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Clinical and genomic characterization of neutral tumor evolution in Head and Neck Squamous Cell Carcinoma. Genomics 2020; 112:3448-3454. [PMID: 32569729 DOI: 10.1016/j.ygeno.2020.06.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
Recent studies suggest that a significant proportion of cancers undergo neutral tumor evolution. We applied neutral evolution model in HNSCC patients from The Cancer Genome Atlas (TCGA). To ensure the accuracy of classification results, a sample with the purity of tumor <0.7 was excluded. A tumor sample was considered to evolve neutrally if R2 ≥ 0.98. We found that about 16% of HNSCC patients undergo neutral tumor evolution. We showed that neutral evolution HNSCC patients have better prognosis and higher activities of immune response pathways, and the numbers of co-occurring mutation events and significantly positive selection mutations are significantly less than non-neutral evolution HNSCC patients. In conclusion, we described a comprehensive clinical and genomic characteristics of neutral tumor evolution in Head and Neck Squamous Cell Carcinoma (HNSCC), and provided evidence that the evolution history of HNSCC has both clinical and biological implications.
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Gatti V, Bernassola F, Talora C, Melino G, Peschiaroli A. The Impact of the Ubiquitin System in the Pathogenesis of Squamous Cell Carcinomas. Cancers (Basel) 2020; 12:cancers12061595. [PMID: 32560247 PMCID: PMC7352818 DOI: 10.3390/cancers12061595] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin system is a dynamic regulatory pathway controlling the activity, subcellular localization and stability of a myriad of cellular proteins, which in turn affects cellular homeostasis through the regulation of a variety of signaling cascades. Aberrant activity of key components of the ubiquitin system has been functionally linked with numerous human diseases including the initiation and progression of human tumors. In this review, we will contextualize the importance of the two main components of the ubiquitin system, the E3 ubiquitin ligases (E3s) and deubiquitinating enzymes (DUBs), in the etiology of squamous cell carcinomas (SCCs). We will discuss the signaling pathways regulated by these enzymes, emphasizing the genetic and molecular determinants underlying their deregulation in SCCs.
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Affiliation(s)
- Veronica Gatti
- National Research Council of Italy, Institute of Translational Pharmacology, 00133 Rome, Italy;
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy; (F.B.); (G.M.)
| | - Claudio Talora
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy;
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy; (F.B.); (G.M.)
| | - Angelo Peschiaroli
- National Research Council of Italy, Institute of Translational Pharmacology, 00133 Rome, Italy;
- Correspondence:
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Wang H, Yan C, Ye H. Overexpression of MUC16 predicts favourable prognosis in MUC16-mutant cervical cancer related to immune response. Exp Ther Med 2020; 20:1725-1733. [PMID: 32765681 PMCID: PMC7388571 DOI: 10.3892/etm.2020.8836] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer (CC) is the fourth ranking gynaecologic tumour in women worldwide, with respect to both incidence and mortality. MUC16 is one of the most frequently mutated genes, which functions as a tumour marker in CC. In the present study, mutation, clinical and RNA-Seq data collected from The Cancer Genome Atlas database were used to investigate the association between MUC16 mutation, immune response and clinical prognosis in CC. mRNA expression levels from the TCGA datasets and the results from the present study demonstrated that MUC16 was overexpressed in CC samples; however, there was no difference between mutant and wild-type CC samples. Furthermore, the results indicated that patients with MUC16-mutant overexpression had a prolonged survival time. In addition, overexpression of MUC16 was associated with immune responses in the microenvironment of MUC16-mutant CC. Immune responses were upregulated in patients with early-stage MUC16-mutant. The results from the present study provided novel biomarkers for potential immunotherapy approaches for CC.
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Affiliation(s)
- Hao Wang
- Department of Gynaecology and Obstetrics, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443000, P.R. China
| | - Chao Yan
- Department of Orthopaedics, The People's Hospital of China Three Gorges University, Yichang, Hubei 443000, P.R. China
| | - Hong Ye
- Department of Gynaecology and Obstetrics, The First College of Clinical Medical Science, China Three Gorges University, Yichang, Hubei 443000, P.R. China
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Liu Z, Deng M, Wu L, Zhang S. An integrative investigation on significant mutations and their down-stream pathways in lung squamous cell carcinoma reveals CUL3/KEAP1/NRF2 relevant subtypes. Mol Med 2020; 26:48. [PMID: 32434476 PMCID: PMC7240936 DOI: 10.1186/s10020-020-00166-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/16/2020] [Indexed: 01/10/2023] Open
Abstract
Background Molecular mechanism of lung squamous cell carcinoma (LUSC) remains poorly understood, hampering effective targeted therapies or precision diagnosis about LUSC. We devised an integrative framework to investigate on the molecular patterns of LUSC by systematically mining the genomic, transcriptional and clinical information. Methods We utilized the genomics and transcriptomics data for the LUSC cohorts in The Cancer Genome Atlas.. Both kinds of omics data for 33 types of cancers were downloaded from The NCI’s Genomic Data Commons (GDC) (https://gdc.cancer.gov/about-data/publications/pancanatlas). The genomics data were processed in mutation annotation format (maf), and the transcriptomics data were determined by RNA-seq method. Mutation significance was estimated by MutSigCV. Prognosis analysis was based on the cox proportional hazards regression (Coxph) model. Results Significant somatic mutated genes (SMGs) like NFE2L2, RASA1 and COL11A1 and their potential down-stream pathways were recognized. Furthermore, two LUSC-specific and prognosis-meaningful subtypes were identified. Interestingly, the good prognosis subtype was enriched with mutations in CUL3/KEAP1/NRF2 pathway and with markedly suppressed expressions of multiple down-stream pathways like epithelial mesenchymal transition. The subtypes were verified by the other two cohorts. Additionally, primarily regulated down-stream elements of different SMGs were also estimated. NFE2L2, KEAP1 and RASA1 mutations showed remarkable effects on the subtype-determinant gene expressions, especially for the inflammatory relevant genes. Conclusions This study supplies valuable references on potential down-stream processes of SMGs and an alternative way to classify LUSC.
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Affiliation(s)
- Zongang Liu
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District Shenyang, Liaoning, 110004, People's Republic of China
| | - Meiyan Deng
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District Shenyang, Liaoning, 110004, People's Republic of China
| | - Lin Wu
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District Shenyang, Liaoning, 110004, People's Republic of China.
| | - Suning Zhang
- Department of Thoracic Surgery, Shengjing Hospital of China Medical University, No.36 Sanhao Street, Heping District Shenyang, Liaoning, 110004, People's Republic of China
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Ju Q, Zhao YJ, Ma S, Li XM, Zhang H, Zhang SQ, Yang YM, Yan SX. Genome-wide analysis of prognostic-related lncRNAs, miRNAs and mRNAs forming a competing endogenous RNA network in lung squamous cell carcinoma. J Cancer Res Clin Oncol 2020; 146:1711-1723. [PMID: 32356177 DOI: 10.1007/s00432-020-03224-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE As a type of cancer with the highest morbidity and mortality, lung squamous cell carcinoma (LUSC) has a very poor prognosis. Long-non-coding RNA (lncRNA) has recently attracted attentions because it can play the role of competing endogenous RNA (ceRNA) to inhibit microRNA (miRNA) functions. In this study, we aimed to find prognosis-related lncRNAs, miRNAs and mRNAs and construct a prognosis-related ceRNA network. METHODS The original LUSC RNA-sequencing data and miRNA profiles data were downloaded from the cancer genome atlas (TCGA) database. Differentially expressed lncRNAs, miRNAs and mRNAs were then identified between patients with lymph node metastasis and no lymph node metastasis. Univariate Cox regression analysis was performed to find the survival-associated lncRNAs, miRNAs and mRNAs. Subsequently, prognostic-related ceRNA network was established. By multivariate Cox regression analysis, three lncRNA signatures and three mRNA signatures were developed and used for predicting LUSC patients' survival. RESULTS A total of 224 lncRNAs, 160 miRNAs, 913 mRNAs were identified between samples with lymph node metastasis and no lymph node metastasis. Univariate Cox regression analysis showed that, among them, 28 lncRNAs, 8 miRNAs, 105 mRNAs were significantly associated with patients' overall survival time. Further pathway and enrichment analysis suggested that these mRNAs were associated with the regulation of transmembrane transport, regulation of blood circulation, plasma lipoprotein particle organization. Then we constructed a survival-related ceRNA network including 9 lncRNAs, 8 miRNAs and 23 mRNAs. Additionally, a multivariate Cox regression analysis demonstrated that three lncRNAs (AL161431.1, LINC02389, APCDD1L.DT) and three mRNAs (KLK6, SLITRK5, CCDC177) had a significant prognostic value. Risk score indicated that lncRNA signature and mRNA signature could independently predict overall survival in LUSC patients. CONCLUSION The current study provided a better understanding of the ceRNA network in the progression of LUSC and laid a theoretical foundation for LUSC prognosis.
