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Deakin S, Coltman DW. Development of a high-density sub-species-specific targeted SNP assay for Rocky Mountain bighorn sheep ( Ovis canadensis canadensis). PeerJ 2024; 12:e16946. [PMID: 38426129 PMCID: PMC10903336 DOI: 10.7717/peerj.16946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Due to their abundance and relative ease of genotyping, single nucleotide polymorphisms (SNPs) are a commonly used molecular marker for contemporary population genetic and genomic studies. A high-density and cost-effective way to type SNP loci is Allegro targeted genotyping (ATG), which is a form of targeted genotyping by sequencing developed and offered by Tecan genomics. One major drawback of this technology is the need for a reference genome and information on SNP loci when designing a SNP assay. However, for some non-model species genomic information from other closely related species can be used. Here we describe our process of developing an ATG assay to target 50,000 SNPs in Rocky Mountain bighorn sheep, using a reference genome from domestic sheep and SNP resources from prior bighorn sheep studies. We successfully developed a high accuracy, high-density, and relatively low-cost SNP assay for genotyping Rocky Mountain bighorn sheep that genotyped ~45,000 SNP loci. These loci were relatively evenly distributed throughout the genome. Furthermore, the assay produced genotypes at tens of thousands of SNP loci when tested on other mountain sheep species and subspecies.
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Affiliation(s)
- Samuel Deakin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David W. Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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2
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Lu J, Feng Y, Guo K, Sun L, Ruan S, Zhang K. Prognostic value of preoperative circulating tumor DNA in non-small cell lung cancer: a systematic review and meta-analysis. J Cancer Res Clin Oncol 2024; 150:25. [PMID: 38252173 PMCID: PMC10803397 DOI: 10.1007/s00432-023-05550-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/03/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND Several recent studies have reported the increasing application of preoperative circulating tumor DNA (ctDNA) as a biomarker of tumor burden for guiding potential postoperative treatment strategies. METHODS A meta-analysis of prospective/retrospective cohort studies was conducted to compare the prognosis of preoperatively genetically positive and genetically negative NSCLC patients. The endpoints used in the included studies were overall survival (OS) and recurrence-free survival (RFS). The objective of the meta-analysis was to comprehensively explore the prognostic value of preoperative ctDNA for patients with non-small-cell lung cancer (NSCLC) and its significance in guiding postoperative adjuvant therapy (AT) in patients with NSCLC. RESULTS The preliminary analysis identified 1565 studies, among which only 11 studies fulfilled the eligibility criteria and were finally included in the present systematic review and meta-analysis. The statistical results revealed that the expression of preoperative ctDNA was associated with worse RFS (HR = 3.00; 95% CI 2.26-3.98; I2 = 0%) and OS (HR = 2.77; 95% CI 1.67-4.58; I2 = 0%), particularly in lung adenocarcinoma (LUAD) patients (RFS: HR = 3.46; 95% CI 2.37-5.05; I2 = 0%; OS: HR = 3.52; 95% CI 1.91-6.49; I2 = 0%) and patients with I-II stage of NSCLC (RFS: HR = 2.84; 95% CI 1.88-4.29; I2 = 0%; OS: HR = 2.60; 95% CI 1.43-4.74; I2 = 0%). Moreover, compared to patients with negative preoperative ctDNA, patients with positive preoperative ctDNA presented greater survival benefits (HR = 0.39; 95% CI 0.22-0.67; I2 = 2%) from postoperative AT. CONCLUSION The evaluation of the prognostic value of preoperative ctDNA revealed that preoperative ctDNA might be used as a prognostic biomarker for patients with LUAD or those with stage I-II NSCLC. In addition, postoperative AT is recommended for NSCLC patients with positive preoperative ctDNA, regardless of the disease stage and subtype.
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Affiliation(s)
- Jiamin Lu
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Yuqian Feng
- Hangzhou TCM Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Kaibo Guo
- Department of Oncology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Leitao Sun
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
| | - Shanming Ruan
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
| | - Kai Zhang
- The First Affiliated Hospital of Zhejiang, Chinese Medical University, (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China.
- Anji Traditional Chinese Medical Hospital, Huzhou, Zhejiang, China.
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3
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Chaudhary M, Sharma P, Mukherjee TK. Applications of CRISPR/Cas technology against drug-resistant lung cancers: an update. Mol Biol Rep 2022; 49:11491-11502. [PMID: 36097111 DOI: 10.1007/s11033-022-07766-7] [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: 03/28/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022]
Abstract
Out of all the cancer types, the most prevalent one is lung cancer. Multiple genes and signaling pathways play role in the progression of lung cancer. Considering the wider prevalence and fatality of lung cancer it has become the focus of current cancer research. Though currently used approaches have shown positive results against lung cancer but success against non-small cell lung cancer (NSCLC) still looms as an enigma for the entire research fraternity. The development of resistance against inhibitors within a short span is one of the reasons responsible for the failure and relapse of lung cancer. Under these prevailing conditions genome/gene-editing technology using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated proteins (Cas), popularly known as CRISPR/Cas technology offers a convenient and flexible method for inducing precise changes within the lung cancer cell. Additionally, CRISPR-barcoding and CRISPR knockout screens at the genome-wide level can help in the functional investigation of specific mutations and identification of novel cancer drivers respectively. Several variants of the CRISPR/Cas system are being developed to limit off-targeting with enhanced precision. The present review article updates the usefulness of CRISPR/Cas technology against various types of lung cancers.
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Affiliation(s)
- Mayank Chaudhary
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Pooja Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India
| | - Tapan Kumar Mukherjee
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala, Haryana, 133207, India.
