51
|
Thorenoor N, Kawasawa YI, Gandhi CK, Floros J. Sex-Specific Regulation of Gene Expression Networks by Surfactant Protein A (SP-A) Variants in Alveolar Macrophages in Response to Klebsiella pneumoniae. Front Immunol 2020; 11:1290. [PMID: 32670284 PMCID: PMC7326812 DOI: 10.3389/fimmu.2020.01290] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/21/2020] [Indexed: 01/01/2023] Open
Abstract
Surfactant protein A (SP-A) in addition to its surfactant-related functions interacts with alveolar macrophages (AM), the guardian cells of innate immunity in the lungs, and regulates many of its functions under basal condition and in response to various pressures, such as infection and oxidative stress. The human SP-A locus consists of two functional genes, SFTPA1 and SFTPA2, and one pseudogene. The functional genes encode human SP-A1 and SP-A2 proteins, respectively, and each has been identified with several genetic variants. SP-A variants differ in their ability to regulate lung function mechanics and survival in response to bacterial infection. Here, we investigated the effect of hSP-A variants on the AM gene expression profile in response to Klebsiella pneumoniae infection. We used four humanized transgenic (hTG) mice that each carried SP-A1 (6A2, 6A4) or SP-A2 (1A0, 1A3), and KO. AM gene expression profiling was performed after 6 h post-infection. We found: (a) significant sex differences in the expression of AM genes; (b) in response to infection, 858 (KO), 196 (6A2), 494 (6A4), 276 (1A0), and 397 (1A3) genes were identified (P < 0.05) and some of these were differentially expressed with ≥2 fold, specific to either males or females; (c) significant SP-A1 and SP-A2 variant-specific differences in AM gene expression; (d) via Ingenuity Pathway Analysis (IPA), key pathways and molecules were identified that had direct interaction with TP53, TNF, and cell cycle signaling nodes; (e) of the three pathways (TNF, TP-53, and cell cycle signaling nodes) studied here, all variants except SP-A2 (1A3) female, showed significance for at least 2 of these pathways, and KO male showed significance for all three pathways; (f) validation of key molecules exhibited variant-specific significant differences in the expression between sexes and a similarity in gene expression profile was observed between KO and SP-A1. These results reveal for the first time a large number of biologically relevant functional pathways influenced in a sex-specific manner by SP-A variants in response to infection. These data may assist in studying molecular mechanisms of SP-A-mediated AM gene regulation and potentially identify novel therapeutic targets for K. pneumoniae infection.
Collapse
Affiliation(s)
- Nithyananda Thorenoor
- Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, United States.,Biochemistry & Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Yuka Imamura Kawasawa
- Pharmacology & Biochemistry & Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Chintan K Gandhi
- Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Joanna Floros
- Center for Host Defense, Inflammation, and Lung Disease (CHILD) Research, Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, United States.,Obstetrics & Gynecology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| |
Collapse
|
52
|
Lee TY, Huang KY, Chuang CH, Lee CY, Chang TH. Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication. Comput Biol Chem 2020; 87:107277. [PMID: 32512487 DOI: 10.1016/j.compbiolchem.2020.107277] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/30/2020] [Indexed: 12/25/2022]
Abstract
Lung cancer is the most occurring cancer type, and its mortality rate is also the highest, among them lung adenocarcinoma (LUAD) accounts for about 40 % of lung cancer. There is an urgent need to develop a prognosis prediction model for lung adenocarcinoma. Previous LUAD prognosis studies only took single-omics data, such as mRNA or miRNA, into consideration. To this end, we proposed a deep learning-based autoencoding approach for combination of four-omics data, mRNA, miRNA, DNA methylation and copy number variations, to construct an autoencoder model, which learned representative features to differentiate the two optimal patient subgroups with a significant difference in survival (P = 4.08e-09) and good consistency index (C-index = 0.65). The multi-omics model was validated though four independent datasets, i.e. GSE81089 for mRNA (n = 198, P = 0.0083), GSE63805 for miRNA (n = 32, P = 0.018), GSE63384 for DNA methylation (n = 35, P = 0.009), and TCGA independent samples for copy number variations (n = 94, P = 0.0052). Finally, a functional analysis was performed on two survival subgroups to discover genes involved in biological processes and pathways. This is the first study incorporating deep autoencoding and four-omics data to construct a robust survival prediction model, and results show the approach is useful at predicting LUAD prognostication.
Collapse
Affiliation(s)
- Tzong-Yi Lee
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China; School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen, China; School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China.
| | - Kai-Yao Huang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, China; School of Life and Health Science, The Chinese University of Hong Kong, Shenzhen, China; School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, China.
| | - Cheng-Hsiang Chuang
- Department of Computer Science and Engineering, Yuan Ze University, Taoyuan 320, Taiwan.
| | - Cheng-Yang Lee
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei City, Taiwan.