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Affiliation(s)
- Qiang Ju
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
| | - Yan-Jie Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Sai Ma
- Qingdao International Travel Health Center, Qingdao, China
| | - Xin-Mei Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Heng Zhang
- School of Public Health, Qingdao University, Qingdao, China
| | - Shao-Qiang Zhang
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yuan-Ming Yang
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Song-Xia Yan
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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Lingling Z, Jiewei L, Li W, Danli Y, Jie Z, Wen L, Dan P, Lei P, Qinghua Z. Molecular regulatory network of PD-1/PD-L1 in non-small cell lung cancer. Pathol Res Pract 2020; 216:152852. [DOI: 10.1016/j.prp.2020.152852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 01/03/2020] [Accepted: 02/04/2020] [Indexed: 12/18/2022]
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Remon J, Passiglia F, Ahn MJ, Barlesi F, Forde PM, Garon EB, Gettinger S, Goldberg SB, Herbst RS, Horn L, Kubota K, Lu S, Mezquita L, Paz-Ares L, Popat S, Schalper KA, Skoulidis F, Reck M, Adjei AA, Scagliotti GV. Immune Checkpoint Inhibitors in Thoracic Malignancies: Review of the Existing Evidence by an IASLC Expert Panel and Recommendations. J Thorac Oncol 2020; 15:914-947. [PMID: 32179179 DOI: 10.1016/j.jtho.2020.03.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/29/2020] [Accepted: 03/06/2020] [Indexed: 02/07/2023]
Abstract
In the past 10 years, a deeper understanding of the immune landscape of cancers, including immune evasion processes, has allowed the development of a new class of agents. The reactivation of host antitumor immune response offers the potential for long-term survival benefit in a portion of patients with thoracic malignancies. The advent of programmed cell death protein 1/programmed death ligand-1 immune checkpoint inhibitors (ICIs), both as single agents and in combination with chemotherapy, and more recently, the combination of ICI, anti-programmed cell death protein 1, and anticytotoxic T-lymphocyte antigen 4 antibody, have led to breakthrough therapeutic advances for patients with advanced NSCLC, and to a lesser extent, patients with SCLC. Encouraging activity has recently emerged in pretreated patients with thymic carcinoma (TC). Conversely, in malignant pleural mesothelioma, pivotal positive signs of activity have not been fully confirmed in randomized trials. The additive effects of chemoradiation and immunotherapy suggested intriguing potential for therapeutic synergy with combination strategies. This has led to the introduction of ICI consolidation therapy in stage III NSCLC, creating a platform for future therapeutic developments in earlier-stage disease. Despite the definitive clinical benefit observed with ICI, primary and acquired resistance represent well-known biological phenomena, which may affect the therapeutic efficacy of these agents. The development of innovative strategies to overcome ICI resistance, standardization of new patterns of ICI progression, identification of predictive biomarkers of response, optimal treatment duration, and characterization of ICI efficacy in special populations, represent crucial issues to be adequately addressed, with the aim of improving the therapeutic benefit of ICI in patients with thoracic malignancies. In this article, an international panel of experts in the field of thoracic malignancies discussed these topics, evaluating currently available scientific evidence, with the final aim of providing clinical recommendations, which may guide oncologists in their current practice and elucidate future treatment strategies and research priorities.
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Affiliation(s)
- Jordi Remon
- Department of Medical Oncology, Centro Integral Oncológico Clara Campal (HM-CIOCC), Hospital HM Delfos, HM Hospitales, Barcelona, Spain
| | - Francesco Passiglia
- Department of Oncology, University of Torino, AOU S. Luigi Gonzaga, Orbassano, Italy
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Fabrice Barlesi
- Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille University, CNRS, INSERM, CRCM, APHM, Marseille, France
| | - Patrick M Forde
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward B Garon
- David Geffen School of Medicine at University of California Los Angeles, Translational Research in Oncology US Network, Los Angeles, California
| | - Scott Gettinger
- Department of Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, Connecticut
| | - Sarah B Goldberg
- Department of Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, Connecticut
| | - Roy S Herbst
- Department of Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, Connecticut
| | - Leora Horn
- Department of Hematology and Oncology, Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Kaoru Kubota
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, People's Republic of China
| | - Laura Mezquita
- Department of Cancer Medicine, Gustave Roussy Cancer Campus, Villejuif, France
| | - Luis Paz-Ares
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Sanjay Popat
- Medical Oncology Department, The Royal Marsden Hospital, London, United Kingdom; Medical Oncology Department, The Institute of Cancer Research, London, United Kingdom; National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Kurt A Schalper
- Departments of Pathology and Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, Connecticut
| | - Ferdinandos Skoulidis
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Martin Reck
- Lung Clinic Grosshansdorf, Airway Research Center North, German Center of Lung Research, Grosshansdorf, Germany
| | - Alex A Adjei
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - Giorgio V Scagliotti
- Department of Oncology, University of Torino, AOU S. Luigi Gonzaga, Orbassano, Italy.
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Zhu Q, Wang J, Zhang Q, Wang F, Fang L, Song B, Xie C, Liu J. Methylation‑driven genes PMPCAP1, SOWAHC and ZNF454 as potential prognostic biomarkers in lung squamous cell carcinoma. Mol Med Rep 2020; 21:1285-1295. [PMID: 32016477 PMCID: PMC7002985 DOI: 10.3892/mmr.2020.10933] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023] Open
Abstract
Of the different types of lung cancer, lung squamous cell cancer (LUSC) has the second highest rates of morbidity and mortality, which have been increasing in recent years. Epigenetic abnormalities may serve as potential biomarkers and diagnostic and/or therapeutic targets, which may help to monitor and improve the prognosis of patients with cancer. In the present study, data were obtained from The Cancer Genome Atlas database and survival and joint survival analyses were conducted using the R MethylMix package. Peptidase, mitochondrial processing a subunit pseudogene 1 (PMPCAP1), sosondowah ankyrin repeat domain family member C (SOWAHC) and zinc finger protein (ZNF) 454 were identified as independent prognosis‑related hub methylation‑driven genes (MDGs). Of these three genes, PMPCAP1 and SOWAHC, characterized by hypomethylation and high expression levels, were associated with poor prognosis in patients with LUSC, whilst ZNF454 was associated with an improved prognosis. In addition, pathway enrichment analysis suggested that PMPCAP1, SOWAHC and ZNF454 were primarily involved in gene expression or transcription pathways. Furthermore, 5, 1 and 10 key methylation sites of PMPCAP1, SOWAHC and ZNF454, respectively, were confirmed to be significantly relevant to gene expression, establishing a basis for further investigation into the mechanisms and more precise targets of these 3 genes. In conclusion, the MDGs PMPCAP1, SOWAHC and ZNF454 may be potential prognostic biomarkers of LUSC for guiding diagnosis and therapy options, as well as providing a theoretical basis for further investigation.
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Affiliation(s)
- Qingqing Zhu
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250022, P.R. China
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| | - Jia Wang
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
- Department of Oncology, Zibo Maternal and Child Health Hospital, Zibo, Shandong 255000, P.R. China
| | - Qiujing Zhang
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Sciences, Jinan, Shandong 250022, P.R. China
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| | - Fuxia Wang
- Department of Oncology, Yun Cheng Country People's Hospital, Heze, Shandong 274700, P.R. China
| | - Lihua Fang
- Department of Oncology, Chang Qing District People's Hospital, Jinan, Shandong 250300, P.R. China
| | - Bao Song
- Basic Laboratory, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| | - Chao Xie
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
| | - Jie Liu
- Department of Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, P.R. China
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Saab S, Zalzale H, Rahal Z, Khalifeh Y, Sinjab A, Kadara H. Insights Into Lung Cancer Immune-Based Biology, Prevention, and Treatment. Front Immunol 2020; 11:159. [PMID: 32117295 PMCID: PMC7026250 DOI: 10.3389/fimmu.2020.00159] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is the number one cause of cancer-related deaths. The malignancy is characterized by dismal prognosis and poor clinical outcome mostly due to advanced-stage at diagnosis, thereby inflicting a heavy burden on public health worldwide. Recent breakthroughs in immunotherapy have greatly benefited a subset of lung cancer patients, and more importantly, they are undauntedly bringing forth a paradigm shift in the drugs approved for cancer treatment, by introducing "tumor-type agnostic therapies". Yet, and to fulfill immunotherapy's potential of personalized cancer treatment, demarcating the immune and genomic landscape of cancers at their earliest possible stages will be crucial to identify ideal targets for early treatment and to predict how a particular patient will fare with immunotherapy. Recent genomic surveys of premalignant lung cancer have shed light on early alterations in the evolution of lung cancer. More recently, the advent of immunogenomic technologies has provided prodigious opportunities to study the multidimensional landscape of lung tumors as well as their microenvironment at the molecular, genomic, and cellular resolution. In this review, we will summarize the current state of immune-based therapies for cancer, with a focus on lung malignancy, and highlight learning outcomes from clinical and preclinical studies investigating the naïve immune biology of lung cancer. The review also collates immunogenomic-based evidence from seminal reports which collectively warrant future investigations of premalignancy, the tumor-adjacent normal-appearing lung tissue, pulmonary inflammatory conditions such as chronic obstructive pulmonary disease, as well as systemic microbiome imbalance. Such future directions enable novel insights into the evolution of lung cancers and, thus, can provide a low-hanging fruit of targets for early immune-based treatment of this fatal malignancy.