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Nicoś M, Krawczyk P. Genetic Clonality as the Hallmark Driving Evolution of Non-Small Cell Lung Cancer. Cancers (Basel) 2022; 14:1813. [PMID: 35406585 PMCID: PMC8998004 DOI: 10.3390/cancers14071813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/12/2022] Open
Abstract
Data indicate that many driver alterations from the primary tumor of non-small cell lung cancer (NSCLC) are predominantly shared across all metastases; however, disseminating cells may also acquire a new genetic landscape across their journey. By comparing the constituent subclonal mutations between pairs of primary and metastatic samples, it is possible to derive the ancestral relationships between tumor clones, rather than between tumor samples. Current treatment strategies mostly rely on the theory that metastases are genetically similar to the primary lesions from which they arise. However, intratumor heterogeneity (ITH) affects accurate diagnosis and treatment decisions and it is considered the main hallmark of anticancer therapy failure. Understanding the genetic changes that drive the metastatic process is critical for improving the treatment strategies of this deadly condition. Application of next generation sequencing (NGS) techniques has already created knowledge about tumorigenesis and cancer evolution; however, further NGS implementation may also allow to reconstruct phylogenetic clonal lineages and clonal expansion. In this review, we discuss how the clonality of genetic alterations influence the seeding of primary and metastatic lesions of NSCLC. We highlight that wide genetic analyses may reveal the phylogenetic trajectories of NSCLC evolution, and may pave the way to better management of follow-up and treatment.
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Affiliation(s)
- Marcin Nicoś
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-954 Lublin, Poland;
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5
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Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs. CONSERV GENET RESOUR 2022; 14:203-213. [PMID: 35673611 PMCID: PMC9162989 DOI: 10.1007/s12686-022-01259-2] [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: 09/01/2021] [Accepted: 02/24/2022] [Indexed: 11/22/2022]
Abstract
The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of single nucleotide polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA isolated from fecal swabs. Total and host-specific DNA were quantified for 989 samples collected as part of a long-term individual-based study of feral horses on Sable Island, Nova Scotia, Canada, using dsDNA fluorescence and a host-specific qPCR assay, respectively. Forty-eight samples representing 44 individuals containing at least 10 ng of host DNA (ATG’s recommended minimum input) were genotyped using a custom multiplex panel targeting 279 SNPs. Genotyping accuracy and consistency were assessed by contrasting ATG genotypes with those obtained from the same individuals with SNP microarrays, and from multiple samples from the same horse, respectively. 62% of swabs yielded the minimum recommended amount of host DNA for ATG. Ignoring samples that failed to amplify, ATG recovered an average of 88.8% targeted sites per sample, while genotype concordance between ATG and SNP microarrays was 98.5%. The repeatability of genotypes from the same individual approached unity with an average of 99.9%. This study demonstrates the suitability of ATG for genome-wide, non-invasive targeted SNP genotyping, and will facilitate further ecological and conservation genetics research in equids and related species.
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Mota A, Oltra SS, Selenica P, Moiola CP, Casas-Arozamena C, López-Gil C, Diaz E, Gatius S, Ruiz-Miro M, Calvo A, Rojo-Sebastián A, Hurtado P, Piñeiro R, Colas E, Gil-Moreno A, Reis-Filho JS, Muinelo-Romay L, Abal M, Matias-Guiu X, Weigelt B, Moreno-Bueno G. Intratumor genetic heterogeneity and clonal evolution to decode endometrial cancer progression. Oncogene 2022; 41:1835-1850. [PMID: 35145232 PMCID: PMC8956509 DOI: 10.1038/s41388-022-02221-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/12/2022] [Accepted: 01/27/2022] [Indexed: 12/12/2022]
Abstract
Analyzing different tumor regions by next generation sequencing allows the assessment of intratumor genetic heterogeneity (ITGH), a phenomenon that has been studied widely in some tumor types but has been less well explored in endometrial carcinoma (EC). In this study, we sought to characterize the spatial and temporal heterogeneity of 9 different ECs using whole-exome sequencing, and by performing targeted sequencing validation of the 42 primary tumor regions and 30 metastatic samples analyzed. In addition, copy number alterations of serous carcinomas were assessed by comparative genomic hybridization arrays. From the somatic mutations, identified by whole-exome sequencing, 532 were validated by targeted sequencing. Based on these data, the phylogenetic tree reconstructed for each case allowed us to establish the tumors’ evolution and correlate this to tumor progression, prognosis, and the presence of recurrent disease. Moreover, we studied the genetic landscape of an ambiguous EC and the molecular profile obtained was used to guide the selection of a potential personalized therapy for this patient, which was subsequently validated by preclinical testing in patient-derived xenograft models. Overall, our study reveals the impact of analyzing different tumor regions to decipher the ITGH in ECs, which could help make the best treatment decision.
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Affiliation(s)
- Alba Mota
- MD Anderson International Foundation, 28033, Madrid, Spain.,Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), IdiPaz, 28029, Madrid, Spain
| | - Sara S Oltra
- MD Anderson International Foundation, 28033, Madrid, Spain.,Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), IdiPaz, 28029, Madrid, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Cristian P Moiola
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Carlos Casas-Arozamena
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706, Santiago de Compostela, Spain
| | - Carlos López-Gil
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Eva Diaz
- MD Anderson International Foundation, 28033, Madrid, Spain
| | - Sonia Gatius
- Department of Pathology, Hospital U Arnau de Vilanova, University of Lleida, IRBLLEIDA, Lleida, Spain
| | | | - Ana Calvo
- Department of Gynecology, Hospital U Arnau de Vilanova, IRBLLEIDA, Lleida, Spain
| | - Alejandro Rojo-Sebastián
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain.,MD Anderson Cancer Center, Madrid, Spain
| | - Pablo Hurtado
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - Roberto Piñeiro
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), Travesía da Choupana s/n, 15706, Santiago de Compostela, Spain
| | - Eva Colas
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain
| | - Antonio Gil-Moreno
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, 08035, Barcelona, Spain.,Gynaecological Department, Vall Hebron University Hospital, 08035, Barcelona, Spain
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Laura Muinelo-Romay
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706, Santiago de Compostela, Spain
| | - Miguel Abal
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Hospital of Santiago de Compostela (SERGAS), Trav. Choupana s/n, 15706, Santiago de Compostela, Spain
| | - Xavier Matias-Guiu
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.,Department of Pathology, Hospital U Arnau de Vilanova, University of Lleida, IRBLLEIDA, Lleida, Spain.,Departments of Pathology, Hospital U. de Bellvitge, Universities of Lleida and Barcelona, IDIBELL Lleida and Barcelona, Spain
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Gema Moreno-Bueno
- MD Anderson International Foundation, 28033, Madrid, Spain. .,Biochemistry Department, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), IdiPaz, 28029, Madrid, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28029, Madrid, Spain.