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei City, Taiwan; Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei City, Taiwan.
| |
Collapse
|
53
|
Canale M, Petracci E, Delmonte A, Bronte G, Chiadini E, Ludovini V, Dubini A, Papi M, Baglivo S, De Luigi N, Verlicchi A, Chiari R, Landi L, Metro G, Burgio MA, Crinò L, Ulivi P. Concomitant TP53 Mutation Confers Worse Prognosis in EGFR-Mutated Non-Small Cell Lung Cancer Patients Treated with TKIs. J Clin Med 2020; 9:E1047. [PMID: 32272775 PMCID: PMC7230306 DOI: 10.3390/jcm9041047] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is the primary cause of cancer-related deaths worldwide. Epidermal Growth Factor Receptor (EGFR)-mutated patients usually benefit from TKIs treatment, but a significant portion show unresponsiveness due to primary resistance mechanisms. We investigated the role of TP53 mutations in predicting survival and response to EGFR-TKIs in EGFR-mutated NSCLC patients, to confirm, on an independent case series, our previous results. METHODS An independent retrospective cohort study was conducted, on a case series of 136 EGFR-mutated NSCLC patients receiving first or second generation TKIs as a first line therapy, and a smaller fraction of patients who acquired the T790M resistance mutation and were treated with third generation TKIs in the second or further line of treatment. TP53 mutations were evaluated in relation to disease control rate (DCR), objective response rate (ORR), progression-free survival (PFS) and overall survival (OS) of the patients. RESULTS Forty-two patients (30.9%) showed a TP53 mutation. Considered together, TP53 mutations had no significant impact on time-to-event endpoints. Considering the different TP53 mutations separately, exon 8 mutations confirmed their negative effect on PFS (HR 3.16, 95% 1.59-6.28, p = 0.001). In patients who developed the T790M resistance mutation, treated with third generation TKIs, the TP53 exon 8 mutations predicted worse PFS (even though not statistically significant), and OS (HR 4.86, 95% CI: 1.25-18.90, p = 0.023). CONCLUSIONS TP53 exon 8 mutations confirmed their negative prognostic impact in patients treated with first and second generation TKIs and demonstrated a role in affecting clinical outcome in patients treated with third generation TKIs.
Collapse
Affiliation(s)
- Matteo Canale
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (M.C.); (E.C.)
| | - Elisabetta Petracci
- Biostatistics and Clinical Trials Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy;
| | - Angelo Delmonte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (A.D.); (G.B.); (A.V.); (M.A.B.); (L.C.)
| | - Giuseppe Bronte
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (A.D.); (G.B.); (A.V.); (M.A.B.); (L.C.)
| | - Elisa Chiadini
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (M.C.); (E.C.)
| | - Vienna Ludovini
- Department of Medical Oncology, Santa Maria della Misericordia Hospital, 06129 Perugia, Italy; (V.L.); (S.B.); (G.M.)
| | - Alessandra Dubini
- Department of Pathology, Morgagni-Pierantoni Hospital, 47121 Forlì, Italy;
| | - Maximilian Papi
- Department of Medical Oncology, Per gli Infermi Hospital, Rimini 47923, Italy;
| | - Sara Baglivo
- Department of Medical Oncology, Santa Maria della Misericordia Hospital, 06129 Perugia, Italy; (V.L.); (S.B.); (G.M.)
| | - Nicoletta De Luigi
- UOS Oncology, Istituto per la Sicurezza Sociale, State Hospital, Cailungo 47893, San Marino, Italy;
| | - Alberto Verlicchi
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (A.D.); (G.B.); (A.V.); (M.A.B.); (L.C.)
| | - Rita Chiari
- Department of Medical Oncology, Ospedali Riuniti Padova Sud “M. Teresa di Calcutta”, ULSS6 Euganea, 35131 Padova, Italy;
| | - Lorenza Landi
- Department of Medical Oncology, S. Maria delle Croci Hospital, 48121 Ravenna, Italy;
| | - Giulio Metro
- Department of Medical Oncology, Santa Maria della Misericordia Hospital, 06129 Perugia, Italy; (V.L.); (S.B.); (G.M.)
| | - Marco Angelo Burgio
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (A.D.); (G.B.); (A.V.); (M.A.B.); (L.C.)
| | - Lucio Crinò
- Department of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (A.D.); (G.B.); (A.V.); (M.A.B.); (L.C.)
| | - Paola Ulivi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, 47014 Meldola, Italy; (M.C.); (E.C.)