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Affiliation(s)
- Sara Saab
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hussein Zalzale
- School of Medicine, American University of Beirut, Beirut, Lebanon
| | - Zahraa Rahal
- School of Medicine, American University of Beirut, Beirut, Lebanon
| | - Yara Khalifeh
- School of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Humam Kadara
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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Comprehensive T cell repertoire characterization of non-small cell lung cancer. Nat Commun 2020; 11:603. [PMID: 32001676 PMCID: PMC6992630 DOI: 10.1038/s41467-019-14273-0] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Immunotherapy targeting T cells is increasingly utilized to treat solid tumors including non-small cell lung cancer (NSCLC). This requires a better understanding of the T cells in the lungs of patients with NSCLC. Here, we report T cell repertoire analysis in a cohort of 236 early-stage NSCLC patients. T cell repertoire attributes are associated with clinicopathologic features, mutational and immune landscape. A considerable proportion of the most prevalent T cells in tumors are also prevalent in the uninvolved tumor-adjacent lungs and appear specific to shared background mutations or viral infections. Patients with higher T cell repertoire homology between the tumor and uninvolved tumor-adjacent lung, suggesting a less tumor-focused T cell response, exhibit inferior survival. These findings indicate that a concise understanding of antigens and T cells in NSCLC is needed to improve therapeutic efficacy and reduce toxicity with immunotherapy, particularly adoptive T cell therapy. Relevant features of T cell repertoire in human cancer remain to be delineated. Here the authors show, by TCR sequencing in a large cohort of lung cancer patients, that while a majority of T cell clones are shared between tumor and adjacent lung tissue, less frequent tumor-unique T cell clones correlate with worse prognosis.
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Lv Z, Lei T. Systematical identifications of prognostic meaningful lung adenocarcinoma subtypes and the underlying mutational and expressional characters. BMC Cancer 2020; 20:56. [PMID: 31987030 PMCID: PMC6983970 DOI: 10.1186/s12885-019-6462-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/15/2019] [Indexed: 01/10/2023] Open
Abstract
Background Lung adenocarcinoma (LUAD) is one of the most common cancer types, threatening the human health around the world. However, the high heterogeneity and complexity of LUAD limit the benefits of targeted therapies. This study aimed to identify the key prognosis impacting genes and relevant subtypes for LUAD. Methods We recognized significant mutations and prognosis-relevant genes based on the omics data of 515 LUAD samples from The Cancer Genome Atlas. Mutation significance was estimated by MutSigCV. Prognosis analysis was based on the cox proportional hazards regression (Coxph) model. Specifically, the Coxph model was combined with a causal regulatory network to help reveal which genes play master roles among numerous prognosis impacting genes. Based on expressional profiles of the master genes, LUAD patients were clustered into different sub-types by a consensus clustering method and the importance of master genes were further evaluated by random forest. Results Significant mutations did not influence the prognosis directly. However, a collection of prognosis relevant genes were recognized, where 75 genes like GAPDH and GGA2 which are involved in mTOR signaling, lysosome or other key pathways are further identified as the master ones. Interestingly, the master gene expressions help separate LUAD patients into two sub-types displaying remarkable differences in expressional profiles, prognostic outcomes and genomic mutations in certain genes, like SMARCA4 and COL11A1. Meanwhile, the subtypes were re-discovered from two additional LUAD cohorts based on the top-10 important master genes. Conclusions This study can promote precision treatment of LUAD by providing a comprehensive description on the key prognosis-relevant genes and an alternative way to classify LUAD subtypes.
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Affiliation(s)
- Zhenyang Lv
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People's Republic of China
| | - Ting Lei
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People's Republic of China.
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Zhu N, Ding L, Fu Y, Yang Y, Chen S, Chen W, Zhao M, Zhao X, Lu Z, Ni Y, Hu Q. Tumor-infiltrating lymphocyte-derived MLL2 independently predicts disease-free survival for patients with early-stage oral squamous cell carcinoma. J Oral Pathol Med 2019; 49:126-136. [PMID: 31660637 DOI: 10.1111/jop.12969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/04/2019] [Accepted: 10/18/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND MLL2 (mixed-lineage leukemia 2) is recognized as an essential role in regulating histone 3 lysine 4 tri-methylation (H3K4me3) in mammalian cells. It is frequently mutated to promote developmental diseases and tumor initiation. However, the expression pattern of MLL2 and its clinical significance for patients with early-stage oral squamous cell carcinoma (OSCC) remain totally unknown. METHODS Eighty-five samples of primary early-stage OSCC were enrolled in this retrospective study, and immunohistochemistry (IHC) was performed to detect the spatial pattern of MLL2. The diagnostic and prognostic value of MLL2 were assessed. RESULTS MLL2 was widely expressed in tumor cells (TCs), fibroblast-like cells (FLCs), and tumor-infiltrating lymphocytes (TILs), both in tumor center and invasive tumor front, and showed no distributive heterogeneity. Moreover, regardless of cell types and microlocalization, patients with high expressed MLL2 had increased depth invasion of tumor (DOI). Besides, upregulation of MLL2TC and MLL2TIL in tumor center were both associated with poor differentiation, but showed no correlation with tumor growth with comparable Ki-67 levels. Prognostic analysis indicated that early-stage OSCC patients with enhanced MLL2TIL in invasive tumor front were susceptible to occur postoperative metastasis and recurrence. Indeed, patients with higher expressed MLL2TIL showed shorter overall survival (OS) and disease-free survival (DFS), and MLL2TIL in invasive tumor front was an independent risk factor of DFS. CONCLUSION TIL-derived MLL2 in invasive tumor front was an independent prognostic factor of DFS for early-stage OSCC patients.
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Affiliation(s)
- Nisha Zhu
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Liang Ding
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yong Fu
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yan Yang
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Sheng Chen
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wantao Chen
- Department of Oral and Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengxiang Zhao
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xingxing Zhao
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Zhanyi Lu
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Yanhong Ni
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
| | - Qingang Hu
- Central Laboratory of Stomatology, Nanjing Stomatological Hospital, Medical School of Nanjing University, Nanjing, China
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Willis C, Fiander M, Tran D, Korytowsky B, Thomas JM, Calderon F, Zyczynski TM, Brixner D, Stenehjem DD. Tumor mutational burden in lung cancer: a systematic literature review. Oncotarget 2019; 10:6604-6622. [PMID: 31762941 PMCID: PMC6859921 DOI: 10.18632/oncotarget.27287] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/16/2019] [Indexed: 01/24/2023] Open
Abstract
Purpose: To assess the association of tumor mutational burden (TMB) with clinical outcomes, other biomarkers and patient/disease characteristics in patients receiving therapy for lung cancer. Results: In total, 4,303 publications were identified; 81 publications were included. The majority of publications assessing clinical efficacy of immunotherapy reported an association with high TMB, particularly when assessing progression-free survival and objective response rate. High TMB was consistently associated with TP53 alterations, and negatively associated with EGFR mutations. High TMB was also associated with smoking, squamous cell non-small cell lung carcinoma, and being male. Methods: A systematic literature review based upon an a priori protocol was conducted following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) and Cochrane methodologies. Searches were conducted in EMBASE, SCOPUS, Ovid MEDLINE®, and Emcare (from January 2012 until April 2018) and in two clinical trial registries. Conference abstracts were identified in EMBASE, and in targeted searches of recent major conference proceedings (from January 2016 until April 2018). Publications reporting data in patients receiving therapy for lung cancer that reported TMB and its association with clinical efficacy, or with other biomarkers or patient/disease characteristics, were included. Results are presented descriptively. Conclusion: This systematic literature review identified several clinical outcomes, biomarkers, and patient/disease characteristics associated with high TMB, and highlights the need for standardized definitions and testing practices. Further studies using standardized methodology are required to inform treatment decisions.