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7
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Tong Z, Wang L, Shi W, Zeng Y, Zhang H, Liu L, Zheng Y, Chen C, Xia W, Fang W, Zhao P. Clonal Evolution Dynamics in Primary and Metastatic Lesions of Pancreatic Neuroendocrine Neoplasms. Front Med (Lausanne) 2021; 8:620988. [PMID: 34026777 PMCID: PMC8131504 DOI: 10.3389/fmed.2021.620988] [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: 10/24/2020] [Accepted: 04/06/2021] [Indexed: 02/06/2023] Open
Abstract
Background: Data on inter-tumoral heterogeneity and clonal evolution of pancreatic neuroendocrine neoplasms (panNENs) with liver metastasis are limited. The aim of this study was to explore different patterns of clonal evolution of pancreatic neuroendocrine neoplasms with liver metastasis and the possible distinctive signaling pathways involved between G2 neuroendocrine tumors (NETs) and neuroendocrine carcinomas (NECs). Methods: Tumor tissues of five patients (10 samples) with pancreatic neuroendocrine neoplasms with synchronous liver metastasis were analyzed using next-generation sequencing. PyClone, Gene Ontology, and Reactome pathway enrichment analysis were also applied. Results: Mutated genes varied in individuals, reflecting the inter-tumoral heterogeneity of panNENs. The distribution of subclones varied during tumor metastasis, and different clonal evolution patterns were revealed between NETs and NECs. Gene Ontology and Reactome analyses revealed that in both NETs and NECs, signaling pathways and biological processes shared similarities and differences in the primary and metastatic lesions. In addition, the signaling pathway features were different between NETs and NECs. In the primary lesions, epigenetic changes and post-transcriptional modifications participated in NETs, while FGFR signaling, EGFR signaling, and NTRK2 signaling were largely involved in NECs. Although DNA repair and TP53 regulation were both involved in the metastatic lesions, most of the signaling pathways and biological processes disrupted by the mutated genes were different. Conclusions: Our study revealed spatial inter-tumoral heterogeneity and temporal clonal evolution in PanNENs, providing potential therapeutic targets for further prospective clinical trials.
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Affiliation(s)
- Zhou Tong
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lin Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | | | | | - Hangyu Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lulu Liu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Zheng
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chunlei Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weiliang Xia
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Zhao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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8
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Kong W, Chen Y, Zhao Z, Zhang L, Lin X, Luo X, Wang S, Song Z, Lin X, Lai G, Yu Z. EXT1 methylation promotes proliferation and migration and predicts the clinical outcome of non-small cell lung carcinoma via WNT signalling pathway. J Cell Mol Med 2021; 25:2609-2620. [PMID: 33565239 PMCID: PMC7933929 DOI: 10.1111/jcmm.16277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 01/15/2023] Open
Abstract
DNA methylation is important for lung cancer prognosis. In this work, it is aimed to seek novel biomarkers with DNA methylation‐expression‐pathway pattern and explore its underlying mechanism. Prognostic DNA methylation sites and mRNAs were screened in NSCLC data set from TCGA, and further validated using the samples retrospectively collected, and EXT1 was identified as a potential target. Gene body methylation of three CpG sites (cg03276982, cg11592677, cg16286281) on EXT1 was significantly associated with clinical outcome, and the EXT1 gene expression also predicted prognosis. The expression level of EXT1 was also correlated with its DNA methylation level. This observation was further validated in a new data set consist of 170 samples. Knocking down of EXT1 resulted in decreased proliferation and migration. EXT1 targets were analysed using GSEA. It is found that the WNT signalling is the potential downstream target of EXT1. Further analyses revealed that the EXT1 targets the beta‐catenin and effect migration rate of NSCLC cell lines. The WNT signalling inhibitor, XAV‐939, effectively disrupted the migration promotion effect induced by EXT1. In summary, EXT1 methylation regulates the gene expression, effects the proliferation and migration via WNT pathway and predicted a poor prognosis for NSCLC.
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Affiliation(s)
- Wencui Kong
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Ying Chen
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Zhongquan Zhao
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Lei Zhang
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Xiandong Lin
- Laboratory of Radiation Oncology and Radiobiology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Xingguang Luo
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA
| | - Shuiliang Wang
- Department of Urology, 900th Hospital of the Joint Logistics Team Support Force, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Transplant Biology, Affiliated Dongfang Hospital, Xiamen University School of Medicine, Fuzhou, China
| | - Zhengbo Song
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou, China.,Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, China.,Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Xiangwu Lin
- Medical Oncology, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Guoxiang Lai
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fuzhou, China
| | - Zongyang Yu
- Department of Respiratory Medicine and Critical Care Medicine, The 900th Hospital of Joint Logistic Support Force, PLA, Fujian Medical University,Affiliated Dongfang Hospital, Xiamen University School of Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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9
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Predictors of prognosis of synchronous brain metastases in small-cell lung cancer patients. Clin Exp Metastasis 2020; 37:531-539. [PMID: 32500410 DOI: 10.1007/s10585-020-10040-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/29/2020] [Indexed: 10/24/2022]
Abstract
Patients with small cell lung cancer (SCLC) are more likely to have synchronous brain metastasis (SBM) at the time of diagnosis than patients with any other extracranial primary malignancy. We sought to identify which factors predicted an increased risk of SBM in SCLC as well as which factors affected the prognosis of these patients. 38,956 Patients in the Surveillance, Epidemiology, and End Results (SEER) database with microscopically confirmed SCLC from 2010 to 2016 were identified. 6264 (16.1%) Patients with SCLC had SBM at the time of diagnosis. In the multivariable logistic regression, disease specific factors that were predictive of SBM were primary tumor size > 7 cm (adjusted OR = 1.14, 95% CI [1.02, 1.28], p = 0.02), synchronous lung metastases, and synchronous bone metastases. Demographic specific factors predictive of increased SBM risk in this model were younger age, male sex, and race (American Indian/Alaska Native and black patients). Patients insured through Medicaid were less likely to present with SBM. In the multivariate Cox proportional hazards model, lack of insurance was the strongest predictor of mortality (adjusted HR = 1.47, 95% CI [1.26, 1.73], p < 0.001). Other factors associated with an increased risk of mortality include male sex, older age, health insurance coverage through Medicaid, synchronous liver metastasis, synchronous lung metastasis, and primary tumor size > 7 cm. In contrast, Asian patients had a lower risk of mortality. This study identifies risk factors for SBM among patients with SCLC, as well as indicators of prognosis among this patient population.