| |
Collapse
|
54
|
Oduah EI, Grossman SR. Harnessing the vulnerabilities of p53 mutants in lung cancer - Focusing on the proteasome: a new trick for an old foe? Cancer Biol Ther 2020; 21:293-302. [PMID: 32041464 PMCID: PMC7515531 DOI: 10.1080/15384047.2019.1702403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 11/02/2019] [Accepted: 12/01/2019] [Indexed: 12/25/2022] Open
Abstract
Gain-of-function (GOF) p53 mutations occur commonly in human cancer and lead to both loss of p53 tumor suppressor function and acquisition of aggressive cancer phenotypes. The oncogenicity of GOF mutant p53 is highly related to its abnormal protein stability relative to wild type p53, and overall stoichiometric excess. We provide an overview of the mechanisms of dysfunction and abnormal stability of GOF p53 specifically in lung cancer, the leading cause of cancer-related mortality, where, depending on histologic subtype, 33-90% of tumors exhibit GOF p53 mutations. As a distinguishing feature and oncogenic mechanism in lung and many other cancers, GOF p53 represents an appealing and cancer-specific therapeutic target. We review preclinical evidence demonstrating paradoxical depletion of GOF p53 by proteasome inhibitors, as well as preclinical and clinical studies of proteasome inhibition in lung cancer. Finally, we provide a rationale for a reexamination of proteasome inhibition in lung cancer, focusing on tumors expressing GOF p53 alleles.
Collapse
Affiliation(s)
- Eziafa I. Oduah
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Steven R. Grossman
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| |
Collapse
|
55
|
TP53 co-mutations in EGFR mutated patients in NSCLC stage IV: A strong predictive factor of ORR, PFS and OS in EGFR mt+ NSCLC. Oncotarget 2020; 11:250-264. [PMID: 32076486 PMCID: PMC6980625 DOI: 10.18632/oncotarget.27430] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/16/2019] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION The impact of TP53 co-mutations in EGFR mutated patients on PFS and OS is controversial. Different classifications of TP53 mutations with respect to functional and potential clinical impact have been published. Therefore, we retrospectively analyzed the impact of TP53 co-mutations on ORR, PFS and OS in a cohort of EGFR mutated NSCLC IV patients (UICC 7) using different classifications of TP53 mutations. METHODS 75 EGFR mutated NSCLC IV patients homogeneously treated with 1st line EGFR TKI were analyzed for TP53 co-mutations. TP53 mutations were classified according to three different types of classifications. The endpoints ORR, PFS and OS were investigated. RESULTS TP53 co-mutations were found in 29/59 patients (49.2%). TP53 co-mutations were a statistically significant independent negative predictive factor for ORR, PFS and OS. TP53 co-mutations were associated with inferior mPFS and mOS: mPFS/mOS 12 vs. 18/24 vs. 42 months for non-disruptive/disruptive mutations vs. WT (p < 0.004)/(p < 0.009), 11 vs. 17/23 vs. 42 months for pathogenic vs. non-pathogenic/WT (p < 0.001)/(p < 0.001), and 7 vs. 12 vs. 18/12 vs. 28 vs. 42 months for exon 8 vs. non-exon 8 vs. WT (p < 0.001)/(p < 0.002). CONCLUSIONS TP53 co-mutations are frequent in EGFR mt+ NSCLC and have a strong negative impact on all clinical endpoints of TKI therapy.
Collapse
|
56
|
Löfling L, Karimi A, Sandin F, Bahmanyar S, Kieler H, Lambe M, Lamberg K, Wagenius G. Clinical characteristics and survival in non-small cell lung cancer patients by smoking history: a population-based cohort study. Acta Oncol 2019; 58:1618-1627. [PMID: 31373239 DOI: 10.1080/0284186x.2019.1638521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Introduction: Approximately, 10-15% of lung cancer patients have never smoked. Previous epidemiological studies on non-tobacco associated lung cancer have been hampered by selected data from a small number of hospitals or limited numbers of patients. By use of data from large population-based registers with national coverage, this study aims to compare characteristics and survival of patients with non-small cell lung cancer (NSCLC) with different smoking histories.Methods: Swedish national population-based registers were used to retrieve data on patients diagnosed with primary NSCLC between 2002 and 2016. The Kaplan-Meier method and Cox proportional hazard models were used to estimate overall survival and lung cancer-specific survival by smoking history.Results: In total, 41,262 patients with NSCLC were included. Of those, 4624 (11%) had never smoked. Never-smokers were more often women and older compared to ever smokers (current and former). Adenocarcinoma was proportionally more common in never-smokers (77%) compared to current (52%) and former smokers (57%). Stage IV disease was more common in never-smokers (57%) than in current (48%) and former smokers (48%). Epidermal growth factor receptor mutation was observed more in never-smokers (37%) compared to current (5%) and former smokers (9%). Both lung cancer-specific and overall survival were higher for never-smokers compared to current smokers.Conclusions: The observed differences in characteristics between never-smokers and smokers, and the higher survival in never-smokers compared to smokers from this large population-based study provide further evidence that lung cancer in never-smokers is clinically different to tobacco-associated lung cancer. The findings from this study emphasise the need for an improved understanding of genetics, pathogenesis, mechanisms and progression of non-tobacco associated lung cancer that may help prevent lung cancer or identify individually targeted treatments.
