexed: 12/25/2022]
Abstract
Depending on disease stage follicular lymphoma (FL) lack the t(14;18) in ~15-~50% of cases. Nevertheless, most of these cases express BCL2. To elucidate mechanisms triggering BCL2 expression and promoting pathogenesis in t(14;18)-negative FL, exonic single-nucleotide variant (SNV) profiles of 28 t(14;18)-positive and 13 t(14;18)-negative FL were analyzed, followed by the integration of copy-number changes, copy-neutral LOH and published gene-expression data as well as the assessment of immunoglobulin N-glycosylation sites. Typical FL mutations also affected t(14;18)-negative FL. Curated gene set/pathway annotation of genes mutated in either t(14;18)-positive or t(14;18)-negative FL revealed a strong enrichment of same or similar gene sets but also a more prominent or exclusive enrichment of immune response and N-glycosylation signatures in t(14;18)-negative FL. Mutated genes showed high BCL2 association in both subgroups. Among the genes mutated in t(14;18)-negative FL 555 were affected by copy-number alterations and/or copy-neutral LOH and 96 were differently expressed between t(14;18)-positive and t(14;18)-negative FL (P<0.01). N-glycosylation sites were detected considerably less frequently in t(14;18)-negative FL. These results suggest a diverse portfolio of genetic alterations that may induce or regulate BCL2 expression or promote pathogenesis of t(14;18)-negative FL as well as a less specific but increased crosstalk with the microenvironment that may compensate for the lack of N-glycosylation.
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Affiliation(s)
- A Zamò
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Department of Diagnostic and Public Health, University of Verona, Verona, Italy.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - J Pischimarov
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - M Schlesner
- Theoretical Bioinformatics (B080), Computational Oncology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - P Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - R Bomben
- Department of Translational Research, CRO, Aviano, Italy
| | - H Horn
- Dr Margarete Fischer-Bosch-Institute for Clinical Pharmacology, Stuttgart, Germany
| | - T Grieb
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - T Nedeva
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - C López
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany.,Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Haake
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - J Richter
- Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany.,Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - L Trümper
- Department of Hematology and Medical Oncology, University Hospital, Göttingen, Germany
| | - C Lawerenz
- Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - W Klapper
- Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - P Möller
- Institute of Pathology, University Hospital Ulm, Ulm, Germany
| | - M Hummel
- Institute of Pathology, Charité-University Hospital Berlin, Germany
| | - D Lenze
- Institute of Pathology, Charité-University Hospital Berlin, Germany
| | - M Szczepanowski
- Institute of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - L Flossbach
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - M Schreder
- Medizinische Klinik und Poliklinik II, University Hospital Würzburg, Würzburg, Germany
| | - V Gattei
- Department of Translational Research, CRO, Aviano, Italy
| | - G Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, Stuttgart, Germany
| | - R Siebert
- Institute for Human Genetics, University Hospital Ulm, Ulm, Germany.,Institute for Human Genetics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - A Rosenwald
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
| | - E Leich
- Institute of Pathology, University of Würzburg, Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, Würzburg, Germany
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50
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Sundaresan V, Lin VT, Liang F, Kaye FJ, Kawabata-Iwakawa R, Shiraishi K, Kohno T, Yokota J, Zhou L. Significantly mutated genes and regulatory pathways in SCLC-a meta-analysis. Cancer Genet 2017; 216-217:20-28. [PMID: 29025592 DOI: 10.1016/j.cancergen.2017.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/06/2017] [Accepted: 05/31/2017] [Indexed: 02/08/2023]
Abstract
Small cell lung cancer (SCLC) accounts for approximately 15% of all lung cancers and demands effective targeted therapeutic strategies. In this meta-analysis study, we aim to identify significantly mutated genes and regulatory pathways to help us better understand the progression of SCLC and to identify potential biomarkers. Besides ranking genes based on their mutation frequencies, we sought to identify statistically significant mutations in SCLC with the MutSigCV software. Our analysis identified several genes with relatively low mutation frequency, including PTEN, as highly significant (p < 0.001), suggesting these genes may play an important role in the progression of SCLC. Our results also indicated mutations in genes involved in the axon guidance pathways likely play an important role in SCLC progression. In addition, we observed that the mutation rate was significantly higher in samples with RB1 gene mutated when compared to samples with wild type RB1, suggesting that RB1 status has significant impact on the mutation profile and disease progression in SCLC.
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Affiliation(s)
- Varsha Sundaresan
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA; UF Health Cancer Center, University of Florida, Gainesville, FL, USA
| | - Victor T Lin
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Faming Liang
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Frederic J Kaye
- UF Health Cancer Center, University of Florida, Gainesville, FL, USA; Department of Medicine, University of Florida, Gainesville, FL, USA; UF Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Reika Kawabata-Iwakawa
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo 104-0045, Japan
| | - Jun Yokota
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Cancer Genome Biology Group, Institute of Predictive and Personalized Medicine of Cancer, Barcelona 08916, Spain
| | - Lei Zhou
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA; UF Health Cancer Center, University of Florida, Gainesville, FL, USA; UF Genetics Institute, University of Florida, Gainesville, FL, USA.
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