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10
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Saber A, Liu B, Ebrahimi P, Haisma HJ. CRISPR/Cas9 for overcoming drug resistance in solid tumors. Daru 2020; 28:295-304. [PMID: 30666557 PMCID: PMC7214581 DOI: 10.1007/s40199-019-00240-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/04/2019] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES In this review, we focus on the application of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated nuclease 9 (Cas9), as a powerful genome editing system, in the identification of resistance mechanisms and in overcoming drug resistance in the most frequent solid tumors. DATA ACQUISITION Data were collected by conducting systematic searching of scientific English literature using specific keywords such as "cancer", "CRISPR" and related combinations. RESULTS The review findings revealed the importance of CRISPR/Cas9 system in understanding drug resistance mechanisms and identification of resistance-related genes such as PBRM1, SLFN11 and ATPE1 in different cancers. We also provided an overview of genes, including RSF1, CDK5, and SGOL1, whose disruption can synergize with the currently available drugs such as paclitaxel and sorafenib. CONCLUSION The data suggest CRISPR/Cas9 system as a useful tool in elucidating the molecular basis of drug resistance and improving clinical outcomes. Graphical abstract The mechanisms of CRISPR/Cas9-mediated genome editing and double-strand breaks (DSBs) repair.
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Affiliation(s)
- Ali Saber
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Bin Liu
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Pirooz Ebrahimi
- Universal Scientific Education and Research Network, Tehran, Iran
- Parseh Medical Genetics Clinic, Tehran, Iran
| | - Hidde J Haisma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands.
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11
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Lohinai Z, Megyesfalvi Z, Suda K, Harko T, Ren S, Moldvay J, Laszlo V, Rivard C, Dome B, Hirsch FR. Comparative expression analysis in small cell lung carcinoma reveals neuroendocrine pattern change in primary tumor versus lymph node metastases. Transl Lung Cancer Res 2019; 8:938-950. [PMID: 32010572 DOI: 10.21037/tlcr.2019.11.30] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Recent preclinical data suggest that neuroendocrine (NE) subtype of small cell lung cancer (SCLC) has strong therapeutic relevance. NE high tumors are associated with immune desert and NE low tumors are considered to have an immune oasis phenotype. Our aim was to investigate the NE phenotypes of surgically resected SCLC tumors according to inter-tumor heterogeneity. Methods Expression analysis for 2,560 genes was performed in 32 surgically resected SCLC patients' primary tumors and corresponding lymph node (LN) metastases. To analyze tumor heterogeneity, we examined the differences in the gene expression of primary tumors versus LN metastases. We performed cluster analysis and heat map to divide patients into NE high and low subtypes by using the top NE-associated genes described in preclinical studies. Results We found 6% (n=154) genes with significant differences and only 13.1% (n=336) of all genes in the panel had a strong correlation between the primary tumor and LN metastases. Cluster analysis clearly distinguished SCLC NE high versus low subtypes both in primary tumor (20 vs. 12, respectively) and LNs (23 vs. 9, respectively). As for inter-tumor heterogeneity, in case of five patients, a change in the NE pattern was observed. Specifically, we found significant downregulation of the NE-associated genes CAV1 (P=0.004), CAV2 (P=0.029) and ANXA3 (P=0.035) in their LN metastases compared to their primary tumor. Conclusions Our data confirm the results of preclinical studies and clearly distinguish NE low and high differentiation clusters in SCLC. Moreover, they highlight the gene expression discordance between primary tumors and corresponding LN metastases suggesting that the NE pattern of metastatic LNs might not reflect that of the primary tumor. Altogether, by shedding light on the diversity of SCLC, the current study might help to improve patient selection and treatment in this devastating disease. Keywords Small cell lung cancer (SCLC); neuroendocrine tumor; lymph node metastasis; tumor heterogeneity; RNA sequencing.
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Affiliation(s)
- Zoltan Lohinai
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Zsolt Megyesfalvi
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Kenichi Suda
- Division of Thoracic Surgery, Department of Surgery, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Tunde Harko
- Department of Pathology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Judit Moldvay
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Viktoria Laszlo
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary.,Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Christopher Rivard
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Balazs Dome
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, Vienna, Austria
| | - Fred R Hirsch
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Tisch Cancer Institute, Center for Thoracic Oncology, Mount Sinai Health System, New York, NY, USA
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12
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Meng P, Wei J, Geng Y, Chen S, Terpstra MM, Huang Q, Zhang Q, Su Z, Yu W, Su M, Kok K, van den Berg A, Gu J. Targeted sequencing of circulating cell-free DNA in stage II-III resectable oesophageal squamous cell carcinoma patients. BMC Cancer 2019; 19:818. [PMID: 31429737 PMCID: PMC6701116 DOI: 10.1186/s12885-019-6025-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/08/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The aim of this study was to investigate the potential of cell-free DNA (cfDNA) as a disease biomarker in oesophageal squamous cell carcinoma (ESCC) that can be used for treatment response evaluation and early detection of tumour recurrence. METHODS Matched tumour tissue, pre- and post-surgery plasma and WBCs obtained from 17 ESCC patients were sequenced using a panel of 483 cancer-related genes. RESULTS Somatic mutations were detected in 14 of 17 tumour tissues. Putative harmful mutations were observed in genes involved in well-known cancer-related pathways, including PI3K-Akt/mTOR signalling, Proteoglycans in cancer, FoxO signalling, Jak-STAT signalling, Chemokine signalling and Focal adhesion. Forty-six somatic mutations were found in pre-surgery cfDNA in 8 of 12 patients, with mutant allele frequencies (MAF) ranging from 0.24 to 4.91%. Three of the 8 patients with detectable circulating tumour DNA (ctDNA) had stage IIA disease, whereas the others had stage IIB-IIIB disease. Post-surgery cfDNA somatic mutations were detected in only 2 of 14 patients, with mutant allele frequencies of 0.28 and 0.36%. All other somatic mutations were undetectable in post-surgery cfDNA, even in samples collected within 3-4 h after surgery. CONCLUSION Our study shows that somatic mutations can be detected in pre-surgery cfDNA in stage IIA to IIIB patients, and at a lower frequency in post-surgery cfDNA. This indicates that cfDNA could potentially be used to monitor disease load, even in low disease-stage patients.