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Affiliation(s)
- Connor Willis
- Department of Pharmacotherapy, University of Utah, Salt Lake City, UT, USA
| | - Michelle Fiander
- Department of Pharmacotherapy, University of Utah, Salt Lake City, UT, USA
| | - Dao Tran
- Department of Pharmacy Practice and Pharmaceutical Sciences, University of Minnesota, Duluth, MN, USA
| | | | | | | | | | - Diana Brixner
- Department of Pharmacotherapy, University of Utah, Salt Lake City, UT, USA
| | - David D. Stenehjem
- Department of Pharmacotherapy, University of Utah, Salt Lake City, UT, USA
- Department of Pharmacy Practice and Pharmaceutical Sciences, University of Minnesota, Duluth, MN, USA
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Fan Y, Mu J, Huang M, Imani S, Wang Y, Lin S, Fan J, Wen Q. Epigenetic identification of ADCY4 as a biomarker for breast cancer: an integrated analysis of adenylate cyclases. Epigenomics 2019; 11:1561-1579. [PMID: 31584294 DOI: 10.2217/epi-2019-0207] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: To explore the role of adenylyl cyclase isoforms and its epigenetics in cancer. Materials & methods: Adenylyl cyclase expression profiles, epigenetic alterations, prognostic value and molecular networks were assessed by use of public omics datasets. Results: ADCY4 was significantly downregulated in breast cancer. This downregulation was associated with promoter hypermethylation. High ADCY4 expression was correlated with better survival of patients with breast cancer and its different intrinsic subtypes and tumor stages. ADCY4 was shown to be strongly associated with G protein coupled receptors and the downstream cAMP signaling pathway, which was also significantly enriched in newly identified lysophosphatidic acid receptor 4 and glucagon-like peptide-1. Conclusion: ADCY4 may be used as an epigenetic biomarker for breast cancer, as well as a possible target for therapy.
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Affiliation(s)
- Yu Fan
- Oncology Department, The Affiliated Hospital of Southwest Medical University, 646000 Luzhou, PR China
| | - Junhao Mu
- Chongqing Key Laboratory of Molecular Oncology & Epigenetics, The First Affiliated Hospital of Chongqing Medical University, 400010 Chongqing, PR China
| | - Mingquan Huang
- Breast Surgery Department, The Affiliated Hospital of Southwest Medical University, 646000 Luzhou, PR China
| | - Saber Imani
- Oncology Department, The Affiliated Hospital of Southwest Medical University, 646000 Luzhou, PR China
| | - Yu Wang
- Health Examination Department, The Affiliated Hospital of Southwest Medical University, 646000 Luzhou, PR China
| | - Sheng Lin
- Oncology Department, The Affiliated Hospital of Southwest Medical University, 646000 Luzhou, PR China
| | - Juan Fan
- Oncology Department, The Affiliated Hospital of Southwest Medical University, 646000 Luzhou, PR China
| | - Qinglian Wen
- Oncology Department, The Affiliated Hospital of Southwest Medical University, 646000 Luzhou, PR China
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Desrichard A, Kuo F, Chowell D, Lee KW, Riaz N, Wong RJ, Chan TA, Morris LGT. Tobacco Smoking-Associated Alterations in the Immune Microenvironment of Squamous Cell Carcinomas. J Natl Cancer Inst 2019; 110:1386-1392. [PMID: 29659925 DOI: 10.1093/jnci/djy060] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/06/2018] [Indexed: 01/16/2023] Open
Abstract
Background Tobacco smoking creates DNA damage, inducing mutations and potentially altering the tumor immune microenvironment. These types of genetic and immune microenvironment alterations are critical factors known to affect tumor response to immunotherapy. Here we analyze the association between the mutational signature of tobacco smoking, tumor mutational load, and metrics of immune activity in squamous cell carcinomas arising in the head and neck and lung. Methods Using RNA and DNA sequencing data from The Cancer Genome Atlas head and neck (HNSC; n = 287) and lung (LUSC; n = 130) squamous cell carcinoma data sets and two independent gene expression data sets (HNSC, n = 136; LUSC, n = 75), we examined associations between the mutational smoking signature, mutation count, immune cell infiltration, cytolytic activity, and interferon-γ signaling. Results An increasing mutational smoking signature was associated with statistically significantly increased overall mutational load in both HNSC (ρ = .33, P = 1.01 × 10-7) and LUSC (ρ = .49, P = 2.80 × 10-9). In HNSC, a higher mutational smoking signature was associated with lower levels of immune infiltration (ρ = -.37, P = 1.29 × 10-10), cytolytic activity (ρ = -.28, P = 4.07 × 10-6), and interferon-γ pathway signaling (ρ = .39, P = 3.20 × 10-11). In LUSC, these associations were reversed (ρ = .19, P = .03; ρ = .20, P = .02; and ρ = .18, P = .047, respectively). Differentially expressed genes between smoking-high and smoking-low tumors revealed broad tobacco-induced immunosuppression in HNSC, in contrast to a tumor-inflamed microenvironment in smokers with LUSC. Conclusions In squamous cell carcinomas, the genetic smoking signature is associated with higher mutational load, but variable effects on tumor immunity can occur, depending on anatomic site. In HNSC, smoking is predominantly immunosuppressive; in LUSC, more pro-inflammatory. Both tumor mutation load and immune microenvironment affect clinical response to immunotherapy. Thus, the mutational smoking signature is likely to have relevance for immunotherapeutic investigation in smoking-associated cancers.
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Affiliation(s)
- Alexis Desrichard
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diego Chowell
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ken-Wing Lee
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nadeem Riaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Richard J Wong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Timothy A Chan
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luc G T Morris
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
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Qi L, Zhang T, Yao Y, Zhuang J, Liu C, Liu R, Sun C. Identification of lncRNAs associated with lung squamous cell carcinoma prognosis in the competitive endogenous RNA network. PeerJ 2019; 7:e7727. [PMID: 31576252 PMCID: PMC6753923 DOI: 10.7717/peerj.7727] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/22/2019] [Indexed: 12/24/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) play a role in the formation, development, and prognosis of various cancers. Our study aimed to identify prognostic-related lncRNAs in lung squamous cell carcinoma (LUSC), which may provide new perspectives for individualized treatment of patients. Materials and Methods The RNA sequencing (lncRNA, microRNA (miRNA), mRNA) data and clinical information related to LUSC were obtained from The Cancer Genome Atlas (TCGA) database. Differentially expressed RNA sequences were used to construct the competitive endogenous RNA (ceRNA) network. In present study, we mainly used two prognostic verification methods, Cox analysis and survival analysis, to identify the prognostic relevance of specific lncRNAs and construct prognostic model of lncRNA. Results Datasets on 551 samples of lncRNA and mRNA and 523 miRNA samples were retrieved from the TCGA database. Analysis of the normal and LUSC samples identified 170 DElncRNAs, 331 DEmiRNAs, and 417 DEmRNAs differentially expressed RNAs. The ceRNA network contained 27 lncRNAs, 43 miRNAs, and 11 mRNAs. Furthermore, we identified seven specific lncRNAs (ERVH48-1, HCG9, SEC62-AS1, AC022148.1, LINC00460, C5orf17, LINC00261) as potential prognostic factors after correlation analysis, and five of the seven lncRNAs (AC022148.1, HCG9, LINC00460, C5orf17, LINC00261) constructed a prognostic model of LUSC. Conclusion In present study, we identified seven lncRNAs in the ceRNA network that are associated with potential prognosis in LUSC patients, and constructed a prognostic model of LUSC which can be used to assess the prognosis risk of clinical patients. Further biological experiments are needed to elucidate the specific molecular mechanisms underlying them.