Collapse
Affiliation(s)
- Lukas Löfling
- Department of Medicine – Solna, Centre for Pharmacoepidemiology, Karolinska Institutet, T2 Karolinska University Hospital, Solna, Sweden
| | - Annette Karimi
- Department of Medical Science, Uppsala University Hospital, Uppsala, Sweden
| | | | - Shahram Bahmanyar
- Department of Medicine – Solna, Centre for Pharmacoepidemiology, Karolinska Institutet, T2 Karolinska University Hospital, Solna, Sweden
| | - Helle Kieler
- Department of Medicine – Solna, Centre for Pharmacoepidemiology, Karolinska Institutet, T2 Karolinska University Hospital, Solna, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Mats Lambe
- Regional Cancer Centre, Uppsala-Örebro, Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, Sweden
| | - Kristina Lamberg
- Department of Medical Science, Uppsala University Hospital, Uppsala, Sweden
| | - Gunnar Wagenius
- Department of Oncology, Karolinska University Hospital, Solna, Sweden
| |
Collapse
|
57
|
Kim M, Chung YS, Kim KA, Shim HS. Prognostic factors of acinar- or papillary-predominant adenocarcinoma of the lung. Lung Cancer 2019; 137:129-135. [DOI: 10.1016/j.lungcan.2019.09.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/07/2019] [Accepted: 09/28/2019] [Indexed: 10/25/2022]
|
58
|
Simarro J, Murria R, Pérez-Simó G, Llop M, Mancheño N, Ramos D, Juan ID, Barragán E, Laiz B, Cases E, Ansótegui E, Gómez-Codina J, Aparicio J, Salvador C, Juan Ó, Palanca S. Development, Implementation and Assessment of Molecular Diagnostics by Next Generation Sequencing in Personalized Treatment of Cancer: Experience of a Public Reference Healthcare Hospital. Cancers (Basel) 2019; 11:E1196. [PMID: 31426418 PMCID: PMC6721584 DOI: 10.3390/cancers11081196] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/12/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
The establishment of precision medicine in cancer patients requires the study of several biomarkers. Single-gene testing approaches are limited by sample availability and turnaround time. Next generation sequencing (NGS) provides an alternative for detecting genetic alterations in several genes with low sample requirements. Here we show the implementation to routine diagnostics of a NGS assay under International Organization for Standardization (UNE-EN ISO 15189:2013) accreditation. For this purpose, 106 non-small cell lung cancer (NSCLC) and 102 metastatic colorectal cancer (mCRC) specimens were selected for NGS analysis with Oncomine Solid Tumor (ThermoFisher). In NSCLC the most prevalently mutated gene was TP53 (49%), followed by KRAS (31%) and EGFR (13%); in mCRC, TP53 (50%), KRAS (48%) and PIK3CA (16%) were the most frequently mutated genes. Moreover, NGS identified actionable genetic alterations in 58% of NSCLC patients, and 49% of mCRC patients did not harbor primary resistance mechanisms to anti-EGFR treatment. Validation with conventional approaches showed an overall agreement >90%. Turnaround time and cost analysis revealed that NGS implementation is feasible in the public healthcare context. Therefore, NGS is a multiplexed molecular diagnostic tool able to overcome the limitations of current molecular diagnosis in advanced cancer, allowing an improved and economically sustainable molecular profiling.
Collapse
Affiliation(s)
- Javier Simarro
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Rosa Murria
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Gema Pérez-Simó
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Marta Llop
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Nuria Mancheño
- Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - David Ramos
- Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Inmaculada de Juan
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Eva Barragán
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Begoña Laiz
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Enrique Cases
- Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Emilio Ansótegui
- Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - José Gómez-Codina
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Jorge Aparicio
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Carmen Salvador
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Óscar Juan
- Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain
| | - Sarai Palanca
- Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain.
- Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain.
| |
Collapse
|
59
|
Liu Y, Xu F, Wang Y, Wu Q, Wang B, Yao Y, Zhang Y, Han-Zhang H, Ye J, Zhang L, Mao X, Zhang Z, Liu J, Zhu L, Guo R. Mutations in exon 8 of TP53 are associated with shorter survival in patients with advanced lung cancer. Oncol Lett 2019; 18:3159-3169. [PMID: 31452792 PMCID: PMC6676404 DOI: 10.3892/ol.2019.10625] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/05/2019] [Indexed: 12/26/2022] Open
Abstract
Currently, in clinical settings, all TP53 mutations have been considered equally. However, numerous studies have demonstrated that the position and type of mutation have differential effects on prognosis. Such discrepancy can be partially due to the lack of unifying classification system for TP53 mutations. In the present study, two of the most frequently used systems were compared, according to the location of the mutation or its functional effects on p53 protein and the impact of TP53 mutations on the overall survival (OS) time of 379 Chinese patients with advanced lung cancer was analyzed. Capture-based ultra-deep targeted sequencing on plasma samples of 379 patients with advanced lung cancer was performed. The present results suggested that mutations occurring in exon 8 may be associated with shorter OS in tyrosine kinase inhibitor-naïve patients (P=0.013) and in patients previously treated with one line of treatment (P=0.032). The results of the present study provided solid evidence that not all TP53 mutations were associated with a similar prognosis. Mutations in exon 8 were found in a subgroup of patients with unfavorable prognosis across various treatment histories. To the best of our knowledge, the present study is the first to compare different TP53 mutation classification systems in a large cohort of patients with advanced lung cancer.
Collapse
Affiliation(s)
- Yutao Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Fang Xu
- Department of Thoracic Medicine, Hunan Cancer Center and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410006, P.R. China
| | - Yubo Wang
- Department of Respiratory Medicine, Daping Hospital, Third Military Medical University, Chongqing 400042, P.R. China
| | - Qingchen Wu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, P.R. China
| | - Buhai Wang
- Department of Medical Oncology, Subei People's Hospital of Jiangsu Province, Yangzhou, Jiangsu 225001, P.R. China
| | - Yanwen Yao
- Department of Respiratory Medicine, Nanjing General Hospital of Nanjing Military Area Command, Nanjing, Jiangsu 210002, P.R. China
| | - Yu Zhang
- Department of Respiratory Medicine, Nanjing Chest Hospital, Medical School of Southeast University, Nanjing, Jiangsu 210029, P.R. China
| | - Han Han-Zhang
- Burning Rock Biotech, Guangzhou, Guangdong 510300, P.R. China
| | - Junyi Ye
- Burning Rock Biotech, Guangzhou, Guangdong 510300, P.R. China
| | - Lu Zhang
- Burning Rock Biotech, Guangzhou, Guangdong 510300, P.R. China
| | - Xinru Mao
- Burning Rock Biotech, Guangzhou, Guangdong 510300, P.R. China
| | - Zhe Zhang
- Burning Rock Biotech, Guangzhou, Guangdong 510300, P.R. China
| | - Jing Liu
- Burning Rock Biotech, Guangzhou, Guangdong 510300, P.R. China
| | - Liangjun Zhu
- Department of Internal Medicine, Jiangsu Cancer Hospital, Nanjing, Jiangsu 210009, P.R. China
| | - Renhua Guo
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, Jiangsu 210029, P.R. China
| |
Collapse
|
60
|
Mechanisms of Compound Kushen Injection for the Treatment of Lung Cancer Based on Network Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 2019:4637839. [PMID: 31275410 PMCID: PMC6558614 DOI: 10.1155/2019/4637839] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 04/23/2019] [Accepted: 05/20/2019] [Indexed: 12/20/2022]
Abstract
Background Compound Kushen Injection (CKI) is a Chinese patent drug that shows good efficacy in treating lung cancer (LC). However, its underlying mechanisms need to be further clarified. Methods In this study, we adopted a network pharmacology method to gather compounds, predict targets, construct networks, and analyze biological functions and pathways. Moreover, molecular docking simulation was employed to assess the binding potential of selected target-compound pairs. Results Four networks were established, including the compound-putative target network, protein-protein interaction (PPI) network of LC targets, compound-LC target network, and herb-compound-target-pathway network. Network analysis showed that 8 targets (CHRNA3, DRD2, PRKCA, CDK1, CDK2, CHRNA5, MMP1, and MMP9) may be the therapeutic targets of CKI in LC. In addition, molecular docking simulation indicated that CHRNA3, DRD2, PRKCA, CDK1, CDK2, MMP1, and MMP9 had good binding activity with the corresponding compounds. Furthermore, enrichment analysis indicated that CKI might exert a therapeutic role in LC by regulating some important pathways, namely, pathways in cancer, proteoglycans in cancer, PI3K-Akt signaling pathway, non-small-cell lung cancer, and small cell lung cancer. Conclusions This study validated and predicted the mechanism of CKI in treating LC. Additionally, this study provides a good foundation for further experimental studies and promotes the reasonable application of CKI in the clinical treatment of LC.