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Affiliation(s)
- Pei Meng
- Provincial Key laboratory of Infectious Diseases and Molecular Pathology, Department of Pathology and Pathophysiology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, 515041 Guangdong China
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700RB Groningen, Netherlands
| | - Jiacong Wei
- Provincial Key laboratory of Infectious Diseases and Molecular Pathology, Department of Pathology and Pathophysiology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, 515041 Guangdong China
- Department of Genetics, University of Groningen, University Medical Centre Groningen, 9700RB Groningen, Netherlands
| | - Yiqun Geng
- Provincial Key laboratory of Infectious Diseases and Molecular Pathology, Department of Pathology and Pathophysiology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Shaobin Chen
- Department of Thoracic surgery, Cancer Hospital of Shantou University, Shantou, 515041 Guangdong China
| | - Miente Martijn Terpstra
- Department of Genetics, University of Groningen, University Medical Centre Groningen, 9700RB Groningen, Netherlands
| | - Qiongyi Huang
- Provincial Key laboratory of Infectious Diseases and Molecular Pathology, Department of Pathology and Pathophysiology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Qian Zhang
- Provincial Key laboratory of Infectious Diseases and Molecular Pathology, Department of Pathology and Pathophysiology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Zuoqing Su
- Provincial Key laboratory of Infectious Diseases and Molecular Pathology, Department of Pathology and Pathophysiology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Wanchun Yu
- Provincial Key laboratory of Infectious Diseases and Molecular Pathology, Department of Pathology and Pathophysiology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Min Su
- Department of Pathology & Institute of Clinical Pathology, Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Centre Groningen, 9700RB Groningen, Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Centre Groningen, 9700RB Groningen, Netherlands
| | - Jiang Gu
- Provincial Key laboratory of Infectious Diseases and Molecular Pathology, Department of Pathology and Pathophysiology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, 515041 Guangdong China
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066 China
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13
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Prognostic Significance of Somatostatin Receptor Heterogeneity in Progressive Neuroendocrine Tumor Treated with Lu-177 DOTATOC or Lu-177 DOTATATE. Eur J Nucl Med Mol Imaging 2019; 47:881-894. [PMID: 31414209 DOI: 10.1007/s00259-019-04439-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 07/11/2019] [Indexed: 12/21/2022]
Abstract
AIM One of the primary prerequisites for peptide receptor radionuclide therapy (PRRT) in patients with neuroendocrine tumors (NET) is the presence of somatostatin receptors (SSTR) on NET cells. NET are highly heterogeneous and an individual patient as well as separate metastases can harbor cells with different clones, which influence the SSTR expression on NET cells. With this background we looked into our institutional database to assess the prognostic significance of quality of SSTR expression on SSTR PET/CT imaging in patients treated with at least two cycles of Lu-177 DOTATOC or Lu-177 DOTATATE. METHOD Clinical reports and images from 65 (25 females, 40 males; 65 ± 11 years old) patients with progressive grade 1 or grade 2 NET with 2-5 therapy cycles of PRRT with an average administered dose of 6.6 ± 0.97 GBq Lu-177 DOTATOC or Lu-177 DOTATATE were analyzed. All patients were examined with baseline Ga-68 DOTATATE or Ga-68 DOTATOC PET/CT (PET). Quality of SSTR expression as a measure of heterogeneity on indexed lesions was assessed visually. Patients were followed for a median duration of 25 months after the first PRRT (range 5-77 months). RESULTS A total of 70% of the patients received three or more therapy cycles. Twenty-six patients (40%) were treated with PRRT as first or second line while 39 (60%) as third line or more. SSTR expression was heterogeneous in 28 (44.4%) and homogeneous in 35 (55.6%) patients. Disease stabilization could be achieved in 23 patients (35.4%), whereas 17 (26.1%) showed partial remission and 25 patients (38.5%) had disease progression. Median OS was not reached. The 24-month survival rate of the whole study cohort was 83%. In univariate analyses, factors influencing OS were carcinoid heart disease, carcinoid syndrome and quality of SSTR expression (p < 0.05). Patients with heterogeneous SSTR expression on target lesions had a significantly lower OS (p = 0.01). Median time to progression in total patient population was found to be 40 months. Patients with heterogeneous SSTR expression on target lesions had significantly lower TTP (26 months vs 54 months log Rank p = 0.013). By multivariate analyses, quality of SSTR was found to be the only prognostic factor for OS (p = 0.04; HR = 3.68) and also for TTP (p = 0.03; HR = 3.09). CONCLUSION Visual assessment of SSTR heterogeneity has both predictive and prognostic value in progressive grade 1 or grade 2 NET patients undergoing PRRT.