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Affiliation(s)
- Lingyu Qi
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Tingting Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yan Yao
- Clinical Medical Colleges, Weifang Medical University, Weifang, China
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Cun Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Changgang Sun
- Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
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Chan H, Lee H, Yang X, Wang J, Yang X, Gan C, Xiao H, Li Q, Jiao J, Wu D, Zhang G, Wang M, Yang H, Li Q. Relationships between the clinical phenotypes and genetic variants associated with the immunological mechanism in childhood idiopathic nephrotic syndrome: protocol for a prospective observational single-centre cohort study. BMJ Open 2019; 9:e028717. [PMID: 31467050 PMCID: PMC6720149 DOI: 10.1136/bmjopen-2018-028717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION Idiopathic nephrotic syndrome (INS) is the most common glomerulopathy that results in childhood chronic kidney disease in China, but the relationships between different clinical phenotypes and immunological genetic variants observed in patients with INS are ambiguous and have not been well studied. A cohort study combined with whole exome sequencing might further identify the effects of immunological genetic variants on clinical phenotypes and treatment outcomes. METHODS AND ANALYSIS We describe a 3 year prospective observational single-centre cohort study to be conducted in the Children's Hospital of Chongqing Medical University in China. This study will recruit and investigate 336 patients with childhood-onset INS presenting with different clinical phenotypes. Whole exome sequencing will be conducted when patients progress to a confirmed clinical phenotype during follow-up. Relevant clinical and epidemiological data, as well as conventional specimens, will be collected at study entry and 1 month, 3 months, 6 months, 1 year, 2 years and 3 years after disease onset. After this cohort is generated, the immunological genetic variants of steroid-sensitive nephrotic syndrome without frequent relapse, steroid-resistant nephrotic syndrome and steroid-dependent/frequent relapse nephrotic syndrome will be evaluated. ETHICS AND DISSEMINATION The study protocol is approved by Ethics Committee of Children's Hospital of Chongqing Medical University (reference number 2018-140). The results will be disseminated through peer-reviewed journals and conference presentations. TRIAL REGISTRATION NUMBER ChiCTR1800019795.
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Affiliation(s)
- Han Chan
- Department of Nephrology, Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders (Chongqing); China International Science and Technology Cooperation base of Child development and Critical Disorders; Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Hao Lee
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Xia Yang
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Jingzhi Wang
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Xueying Yang
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Chun Gan
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Han Xiao
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Qianqian Li
- China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Jia Jiao
- Department of Nephrology, Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders (Chongqing); China International Science and Technology Cooperation base of Child development and Critical Disorders; Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Daoqi Wu
- Department of Nephrology, Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders (Chongqing); China International Science and Technology Cooperation base of Child development and Critical Disorders; Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Gaofu Zhang
- Department of Nephrology, Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders (Chongqing); China International Science and Technology Cooperation base of Child development and Critical Disorders; Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Mo Wang
- Department of Nephrology, Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders (Chongqing); China International Science and Technology Cooperation base of Child development and Critical Disorders; Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Haiping Yang
- Department of Nephrology, Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders (Chongqing); China International Science and Technology Cooperation base of Child development and Critical Disorders; Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Qiu Li
- Department of Nephrology, Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders (Chongqing); China International Science and Technology Cooperation base of Child development and Critical Disorders; Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Chongqing, China
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Han X, Tan Q, Yang S, Li J, Xu J, Hao X, Hu X, Xing P, Liu Y, Lin L, Gui L, Qin Y, Yang J, Liu P, Wang X, Dai W, Lin D, Lin H, Shi Y. Comprehensive Profiling of Gene Copy Number Alterations Predicts Patient Prognosis in Resected Stages I-III Lung Adenocarcinoma. Front Oncol 2019; 9:556. [PMID: 31448219 PMCID: PMC6691340 DOI: 10.3389/fonc.2019.00556] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/07/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Lung adenocarcinoma (LUAD) possesses a poor prognosis with a low 5-year survival rate even for stages I-III resected patients, it is thus critical to understand the determinants that affect the survival and discover new potentially prognostic biomarkers. Somatic copy number alterations (CNAs) are major source of genomic variations driving tumor evolution, CNAs screening may identify prognostic biomarkers. Methods: Oncoscan MIP array was used to analyze the patterns of CNAs on formalin fixed paraffin embedded(FFPE) tumor specimens from 163 consecutive stage I-III resected LUAD patients, 145 out of which received platinum-based adjuvant chemotherapy. Results: Of the 163 patients, 91(55.8%) were recurred within 3 years after surgery. The most common aberrations in our cohort were 1q, 5p, 5q, 7p, 8q, 14p, 16p, 17q, 20q for copy number gains and 8p, 9p, 13p, 16q, 18q for losses. The GISTIC2 analysis produced 45 amplification peaks and 40 deletion peaks, involving some reported genes TERT, EGFR, MYC, CCND1, CDK4, MDM2, ERBB2, NKX2-1, CCNE1, and CDKN2A, most of which were consistent with TCGA database. The amplifications of 12p12.1 (CMAS, GOLT1B, YS2, LDHB, RECQL, ETNK1, IAPP, PYROXD1, KRAS) and KDM5A were correlated with worse prognosis in our cohort, this result was further validated in 506 LUAD patients from TCGA. In addition, 163 patients could be well-classified into five groups, and the clinical outcomes were significantly different based on threshold copy number at reoccurring alteration peaks. Among the 145 patients who received adjuvant chemotherapy, focal amplification of ERBB2 and deletion of 4q34.3 were found to be specific in relapsed patients, this result was validated in an independent group of Imielinski et al., demonstrating these two CNAs may contribute to resected LUAD recurrence after adjuvant chemotherapy. Conclusion: This study suggests that CNAs profiling may be a potential prognostic classifier in resected LAUD patients. Amplifications of 12p12.1 and KDM5A might be prognostic biomarkers for LUAD, and amplification of ERBB2 and deletion of 4q34.3 predicted early relapse after adjuvant chemotherapy. These novel findings may provide implication for better implementation of precision therapy for lung cancer patients.
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Affiliation(s)
- Xiaohong Han
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qiaoyun Tan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Sheng Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Junling Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Jianping Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Xuezhi Hao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Xingsheng Hu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Puyuan Xing
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Yutao Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Lin Lin
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Lin Gui
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Yan Qin
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Jianliang Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Peng Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Xingyuan Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Wumin Dai
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Dongmei Lin
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hua Lin
- Department of Medical Record, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
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Jiang T, Shi J, Dong Z, Hou L, Zhao C, Li X, Mao B, Zhu W, Guo X, Zhang H, He J, Chen X, Su C, Ren S, Wu C, Zhou C. Genomic landscape and its correlations with tumor mutational burden, PD-L1 expression, and immune cells infiltration in Chinese lung squamous cell carcinoma. J Hematol Oncol 2019; 12:75. [PMID: 31299995 PMCID: PMC6625041 DOI: 10.1186/s13045-019-0762-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/25/2019] [Indexed: 12/16/2022] Open
Abstract
INTRODUCTION To depict the genomic landscape of Chinese early-stage lung squamous cell carcinoma (LUSC) and investigate its correlation with tumor mutation burden (TMB), PD-L1 expression, and immune infiltrates. METHODS Whole-exome sequencing was performed on 189 surgically resected LUSC. TMB was defined as the sum of nonsynonymous single nucleotide and indel variants. CD8+ tumor-infiltrating lymphocyte (TIL) density and PD-L1 expression were evaluated by immunohistochemistry. Six immune infiltrates were estimated using an online database. RESULTS The median TMB was 9.43 mutations per megabase. Positive PD-L1 expression and CD8+ TILs density were identified in 24.3% and 78.8%. PIK3CA amplification was associated with significantly higher TMB (P = 0.036). Frequent genetic alterations had no impact on PD-L1 expression but PIK3CA amplification and KEAP1 mutation were independently associated with significantly lower CD8+ TIL density (P < 0.001, P = 0.005, respectively). Low TMB and high CD8+ TIL density were independently associated with longer disease-free survival (DFS) while none of them could individually predict the overall survival (OS). Combination of TMB and PD-L1 expression or TMB and CD8+ TIL density could stratify total populations into two groups with distinct prognosis. Classifying tumor-immune microenvironment based on PD-L1 expression and CD8+ TIL density showed discrepant genomic alterations but similar TMB, clinical features, and OS. Notably, patients with different smoking status had distinct prognostic factors. CONCLUSION The combination of TMB, PD-L1 expression, immune infiltrates, and smoking status showed the feasibility to subgroup stratification in Chinese patients with early-stage LUSC, which might be helpful for future design of personalized immunotherapy trials in LUSC.
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Affiliation(s)
- Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Zheng Min Road, Shanghai, 200433, China
| | - Jinpeng Shi
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Zheng Min Road, Shanghai, 200433, China
| | - Zhengwei Dong
- Department of Pathology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Likun Hou
- Department of Pathology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China
| | - Chao Zhao
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507, Zheng Min Road, Shanghai, 200433, China
| | - Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, No. 507, Zheng Min Road, Shanghai, 200433, China
| | - Beibei Mao
- Beijing Genecast Biotechnology Co., Beijing, 100191, China
| | - Wei Zhu
- Beijing Genecast Biotechnology Co., Beijing, 100191, China
| | - Xianchao Guo
- Beijing Genecast Biotechnology Co., Beijing, 100191, China
| | - Henghui Zhang
- Beijing Genecast Biotechnology Co., Beijing, 100191, China
| | - Ji He
- Beijing Genecast Biotechnology Co., Beijing, 100191, China
| | - Xiaoxia Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Zheng Min Road, Shanghai, 200433, China
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Zheng Min Road, Shanghai, 200433, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Zheng Min Road, Shanghai, 200433, China
| | - Chunyan Wu
- Department of Pathology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, 200433, China.