Collapse
|
61
|
Quan X, Li X, Yin Z, Ren Y, Zhou B. p53/miR-30a-5p/ SOX4 feedback loop mediates cellular proliferation, apoptosis, and migration of non-small-cell lung cancer. J Cell Physiol 2019; 234:22884-22895. [PMID: 31124131 DOI: 10.1002/jcp.28851] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 04/30/2019] [Accepted: 04/30/2019] [Indexed: 12/31/2022]
Abstract
Many microRNAs (miRNAs) play vital roles in the tumorigenesis and development of cancers. In this study, we aimed to identify the differentially expressed miRNAs and their specific mechanisms in non-small-cell lung cancer (NSCLC). Based on data from the GSE56036 database, miR-30a-5p expression was identified to be downregulated in NSCLC. Further investigations showed that overexpression of miR-30a-5p inhibited cell proliferation, migration, and promoted apoptosis in NSCLC. Increase of miR-30a-5p level could induce the increase of Bax protein level and decrease of Bcl-2 protein level. In addition, chromatin immunoprecipitation assays showed that miR-30a-5p expression was induced by binding of p53 to the promoter of MIR30A. Bioinformatics prediction indicated that miR-30a-5p targets SOX4, and western blot analysis indicated that overexpression of the miRNA decreases the SOX4 protein expression level, which in turn regulated the level of p53. Thus, this study provides evidence for the existence of a p53/miR-30a-5p/SOX4 feedback loop, which likely plays a key role in the regulation of proliferation, apoptosis, and migration in NSCLC, highlighting a new therapeutic target.
Collapse
Affiliation(s)
- Xiaowei Quan
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Xuelian Li
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Yangwu Ren
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention, China Medical University, Liaoning Provincial Department of Education, Liaoning, China
| |
Collapse
|
62
|
Braun CJ, Hemann MT. Functional screens identify coordinators of RNA molecule birth, life, and death as targetable cancer vulnerabilities. Curr Opin Genet Dev 2019; 54:105-109. [PMID: 31121413 DOI: 10.1016/j.gde.2019.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/20/2019] [Accepted: 04/07/2019] [Indexed: 01/04/2023]
Abstract
RNA molecules are subject to a complex co-transcriptional and post-transcriptional life cycle, controlled at all stages by RNA binding proteins (RBPs) and non-coding RNAs that influence mRNA stability, splicing, localization, and decay. Together with mechanisms regulating the process of transcription itself, non-coding RNAs and RBPs contribute to a model of para-transcriptional coordination of gene expression, which is utilized during normal tissue physiology and cancer development in order to execute complex gene expression programs. Several key regulators of RNA biology, such as certain splice factors, represent bona fide cancer vulnerabilities, but our understanding of these processes is still far away from being comprehensive. Genetic forward screens utilizing technologies such as transposons, RNAi and CRISPR aid the field in rapidly establishing functional phenotypes and genetic cancer cell addictions. This review focuses on four individual regulatory gene expression processes governed by regulators of the RNA life cycle, the impact of functional genomics on streamlining the discovery process and the role of such mechanisms in tumor biology.
Collapse
Affiliation(s)
- Christian J Braun
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.
| | - Michael T Hemann
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
63
|
Impact of KRAS mutation subtype and concurrent pathogenic mutations on non-small cell lung cancer outcomes. Lung Cancer 2019; 133:144-150. [PMID: 31200821 DOI: 10.1016/j.lungcan.2019.05.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Concurrent genetic mutations are prevalent in KRAS-mutant non-small cell lung cancer (NSCLC) and may differentially influence patient outcomes. We sought to characterize the effects of KRAS mutation subtypes and concurrent pathogenic mutations on overall survival (OS) and PD-L1 expression, a predictive biomarker for anti-PD-1/PD-L1 immunotherapy. MATERIALS AND METHODS We retrospectively identified patients with KRAS-mutant NSCLC at a single institution and abstracted clinical, molecular, and pathologic data from electronic health records. Cox regression and multinomial logistic regression were used to determine how KRAS mutation subtypes and concurrent pathogenic mutations are associated with OS and tumor PD-L1 expression, respectively. RESULTS A total 186 patients were included. Common KRAS mutation subtypes included G12C (35%) and G12D (17%). Concurrent pathogenic mutations were identified in TP53 (39%), STK11 (12%), KEAP1 (8%), and PIK3CA (4%). On multivariable analysis, KRAS G12D mutations were significantly associated with poor OS (hazard ratio [HR] 2.43, 95% confidence interval [CI] 1.15-5.16; P = 0.021), as were STK11 co-mutations (HR 2.95, 95% CI 1.27-6.88; P = 0.012). Compared to no (<1%) PD-L1 expression, KRAS G12C mutations were significantly associated with positive yet low (1-49%) PD-L1 expression (odds ratio [OR] 4.94, 95% CI 1.07-22.85; P = 0.041), and TP53 co-mutations with high (≥50%) PD-L1 expression (OR 6.36, 95% CI 1.84-22.02; P = 0.004). CONCLUSION KRAS G12D and STK11 mutations confer poor prognoses for patients with KRAS-mutant NSCLC. KRAS G12C and TP53 mutations correlate with a biomarker that predicts benefit from immunotherapy. Concurrent mutations may represent distinct subsets of KRAS-mutant NSCLC; further investigation is warranted to elucidate their role in guiding treatment.