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14
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Lissa D, Robles AI. Comprehensive genomic analysis of circulating tumor DNA for patients with advanced non-small cell lung cancer. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:80. [PMID: 31019930 DOI: 10.21037/atm.2018.12.57] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Delphine Lissa
- Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, USA
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15
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Guberina M, Eberhardt W, Stuschke M, Gauler T, Aigner C, Schuler M, Stamatis G, Theegarten D, Jentzen W, Herrmann K, Pöttgen C. Pretreatment metabolic tumour volume in stage IIIA/B non-small-cell lung cancer uncovers differences in effectiveness of definitive radiochemotherapy schedules: analysis of the ESPATUE randomized phase 3 trial. Eur J Nucl Med Mol Imaging 2019; 46:1439-1447. [PMID: 30710323 DOI: 10.1007/s00259-019-4270-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 01/10/2019] [Indexed: 11/24/2022]
Abstract
PURPOSE According to the ACRIN 6668/RTOG 0235 trial, pretreatment metabolic tumour volume (MTV) as detected by 18F-fluorodeoxyglucose PET/CT is a prognostic factor in patients with stage III non-small-cell lung cancer (NSCLC) after definitive radiochemotherapy (RCT). To validate the prognostic value of MTV in patients with stage III NSCLC after RCT, we analysed mature survival data from the German phase III trial ESPATUE. METHODS This analysis included patients who were staged by PET/CT and who were enrolled in the ESPATUE trial, a randomized study comparing definitive RCT (arm A) with surgery (arm B) after induction chemotherapy and RCT in patients with resectable stage IIIA/IIIB NSCLC. Patients refusing surgery and those with nonresectable disease were scheduled to receive definitive RCT. MTV was measured using a fixed threshold-based approach and a model-based iterative volume thresholding approach. Data were analysed using proportional hazards models and Kaplan-Meier survival functions. RESULTS MTV as a continuous variable did not reveal differences in survival between the 117 patients scheduled to receive definitive RCT and all 169 enrolled patients who underwent pretreatment PET/CT (p > 0.5). Five-year survival rates were 33% (95% CI 17-49%) in patients scheduled for definitive RCT with a high MTV (>95.4 ml) and 32% (95% CI: 22-42%) in those with a low MTV. The hazard ratio for survival was 0.997 (95% CI 0.973-1.022) per 10-ml increase in MTV and the slope was significantly shallower than that in the ACRIN 6668/RTOG 0235 trial (random effects model, p = 0.002). There were no differences in MTV size distributions between the ACRIN and ESPATUE trials (p = 0.97). CONCLUSION Patients with stage III NSCLC and a large MTV in whom definitive RCT had a particularly good survival in the ESPATUE trial. Treatment individualization according to MTV is not supported by this study. The ESPATUE and ACRIN trials differed by the use of cisplatin-containing induction chemotherapy and an intensified radiotherapy regimen that were particularly effective in patients with large MTV disease.
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Affiliation(s)
- Maja Guberina
- Department of Radiation Oncology, West German Cancer Center, University of Duisburg-Essen Medical School, Hufelandstr. 55, 45122, Essen, Germany
| | - Wilfried Eberhardt
- Department of Medical Oncology, West German Cancer Center, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Martin Stuschke
- Department of Radiation Oncology, West German Cancer Center, University of Duisburg-Essen Medical School, Hufelandstr. 55, 45122, Essen, Germany. .,German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45122, Essen, Germany.
| | - Thomas Gauler
- Department of Radiation Oncology, West German Cancer Center, University of Duisburg-Essen Medical School, Hufelandstr. 55, 45122, Essen, Germany
| | - Clemens Aigner
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45122, Essen, Germany.,Department of Thoracic Surgery, Ruhrlandklinik, University of Duisburg-Essen Medical School, 45239, Essen, Germany
| | - Martin Schuler
- Department of Medical Oncology, West German Cancer Center, University of Duisburg-Essen Medical School, 45122, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45122, Essen, Germany
| | - Georgios Stamatis
- Department of Thoracic Surgery, Ruhrlandklinik, University of Duisburg-Essen Medical School, 45239, Essen, Germany
| | - Dirk Theegarten
- Department of Pathology, West German Cancer Center, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Walter Jentzen
- Department of Nuclear Medicine, West German Cancer Center, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Ken Herrmann
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, 45122, Essen, Germany.,Department of Nuclear Medicine, West German Cancer Center, University of Duisburg-Essen Medical School, 45122, Essen, Germany
| | - Christoph Pöttgen
- Department of Radiation Oncology, West German Cancer Center, University of Duisburg-Essen Medical School, Hufelandstr. 55, 45122, Essen, Germany
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16
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Xie X, Luo K, Li Y, Ling Y, Zhang S, Xie X, Wen J. Histone deacetylase 6 expression in metastatic lymph nodes is a valuable prognostic marker for resected node-positive esophageal squamous cell cancer. Cancer Manag Res 2018; 10:5451-5460. [PMID: 30519093 PMCID: PMC6234999 DOI: 10.2147/cmar.s178575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Background Histone deacetylase 6 (HDAC6) exerts enzymatic deacetylation activity on histones and on non-histone substrates and plays a key role in microtubule dynamics and chaperone activities. In addition, previous studies have demonstrated its role in cancer progression. However, its clinical significance in esophageal squamous cell cancer (ESCC) has not been elucidated. We investigated the correlation of HDAC6 expression and clinical outcome in a group of T3N1–3M0 surgically resected ESCCs. Methods Tissue microarrays were conducted on 209 surgically resected T3N1–3M0 ESCC tumors, including 163 pairs of primary tumors (PTs) and their corresponding metastatic lymph nodes (MLNs). Immunohistochemistry was utilized to evaluate HDAC6 protein levels. The relationship between patient outcomes and HDAC6 expression was analyzed statistically. Results The level of HDAC6 expression in ESCC MLNs was found to be significantly lower than that in PTs (P<0.001). Patients with lower MLN HDAC6 expression demonstrated improved overall survival (P=0.011) and disease-free survival (P=0.012) than those with higher HDAC6 expression. HDAC6 expression levels in PTs revealed no prognostic significance. Multivariate analysis showed that the MLN HDAC6 expression level was an independent prognostic factor for both overall survival (HR 1.456, P=0.029) and disease-free survival (HR 1.432, P=0.033). Conclusion High expression of HDAC6 in MLNs but not in PTs suggests a poor prognosis for patients with resected T3N1–3M0 ESCC. We should take into account the protein expression of MLNs when assessing prognosis in patients with lymph-node involvement.