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, Zheng Min Road, Shanghai, 200433, China.
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Owen DH, Williams TM, Bertino EM, Mo X, Webb A, Schweitzer C, Liu T, Roychowdhury S, Timmers CD, Otterson GA. Homologous recombination and DNA repair mutations in patients treated with carboplatin and nab-paclitaxel for metastatic non-small cell lung cancer. Lung Cancer 2019; 134:167-173. [PMID: 31319977 DOI: 10.1016/j.lungcan.2019.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Chemotherapy remains a cornerstone treatment in non-small cell lung cancer either in combination with checkpoint inhibitors or as subsequent therapy. Identifying molecular predictors of response allows for optimal treatment selection. We performed genomic analysis on tumor samples of patients treated with carboplatin and nab-paclitaxel as part of a phase II trial to evaluate the prognostic and predictive value of mutations in DNA repair pathway in patients treated with this regimen. MATERIALS AND METHODS Next-generation sequencing libraries were produced using a capture-based targeted panel covering the coding exons of 278 genes on patients treated on clinical trial NCT00729612. Overall survival (OS) and progression-free survival (PFS) were assessed as part of the clinical outcomes and correlated with mutation analysis. RESULTS Of 63 patients enrolled, 25 patients had sufficient and acceptable DNA isolated from archival tumor samples for targeted sequencing. The most commonly altered pathways included DNA repair (DR) including Fanconi anemia and homologous recombination, JAK-STAT signaling, IGF-1, mTOR, and MAPK-ERK. Four patients with mutations in homologous recombination mutations had a shorter PFS (hazard ratio [HR] = 4.54, 95% CI 1.2, 17.1, p = 0.026) and OS (HR = 6.3, 95% CI 1.8, 21.3, p = 0.003). CONCLUSION In this analysis of patients with predominantly squamous cell non-small cell lung cancer treated with carboplatin and nab-paclitaxel in a phase II trial, patients with mutations in homologous recombination pathways had shorter overall and progression-free survival. Validation on additional datasets of patients treated with platinum-based chemotherapy and immunotherapy combinations is warranted.
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Affiliation(s)
- Dwight H Owen
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States.
| | - Terence M Williams
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Erin M Bertino
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Xiaokui Mo
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, United States
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University Comprehensive Cancer Center, United States
| | - Catherine Schweitzer
- Clinical Trials Office, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Tom Liu
- The Ohio State University Comprehensive Cancer Center, United States
| | - Sameek Roychowdhury
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Cynthia D Timmers
- The Ohio State University Comprehensive Cancer Center, United States; Division of Hematology and Medical Oncology, Department of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Gregory A Otterson
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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Fagan RJ, Dingwall AK. COMPASS Ascending: Emerging clues regarding the roles of MLL3/KMT2C and MLL2/KMT2D proteins in cancer. Cancer Lett 2019; 458:56-65. [PMID: 31128216 DOI: 10.1016/j.canlet.2019.05.024] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/16/2019] [Accepted: 05/19/2019] [Indexed: 12/12/2022]
Abstract
The KMT2 (lysine methyltransferase) family of histone modifying proteins play essential roles in regulating developmental pathways, and mutations in the genes encoding these proteins have been strongly linked to many blood and solid tumor cancers. The KMT2A-D proteins are histone 3 lysine 4 (H3K4) methyltransferases embedded in large COMPASS-like complexes important for RNA Polymerase II-dependent transcription. KMT2 mutations were initially associated with pediatric Mixed Lineage Leukemias (MLL) and found to be the result of rearrangements of the MLL1/KMT2A gene at 11q23. Over the past several years, large-scale tumor DNA sequencing studies have revealed the potential involvement of other KMT2 family genes, including heterozygous somatic mutations in the paralogous MLL3/KMT2C and MLL2(4)/KMT2D genes that are now among the most frequently associated with human cancer. Recent studies have provided a better understanding of the potential roles of disrupted KMT2C and KMT2D family proteins in cell growth aberrancy. These findings, together with an examination of cancer genomics databases provide new insights into the contribution of KMT2C/D proteins in epigenetic gene regulation and links to carcinogenesis.
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Affiliation(s)
- Richard J Fagan
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60521, USA
| | - Andrew K Dingwall
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60521, USA; Department of Cancer Biology and Pathology & Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60521, USA.
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Song J, Tian J, Zhang L, Qu X, Qian W, Zheng B, Zhang L, Zhao J, Niu M, Zhou M, Cui L, Liu Y, Zhao M. Development and validation of a prognostic index for efficacy evaluation and prognosis of first-line chemotherapy in stage III-IV lung squamous cell carcinoma. Eur Radiol 2019; 29:2388-2398. [PMID: 30643941 PMCID: PMC6443600 DOI: 10.1007/s00330-018-5912-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 10/13/2018] [Accepted: 11/23/2018] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To establish a pre-therapy prognostic index model (PIM) of the first-line chemotherapy aiming to achieve accurate prediction of time to progression (TTP) and overall survival among the patients diagnosed with locally advanced (stage III) or distant metastasis (stage IV) lung squamous cell carcinoma (LSCC). METHODS Ninety-six LSCC patients treated with first-line chemotherapy were retrospectively enrolled to build the model. Fourteen epidermal growth factor receptor (EGFR)-mutant LSCC patients treated with first-line EGFR-tyrosine kinase inhibitor (TKI) therapy were enrolled for validation dataset. From CT images, 56,000 phenotype features were initially computed. PIM was constructed by integrating a CT phenotype signature selected by the least absolute shrinkage and selection operator and the significant blood-based biomarkers selected by multivariate Cox regression. PIM was then compared with other four prognostic models constructed by the CT phenotype signature, clinical factors, post-therapy tumor response, and Glasgow Prognostic Score. RESULTS The signature includes eight optimal features extracted from co-occurrence, run length, and Gabor features. By using PIM, chemotherapy efficacy of patients categorized in the low-risk, intermediate-risk, and high-risk progression subgroups (median TTP = 7.2 months, 3.4 months, and 1.8 months, respectively) was significantly different (p < 0.0001, log-rank test). Chemotherapy efficacy of the low-risk progression subgroup was comparable with EGFR-TKI therapy (p = 0.835, log-rank test). Prognostic prediction of chemotherapy efficacy by PIM was significantly higher than other models (p < 0.05, z test). CONCLUSION The study demonstrated that the PIM yielded significantly higher performance to identify individual stage III-IV LSCC patients who can potentially benefit most from first-line chemotherapy, and predict the risk of failure from chemotherapy for individual patients. KEY POINTS • TTP and OS of first-line chemotherapy in individual stage III-IV LSCC patients could be predicted by pre-therapy blood-based biomarkers and image-based signatures. • Risk status of pre-therapy indicators affected the efficacy of first-line chemotherapy in stage III-IV LSCC patients. • Those stage III-IV LSCC patients who were able to achieve similar efficacy to EGFR-TKI therapy through chemotherapy were identified.
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Affiliation(s)
- Jiangdian Song
- School of Medical Informatics, China Medical University, Shenyang, Liaoning, China
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Jie Tian
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Lina Zhang
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Xiujuan Qu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Wei Qian
- College of Engineering, University of Texas, El Paso, TX, USA
- Sino-Dutch Biomedical Engineering School, Northeastern University, Shenyang, Liaoning, China
| | - Bin Zheng
- Sino-Dutch Biomedical Engineering School, Northeastern University, Shenyang, Liaoning, China
- Medicine and Biological Information Engineering, University of Oklahoma, Norman, OK, USA
| | - Lina Zhang
- Department of Radiology, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jia Zhao
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Meng Niu
- Department interventional therapy, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Mu Zhou
- Artificial Intelligence in Medicine and Imaging (AIMI) Center, Department of Radiology, Stanford University, San Francisco, CA, USA
| | - Lei Cui
- School of Medical Informatics, China Medical University, Shenyang, Liaoning, China
| | - Yunpeng Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
| | - Mingfang Zhao
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China.