Collapse
|
64
|
Santeufemia DA, Palmieri G, Cossu A, De Re V, Caggiari L, De Zorzi M, Casula M, Sini MC, Baldino G, Dedola MF, Corona G, Miolo G. Complete and Durable Response to Combined Chemo/Radiation Therapy in EGFR Wild-Type Lung Adenocarcinoma with Diffuse Brain Metastases. Diagnostics (Basel) 2019; 9:diagnostics9020042. [PMID: 30979070 PMCID: PMC6627459 DOI: 10.3390/diagnostics9020042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/02/2019] [Accepted: 04/09/2019] [Indexed: 11/16/2022] Open
Abstract
Most non-small-cell lung cancer (NSCLC) patients are likely to develop brain metastases during the course of their illness. Currently, no consensus on NSCLC patients' treatment with brain metastasis has been established. Although whole brain radiotherapy prolongs the median survival time of approximately 4 months, a cisplatin-pemetrexed combination may also represent a potential option in the treatment of asymptomatic NSCLC patients with brain metastases. Herein, we report the case of a non-smoker male patient with multiple, large and diffuse brain metastases from an "epidermal growth factor receptor (EGFR) wild-type" lung adenocarcinoma who underwent an overly aggressive chemo/radiation therapy. This approach led to a complete and durable remission of the disease and to a long survival of up to 58 months from diagnosis of primary tumor. The uncommon course of this metastatic disease induced us to describe its oncological management and to investigate the molecular features of the tumor.
Collapse
Affiliation(s)
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | - Antonio Cossu
- Operative Unit of Pathology, Azienda Ospedaliero Universitaria Sassari, Via Matteotti 60, 07100 Sassari, Italy.
| | - Valli De Re
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy.
| | - Laura Caggiari
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy.
| | - Mariangela De Zorzi
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy.
| | - Milena Casula
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | - Maria Cristina Sini
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Traversa La Crucca 3, 07100 Sassari, Italy.
| | | | - Maria Filomena Dedola
- Radiotherapy Unit, Azienda Ospedaliero Universitaria Sassari, Via Matteotti 60, 07100 Sassari, Italy.
| | - Giuseppe Corona
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy.
| | - Gianmaria Miolo
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy.
| |
Collapse
|
65
|
Lim SM, Choi JW, Hong MH, Jung D, Lee CY, Park SY, Shim HS, Sheen S, Kwak KI, Kang DR, Cho BC, Kim HR. Indoor radon exposure increases tumor mutation burden in never-smoker patients with lung adenocarcinoma. Lung Cancer 2019; 131:139-146. [PMID: 31027691 DOI: 10.1016/j.lungcan.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 10/27/2022]
Abstract
OBJECTIVES Radon, a natural radiation, is the leading environmental cause of lung cancer in never-smokers. However, the radon exposure impact on the mutational landscape and tumor mutation burden (TMB) of lung cancer in never-smokers has not been explored. The aim of this study was to investigate the mutational landscape of lung adenocarcinoma in never-smokers who were exposed to various degrees of residential radon. MATERIALS AND METHODS To investigate the effect of indoor radon exposure, we estimated the cumulative exposure to indoor radon in each house of patients with lung cancer with a never-smoking history. Patients with at least 2 year-duration of residence before the diagnosis of lung adenocarcinoma were included. Patients were subgrouped based on the median radon exposure level (48 Bq/m3): radon-high vs. radon-low and targeted sequencing of tumor and matched blood were performed in all patients. RESULTS Among 41 patients with lung adenocarcinoma, the TMB was significantly higher in the radon-high group than it was in the radon-low group (mean 4.94 vs. 2.6 mutations/Mb, P = 0.01). The recurrence rates between radon-high and radon-low group did not differ significantly. Mutational signatures of radon-high tumors showed features associated with inactivity of the base excision repair and DNA replication machineries. The analysis of tumor evolutionary trajectories also suggested a series of mutagenesis induced by radon exposure. In addition, radon-high tumors revealed a significant protein-protein interaction of genes involved in DNA damage and repair (P < 0.001). CONCLUSIONS Indoor radon exposure increased the TMB in never-smoker patients with lung adenocarcinoma and their mutational signature was associated with defective DNA mismatch repair.