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Affiliation(s)
- Xuan Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China.,Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Kongjia Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China, .,Guangdong Esophageal Cancer Research Institute, Guangzhou, People's Republic of China, .,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Yi Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China, .,Guangdong Esophageal Cancer Research Institute, Guangzhou, People's Republic of China, .,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Yihong Ling
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China, .,Guangdong Esophageal Cancer Research Institute, Guangzhou, People's Republic of China, .,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Shuishen Zhang
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Xiuying Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China, .,Guangdong Esophageal Cancer Research Institute, Guangzhou, People's Republic of China,
| | - Jing Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China, .,Guangdong Esophageal Cancer Research Institute, Guangzhou, People's Republic of China,
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17
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Xing Z, Wei L, Jiang X, Conroy J, Glenn S, Bshara W, Yu T, Pao A, Tanaka S, Kawai A, Choi C, Wang J, Liu S, Morrison C, Yu YE. Analysis of mutations in primary and metastatic synovial sarcoma. Oncotarget 2018; 9:36878-36888. [PMID: 30627328 PMCID: PMC6305143 DOI: 10.18632/oncotarget.26416] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023] Open
Abstract
Synovial sarcoma is the most common pediatric non-rhabdomyosarcoma soft tissue sarcoma and accounts for about 8-10% of all soft tissue sarcoma in childhood and adolescence. The presence of a chromosomal translocation-associated SS18-SSX-fusion gene is causally linked to development of primary synovial sarcoma. Metastases occur in approximately 50-70% of synovial sarcoma cases with yet unknown mechanisms, which led to about 70-80% mortality rate in five years. To explore the possibilities to investigate metastatic mechanisms of synovial sarcoma, we carried out the first genome-wide search for potential genetic biomarkers and drivers associated with metastasis by comparative mutational profiling of 18 synovial sarcoma samples isolated from four patients carrying the primary tumors and another four patients carrying the metastatic tumors through whole exome sequencing. Selected from the candidates yielded from this effort, we examined the effect of the multiple missense mutations of ADAM17, which were identified solely in metastatic synovial sarcoma. The mutant alleles as well as the wild-type control were expressed in the mammalian cells harboring the SS18-SSX1 fusion gene. The ADAM17-P729H mutation was shown to enhance cell migration, a phenotype associated with metastasis. Therefore, like ADAM17-P729H, other mutations we identified solely in metastatic synovial sarcoma may also have the potential to serve as an entry point for unraveling the metastatic mechanisms of synovial sarcoma.
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Affiliation(s)
- Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program, Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Xiaoling Jiang
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program, Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jeffrey Conroy
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,OmniSeq Inc., Buffalo, NY, USA
| | - Sean Glenn
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,OmniSeq Inc., Buffalo, NY, USA
| | - Wiam Bshara
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Tao Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program, Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, USA.,Department of Medical Genetics, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program, Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Shinya Tanaka
- Department of Cancer Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Christopher Choi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Carl Morrison
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,OmniSeq Inc., Buffalo, NY, USA.,Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program, Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, USA.,Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, USA
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18
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Mutational Evolution in Relapsed Diffuse Large B-Cell Lymphoma. Cancers (Basel) 2018; 10:cancers10110459. [PMID: 30463380 PMCID: PMC6265691 DOI: 10.3390/cancers10110459] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022] Open
Abstract
Current genomic models in diffuse large B-cell lymphoma (DLBCL) are based on single tumor biopsies, which might underestimate heterogeneity. Data on mutational evolution largely remains unknown. An exploratory study using whole exome sequencing on paired (primary and relapse) formalin fixed paraffin embedded DLBCL biopsies (n = 14) of 6 patients was performed to globally assess the mutational evolution and to identify gene mutations specific for relapse samples from patients treated with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisolone. A minority of the mutations detected in the primary sample (median 7.6%, range 4.8–66.2%) could not be detected in the matching relapse sample. Relapsed DLBCL samples showed a mild increase of mutations (median 12.5%, range 9.4–87.6%) as compared to primary tumor biopsies. We identified 264 genes possibly related to therapy resistance, including tyrosine kinases (n = 18), (transmembrane) glycoproteins (n = 73), and genes involved in the JAK-STAT pathway (n = 7). Among the potentially resistance related genes were PIM1, SOCS1, and MYC, which have been reported to convey a risk for treatment failure. In conclusion, we show modest temporal heterogeneity between paired tumor samples with the acquisition of new mutations and identification of genes possibly related to therapy resistance. The mutational evolution could have implications for treatment decisions and development of novel targeted drugs.
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19
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Yu L, Li K, Xu Z, Cui G, Zhang X. Integrated omics and gene expression analysis identifies the loss of metabolite-metabolite correlations in small cell lung cancer. Onco Targets Ther 2018; 11:3919-3929. [PMID: 30013371 PMCID: PMC6039056 DOI: 10.2147/ott.s166149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Small cell lung cancer (SCLC) is the most aggressive type of lung carcinoma with high metastatic potential and chemoresistance upon relapse. Cancer cells remodel the existing metabolic pathways for their benefits and the perturbations in cellular metabolism are the hallmark of cancer. However, the extent of these changes remains largely unknown for SCLC. MATERIALS AND METHODS We characterized the metabolic perturbations in SCLC cells (SCLCC) by metabolomics. Large-scale correlation analysis was performed between metabolites. Targeted proteomics and gene expression analysis were employed to investigate the changes of key enzymes and genes in the disturbed pathways. RESULTS We found dramatic decrease of metabolite-metabolite correlations in SCLCC compared with normal control cells and non-small cell lung cancer cells. Pathway analysis revealed that the loss of correlations was associated with the alternations of fatty acid oxidation, urea cycle, and purine salvage pathway in SCLCC. Targeted proteomics and gene expression analysis confirmed significant changes of the expression for the key enzymes and genes in the pathways in SCLCC including the upregulation of carbamoyl phosphate synthase 1 (urea cycle) and carnitine palmitoyltransferase 1A (fatty acid oxidation), and the downregulation of hypoxanthine-guanine phosphoribosyltransferase and adenine phosphoribosyltransferase in purine salvage pathway. CONCLUSION We demonstrated the loss of metabolite-metabolite correlations in SCLCC associated with the upregulation of fatty acid oxidation and urea cycle and the downregulation of purine salvage pathways. Our findings provide insights into the metabolic reprogramming in SCLCC and highlight the potential therapeutic targets for the treatment of SCLC.