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Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11. Lung Cancer 2019; 130:50-58. [DOI: 10.1016/j.lungcan.2019.01.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/03/2019] [Accepted: 01/08/2019] [Indexed: 11/22/2022]
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Zhang P, Kang B, Xie G, Li S, Gu Y, Shen Y, Zhao X, Ma Y, Li F, Si J, Wang J, Chen J, Yang H, Xu X, Yang Y. Genomic sequencing and editing revealed the GRM8 signaling pathway as potential therapeutic targets of squamous cell lung cancer. Cancer Lett 2018; 442:53-67. [PMID: 30391781 DOI: 10.1016/j.canlet.2018.10.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/18/2018] [Accepted: 10/24/2018] [Indexed: 02/06/2023]
Abstract
The study sought to explore novel genetic aberration driving squamous cell lung carcinoma (LUSC). The whole exome (WES), whole genome (WGS) and target region (TS) sequencings and CRISPR-Cas9 genome editing techniques were integrated to explore and validate novel targeting candidates from LUSC primary tumors and corresponding patient-derived xenografts (PDXs). Seven genes (FGFR2, GRM1,PIK3CG, PIK3CA,ZFHX4, CSMD3, GRM8) with high frequencies of both single nucleotide variants (SNVs) and copy number variants (CNVs), and two genes (CLDN1 and RIT1) only with CNVs were identified by bioinformatics analysis. The functions of these candidates were validated through CRISPR-Cas9 system in primary PDX cells. Furthermore, we focused on the genetic and functional analysis of Metabotropic glutamate receptor 8 (GRM8), whose transcriptional activation was elucidated to promote the survival of LUSC tumor cell through inhibiting cAMP pathway and activating MAPK pathway. The SNV identified in GRM8, A112G, activated downstream signaling pathway and induced cell proliferation, which could be reversed by cAMP stimulator and MEK inhibitor. In conclusion, the components of GRM8 signaling pathway could serve as potential targets of squamous cell lung cancer carrying GRM8 activating variants.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cell Proliferation
- Cell Survival
- Clustered Regularly Interspaced Short Palindromic Repeats
- Cyclic AMP/metabolism
- Gene Editing/methods
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice, Inbred NOD
- Mice, SCID
- Mitogen-Activated Protein Kinases/metabolism
- Molecular Targeted Therapy
- Mutation
- Receptors, Metabotropic Glutamate/genetics
- Receptors, Metabotropic Glutamate/metabolism
- Signal Transduction
- Transcriptional Activation
- Tumor Burden
- Tumor Cells, Cultured
- Exome Sequencing
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Affiliation(s)
- Panpan Zhang
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education/Beijing, Peking University Cancer Hospital and Institute, Beijing, China
| | - Bin Kang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, Shenzhen, 518120, China
| | - Guoyun Xie
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Shaolei Li
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education/Beijing, Peking University Cancer Hospital and Institute, Beijing, China
| | - Ying Gu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, Shenzhen, 518120, China
| | - Yue Shen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, Shenzhen, 518120, China
| | - Xin Zhao
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Yuanyuan Ma
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education/Beijing, Peking University Cancer Hospital and Institute, Beijing, China
| | - Fuqiang Li
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Jiahui Si
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education/Beijing, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jian Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China
| | - Jinfeng Chen
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education/Beijing, Peking University Cancer Hospital and Institute, Beijing, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, Shenzhen, 518120, China
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, 518083, China; China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen, 518120, China; Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, Shenzhen, 518120, China.
| | - Yue Yang
- Department of Thoracic Surgery II, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education/Beijing, Peking University Cancer Hospital and Institute, Beijing, China.
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Identification of aberrantly expressed F-box proteins in squamous-cell lung carcinoma. J Cancer Res Clin Oncol 2018; 144:1509-1521. [PMID: 29728763 DOI: 10.1007/s00432-018-2653-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 04/26/2018] [Indexed: 12/25/2022]
Abstract
PURPOSE F-box proteins, as components of the Skp1-Cullin 1-F-box protein (SCF) E3 ubiquitin ligase, can specifically bind to substrates and regulate multiple tumor behaviors. However, the role of F-box proteins in squamous-cell lung carcinoma (SqCLC) has not been established. METHODS We identified the differentially expressed F-box protein-encoding genes in SqCLC by analyzing data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Prognosis data were evaluated using the Kaplan-Meier (KM) plotter website. The FBXO5 and FBXO45 mRNA levels were analyzed by real time RT-PCR. The impact of the inhibition of these genes with si-RNA on apoptosis and migration was also investigated. RESULTS The FBXO45 and FBXO5 genes were significantly up-regulated in SqCLC compared with normal lung (p values = 0.002 and 0.025, respectively). FBXO45 was significantly elevated in each tumorigenic step, including dysplasia, in situ and SqCLC. The RT-PCR analysis results showed that FBXO5 and FBXO45 were elevated in cancer tissues (p values = 0.024 and 0.004, respectively). Overexpression of FBXO5 and FBXO45 was associated with shorter overall survival (OS) in the SqCLC patients from the K-M plotter database [FBXO5 HR: 1.53 (1.03-2.28), p = 0.036]; [FBXO45 HR: 1.47 (1.03-2.08), p = 0.030]. The GO and KEGG pathway analysis showed that FBXO5 and FBXO45 were associated with cell cycle and adhesion, respectively. Knockdown of FBXO5 leads to increased apoptosis, while knockdown of FBXO45 facilitates the process of epithelial-mesenchymal transition (EMT). CONCLUSIONS Our results provide evidence that FBXO45 and FBXO5 may play a key role in tumorigenesis and prognosis of SqCLC.
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Parra ER, Villalobos P, Zhang J, Behrens C, Mino B, Swisher S, Sepesi B, Weissferdt A, Kalhor N, Heymach JV, Moran C, Zhang J, Lee J, Rodriguez-Canales J, Gibbons D, Wistuba II. Immunohistochemical and Image Analysis-Based Study Shows That Several Immune Checkpoints are Co-expressed in Non-Small Cell Lung Carcinoma Tumors. J Thorac Oncol 2018. [PMID: 29526824 DOI: 10.1016/j.jtho.2018.03.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION The understanding of immune checkpoint molecules' co-expression in non-small cell lung carcinoma (NCLC) is important to potentially design combinatorial immunotherapy approaches. METHODS We studied 225 formalin-fixed, paraffin-embedded tumor tissues from stage I-III NCLCs - 142 adenocarcinomas (ADCs) and 83 squamous cell carcinomas (SCCs) - placed in tissue microarrays. Nine immune checkpoint markers were evaluated; four (programmed death ligand 1 [PD-L1], B7-H3, B7-H4, and indoleamine 2,3-dioxygenase 1 [IDO-1]) expressed predominantly in malignant cells (MCs) and five (inducible T cell costimulator, V-set immunoregulatory receptor, T-cell immunoglobulin mucin family member 3, lymphocyte activating 3, and OX40) expressed mostly in stromal tumor-associated inflammatory cells (TAICs). All markers were examined using a quantitative image analysis and correlated with clinicopathologic features, TAICs, and molecular characteristics. RESULTS Using above the median value as positive expression in MCs and high density of TAICs expressing those markers, we identified higher expression of immune checkpoints in SCC than ADC. Common simultaneous expression by MCs was PD-L1 + B7-H3 + IDO-1 in ADC and PD-L1 + B7-H3, or B7-H3 + B7-H4, in SCC. TAICs expressing checkpoint were significantly higher in current smokers than in never smokers. Almost all the immune checkpoint markers showed positive correlation with TAICs expressing inflammatory cell markers. KRAS-mutant ADC specimens showed higher expression of PD-L1 in MCs and of B7-H3, T-cell immunoglobulin mucin family member 3, and IDO-1 in TAICs than wild type. Kaplan-Meier survival curves showed worse prognosis in ADC patients with higher B7-H4 expression by MCs. CONCLUSIONS We found frequent immunohistochemical co-expression of immune checkpoints in surgically resected NCLC tumors and correlated with tumor histology, smoking history, tumor size, and the density of inflammatory cells and tumor mutational status.