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Affiliation(s)
- Li Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Kefeng Li
- School of Medicine, University of California-San Diego, San Diego, CA, USA
| | - Zhaoguo Xu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Guoyuan Cui
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Xiaoye Zhang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
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Genetic heterogeneity of primary lesion and metastasis in small intestine neuroendocrine tumors. Sci Rep 2018; 8:3811. [PMID: 29491456 PMCID: PMC5830878 DOI: 10.1038/s41598-018-22115-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/16/2018] [Indexed: 01/01/2023] Open
Abstract
Data on intratumoral heterogeneity of small intestine neuroendocrine tumors (SI-NETs) and related liver metastasis are limited. The aim of this study was to characterize genetic heterogeneity of 5 patients with SI-NETs. Therefore, formalin-fixed, paraffin-embedded tissue samples of primary and metastatic lesions as well as benign liver of five patients with synchronously metastasized, well differentiated SI-NETs were analyzed with whole exome sequencing. For one patient, chip based 850k whole DNA methylome analysis was performed of primary and metastatic tumor tissue as well as control tissue. Thereby, 156 single nucleotide variants (SNVs) in 150 genes were identified and amount of mutations per sample ranged from 9–34 (mean 22). The degree of common (0–94%) and private mutations per sample was strongly varying (6–100%). In all patients, copy number variations (CNV) were found and the degree of intratumoral heterogeneity of CNVs corresponded to SNV analysis. DNA methylation analysis of a patient without common SNVs revealed a large overlap of common methylated CpG sites. In conclusion, SI-NET primary and metastatic lesions show a highly varying degree of intratumoral heterogeneity. Driver events might not be detectable with exome analysis only, and further comprehensive studies including whole genome and epigenetic analyses are warranted.
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Abstract
PURPOSE OF REVIEW The pathogenesis of lung cancer and pulmonary fibrotic disorders partially overlaps. This review focuses on the common features of the two disease categories, aimed at advancing our translational understanding of their pathobiology and at fostering the development of new therapies. RECENT FINDINGS Both malignant and collagen-producing lung cells display enhanced cellular proliferation, increased resistance to apoptosis, a propensity for invading and distorting the lung parenchyma, as well as stemness potential. These characteristics are reinforced by the tissue microenvironment and inflammation seems to play an important adjuvant role in both types of disorders. SUMMARY Unraveling the thread of the common and distinct characteristics of lung fibrosis and cancer might contribute to a more comprehensive approach of the pathobiology of both diseases and to a pathfinder for novel and personalized therapeutic strategies.
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Del Re M, Bordi P, Petrini I, Rofi E, Mazzoni F, Belluomini L, Vasile E, Restante G, Di Costanzo F, Falcone A, Frassoldati A, van Schaik RHN, Steendam CMJ, Chella A, Tiseo M, Morganti R, Danesi R. Patients with NSCLC may display a low ratio of p.T790M vs. activating EGFR mutations in plasma at disease progression: implications for personalised treatment. Oncotarget 2017; 8:86056-86065. [PMID: 29156777 PMCID: PMC5689667 DOI: 10.18632/oncotarget.20947] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 07/26/2017] [Indexed: 01/02/2023] Open
Abstract
Introduction NSCLC harboring activating mutations of EGFR is highly sensitive to first-line EGFR-tyrosine kinase inhibitors (TKIs), but drug resistance depending on the EGFR mutation p.T790M will occur in about 50-60% of patients. Detailed information on the amount of p.T790M plasmatic level associated with resistance to EGFR-TKIs and guidance to treatment with p.T790M-effective TKI depending on these levels, is lacking. Methods This study enrolled p.T790M-positive patients (n=49) affected by EGFR-mutated NSCLC at progression to first-line EGFR-TKIs and, in selected cases (n=5), after second-line treatment with osimertinib. Cell-free circulating tumor DNA (cftDNA) was extracted from plasma and the quantitative analysis of EGFR ex19del, p.L858R and p.T790M was performed by digital droplet PCR. Results The mean amount of mutated alleles at progression to first-line EGFR-TKIs was 108,492 copies/ml for ex19del, 97,336 copies/ml for p.L858R, but only 8,754 copies/ml for p.T790M. There was no significant correlation between progression-free survival and the ratio of p.T790M over EGFR activating mutations. The analysis of cftDNA in 5 patients treated with osimertinib revealed a marked decrease of all EGFR mutant alleles. Conclusions The amount of p.T790M in plasma can be much lower than activating EGFR mutations. Despite this finding, osimertinib is effective in p.T790M-positive patients. These results indicate that clones driving resistance to EGFR-TKIs represent a minority among cells bearing activating EGFR-mutations. In addition, the identification of a threshold level of p.T790M is not a strict requirement for the selection of patients to be treated with osimertinib, since treatment showed a decrease in all EGFR mutated cells.
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Affiliation(s)
- Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Paola Bordi
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Iacopo Petrini
- Medical Oncology Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa, Pisa, Italy
| | - Eleonora Rofi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Lorenzo Belluomini
- Medical Oncology Unit, Civil Hospital Arcispedale S. Anna, Ferrara, Italy
| | - Enrico Vasile
- Medical Oncology Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa, Pisa, Italy
| | - Giuliana Restante
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Alfredo Falcone
- Medical Oncology Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa, Pisa, Italy
| | | | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christi M J Steendam
- Department of Pulmonology, Erasmus University Medical Center, Rotterdam, and Amphia Hospital, Breda, The Netherlands
| | - Antonio Chella
- Lung Diseases Unit, Azienda Ospedaliero-Universitaria, Pisa, Italy
| | - Marcello Tiseo
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Riccardo Morganti
- Section of Statistics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Romano Danesi
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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