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Affiliation(s)
- Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pamela Villalobos
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Annika Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Victor Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cesar Moran
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jack Lee
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Deshpande A, Lang W, McDowell T, Sivakumar S, Zhang J, Wang J, San Lucas FA, Fowler J, Kadara H, Scheet P. Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform. BMC Bioinformatics 2018; 19:5. [PMID: 29301485 PMCID: PMC5753459 DOI: 10.1186/s12859-017-1991-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 12/06/2017] [Indexed: 01/10/2023] Open
Abstract
Background ‘Next-generation’ (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in clinical, research and diagnostic settings. However, identifying mutations from IONT deep sequencing with high confidence has remained a challenge. We compared various computational variant-calling methods to derive a variant identification pipeline that may improve the molecular diagnostic and research utility of IONT. Results Using IONT, we surveyed variants from the 409-gene Comprehensive Cancer Panel in whole-section tumors, intra-tumoral biopsies and matched normal samples obtained from frozen tissues and blood from four early-stage non-small cell lung cancer (NSCLC) patients. We used MuTect, Varscan2, IONT’s proprietary Ion Reporter, and a simple subtraction we called “Poor Man’s Caller.” Together these produced calls at 637 loci across all samples. Visual validation of 434 called variants was performed, and performance of the methods assessed individually and in combination. Of the subset of inspected putative variant calls (n=223) in genomic regions that were not intronic or intergenic, 68 variants (30%) were deemed valid after visual inspection. Among the individual methods, the Ion Reporter method offered perhaps the most reasonable tradeoffs. Ion Reporter captured 83% of all discovered variants; 50% of its variants were visually validated. Aggregating results from multiple packages offered varied improvements in performance. Conclusions Overall, Ion Reporter offered the most attractive performance among the individual callers. This study suggests combined strategies to maximize sensitivity and positive predictive value in variant calling using IONT deep sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1991-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aditya Deshpande
- Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,University of Texas School of Public Health, Houston, TX, USA
| | - Wenhua Lang
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tina McDowell
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Smruthy Sivakumar
- Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Jiexin Zhang
- Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - F Anthony San Lucas
- Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jerry Fowler
- Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Humam Kadara
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
| | - Paul Scheet
- Departments of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,University of Texas School of Public Health, Houston, TX, USA. .,University of Texas Graduate School of Biomedical Sciences, Houston, TX, USA.
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Xiong D, Pan J, Yin Y, Jiang H, Szabo E, Lubet RA, Wang Y, You M. Novel mutational landscapes and expression signatures of lung squamous cell carcinoma. Oncotarget 2017; 9:7424-7441. [PMID: 29484121 PMCID: PMC5800913 DOI: 10.18632/oncotarget.23716] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 11/26/2017] [Indexed: 12/15/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is a major subtype of Non-Small Cell Lung Cancer. To increase our understanding of the LUSC pathobiology, we performed exome sequencing and RNA-seq in 16 murine carcinogen-induced LUSC tumors and 8 normal murine lung tissue samples. Additionally, we conducted single-cell RNA-seq on two independent tumors from the same murine model. We identified a list of 59 cancer genes recurrently mutated in the mice LUSC tumors, 47 (80%) of which were also mutated in human LUSCs. At the single cell level, we detected unique clonal mutation patterns for each of the two LUSC tumors, being initiated from clones carrying the mutant Igfbp7 and Trp53 genes, respectively. We also identified an expression signature serving as an effective classifier for LUSC tumors and a strong predictor of survival outcomes of lung cancer patients. Lastly, we found that some of the mutant LUSC genes were associated with the significantly altered tumoral expression of inhibitory immune checkpoint genes such as PD-L1, VISTA, TIM3 and LAG3 in human LUSCs. The novel findings of clonal evolution, mutational landscapes and expression signatures of LUSC suggested new targets for the overall LUSC therapy and the immunotherapy of LUSC.
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Affiliation(s)
- Donghai Xiong
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jing Pan
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yuxin Yin
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hui Jiang
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Eva Szabo
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
| | - Ronald A Lubet
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, USA
| | - Yian Wang
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ming You
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.,Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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79
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Conde E, Caminoa A, Dominguez C, Calles A, Walter S, Angulo B, Sánchez E, Alonso M, Jimenez L, Madrigal L, Hernando F, Sanz-Ortega J, Jimenez B, Garrido P, Paz-Ares L, de Castro J, Hernandez S, Lopez-Rios F. Aligning digital CD8+scoring and targeted next-generation sequencing with programmed death ligand 1 expression: a pragmatic approach in early-stage squamous cell lung carcinoma. Histopathology 2017; 72:270-284. [DOI: 10.1111/his.13346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/16/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Esther Conde
- Pathology-Laboratorio de Dianas Terapeuticas; Hospital Universitario HM Sanchinarro; Universidad CEU San Pablo; Madrid Spain
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC); Madrid Spain
| | - Alejandra Caminoa
- Pathology-Laboratorio de Dianas Terapeuticas; Hospital Universitario HM Sanchinarro; Universidad CEU San Pablo; Madrid Spain
| | - Carolina Dominguez
- Pathology-Laboratorio de Dianas Terapeuticas; Hospital Universitario HM Sanchinarro; Universidad CEU San Pablo; Madrid Spain
| | - Antonio Calles
- Medical Oncology; Hospital Universitario Gregorio Marañón; Madrid Spain
| | - Stefan Walter
- Fundación de Investigación Sanitaria de Getafe; Madrid Spain
- University of California San Francisco; San Francisco CA USA
| | - Barbara Angulo
- Pathology-Laboratorio de Dianas Terapeuticas; Hospital Universitario HM Sanchinarro; Universidad CEU San Pablo; Madrid Spain
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC); Madrid Spain
| | - Elena Sánchez
- Pathology-Laboratorio de Dianas Terapeuticas; Hospital Universitario HM Sanchinarro; Universidad CEU San Pablo; Madrid Spain
| | - Marta Alonso
- Pathology-Laboratorio de Dianas Terapeuticas; Hospital Universitario HM Sanchinarro; Universidad CEU San Pablo; Madrid Spain
| | - Luis Jimenez
- Thoracic Surgery; Hospital Universitario HM Sanchinarro; Madrid Spain
| | - Luis Madrigal
- Thoracic Surgery; Hospital Universitario HM Sanchinarro; Madrid Spain
| | - Florentino Hernando
- Thoracic Surgery; Hospital Clínico San Carlos; Universidad Complutense; Madrid Spain
| | - Julian Sanz-Ortega
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC); Madrid Spain
- Pathology; Hospital Clínico San Carlos; Universidad Complutense; Madrid Spain
| | - Beatriz Jimenez
- Medical Oncology; Hospital Universitario HM Sanchinarro; Madrid Spain
| | - Pilar Garrido
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC); Madrid Spain
- Medical Oncology, IRYCIS; Hospital Universitario Ramón y Cajal; Universidad de Alcalá; Madrid Spain
| | - Luis Paz-Ares
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC); Madrid Spain
- Medical Oncology; Hospital Universitario 12 de Octubre; CNIO and Universidad Complutense; Madrid Spain
| | - Javier de Castro
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC); Madrid Spain
- Medical Oncology; Hospital Universitario HM Sanchinarro; Madrid Spain
| | - Susana Hernandez
- Pathology-Laboratorio de Dianas Terapeuticas; Hospital Universitario HM Sanchinarro; Universidad CEU San Pablo; Madrid Spain
| | - Fernando Lopez-Rios
- Pathology-Laboratorio de Dianas Terapeuticas; Hospital Universitario HM Sanchinarro; Universidad CEU San Pablo; Madrid Spain
- Centro de Investigación Biomedica en Red de Cancer (CIBERONC); Madrid Spain
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80
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Musolf AM, Simpson CL, de Andrade M, Mandal D, Gaba C, Yang P, Li Y, You M, Kupert EY, Anderson MW, Schwartz AG, Pinney SM, Amos CI, Bailey-Wilson JE. Parametric Linkage Analysis Identifies Five Novel Genome-Wide Significant Loci for Familial Lung Cancer. Hum Hered 2017; 82:64-74. [PMID: 28817824 DOI: 10.1159/000479028] [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: 01/20/2017] [Accepted: 06/28/2017] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE One of four American cancer patients dies of lung cancer. Environmental factors such as tobacco smoking are known to affect lung cancer risk. However, there is a genetic factor to lung cancer risk as well. Here, we perform parametric linkage analysis on family-based genotype data in an effort to find genetic loci linked to the disease. METHODS 197 individuals from families with a high-risk history of lung cancer were recruited and genotyped using an Illumina array. Parametric linkage analyses were performed using an affected-only phenotype model with an autosomal dominant inheritance using a disease allele frequency of 0.01. Three types of analyses were performed: single variant two-point, collapsed haplotype pattern variant two-point, and multipoint analysis. RESULTS Five novel genome-wide significant loci were identified at 18p11.23, 2p22.2, 14q13.1, 16p13, and 20q13.11. The families most informative for linkage were also determined. CONCLUSIONS The 5 novel signals are good candidate regions, containing genes that have been implicated as having somatic changes in lung cancer or other cancers (though not in germ line cells). Targeted sequencing on the significant loci is planned to determine the causal variants at these loci.
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Affiliation(s)
- Anthony M Musolf
- National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA
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81
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Paik PK, Hellmann MD. 'Genotype/immunotype' correlations in resected NSCLC. Ann Oncol 2017; 28:7-8. [PMID: 28039156 DOI: 10.1093/annonc/mdw624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- P K Paik
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York
- Weill Cornell Medical College, New York, USA
| | - M D Hellmann
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York
- Weill Cornell Medical College, New York, USA
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