Collapse
Affiliation(s)
- Sun Min Lim
- Division of Medical Oncology, Department of Internal Medicine, CHA Bundang Medical Center, Seongnam-si, Republic of Korea
| | - Jae Woo Choi
- Severance Biomedical Science Institute, Yonsei University of College of Medicine, Seoul, Republic of Korea; Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Hee Hong
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dongmin Jung
- Institute for Cancer Research, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chang Young Lee
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seong Yong Park
- Department of Thoracic and Cardiovascular Surgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seungsoo Sheen
- Department of Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Im Kwak
- Institute of Genomic Cohort, Department of Preventive Medicine, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Dae Ryong Kang
- Center of Biomedical Data Science, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Byoung Chul Cho
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea; JE-UK Institute for Cancer Research, JEUK Co., Ltd., Gumi-City, Kyungbuk, Republic of Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
66
|
Filipczak PT, Leng S, Tellez CS, Do KC, Grimes MJ, Thomas CL, Walton-Filipczak SR, Picchi MA, Belinsky SA. p53-Suppressed Oncogene TET1 Prevents Cellular Aging in Lung Cancer. Cancer Res 2019; 79:1758-1768. [PMID: 30622117 DOI: 10.1158/0008-5472.can-18-1234] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/14/2018] [Accepted: 01/04/2019] [Indexed: 11/16/2022]
Abstract
The role of transcriptional regulator ten-eleven translocation methylcytosine dioxygenease 1 (TET1) has not been well characterized in lung cancer. Here we show that TET1 is overexpressed in adenocarcinoma and squamous cell carcinomas. TET1 knockdown reduced cell growth in vitro and in vivo and induced transcriptome reprogramming independent of its demethylating activity to affect key cancer signaling pathways. Wild-type p53 bound the TET1 promoter to suppress transcription, while p53 transversion mutations were most strongly associated with high TET1 expression. Knockdown of TET1 in p53-mutant cell lines induced senescence through a program involving generalized genomic instability manifested by DNA single- and double-strand breaks and induction of p21 that was synergistic with cisplatin and doxorubicin. These data identify TET1 as an oncogene in lung cancer whose gain of function via loss of p53 may be exploited through targeted therapy-induced senescence. SIGNIFICANCE: These studies identify TET1 as an oncogene in lung cancer whose gain of function following loss of p53 may be exploited by targeted therapy-induced senescence.See related commentary by Kondo, p. 1751.
Collapse
Affiliation(s)
| | - Shuguang Leng
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Carmen S Tellez
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Kieu C Do
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Marcie J Grimes
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Cynthia L Thomas
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | | | - Maria A Picchi
- Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | | |
Collapse
|
67
|
Tfayli AH, Fakhri GB, Al Assaad MS. Prevalence of the epidermal growth factor receptor mutations in lung adenocarcinoma patients from the Middle East region. Ann Thorac Med 2019; 14:173-178. [PMID: 31333766 PMCID: PMC6611202 DOI: 10.4103/atm.atm_344_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Lung cancer remains a major cause of cancer mortality with a 5-year survival in advanced stages around 4%. Platinum-based chemotherapy was routinely used as the standard of care in patients with advanced nonsmall cell lung cancer, but it is being progressively replaced by targeted molecular therapy. One of the molecular aberrations harbored by lung adenocarcinoma is the epidermal growth factor receptor (EGFR). A large ethnic variation has been reported in the prevalence of EGFR mutations in patients with lung adenocarcinoma. Data regarding its prevalence from the Middle East area remains limited. This paper aims at reviewing the data available for the prevalence of this mutation in the Middle Eastern patient population and comparing it with other reported series.
Collapse
Affiliation(s)
- Arafat Hussein Tfayli
- Department of Internal Medicine, Division of Hematology and Oncology, American University of Beirut, Beirut, Lebanon
| | - Ghina Bassam Fakhri
- Department of Internal Medicine, Division of Hematology and Oncology, American University of Beirut, Beirut, Lebanon
| | - Majd Sassine Al Assaad
- Department of Internal Medicine, Division of Hematology and Oncology, American University of Beirut, Beirut, Lebanon
| |
Collapse
|
68
|
Wang Y, Wang Z, Piha-Paul S, Janku F, Subbiah V, Shi N, Hess K, Broaddus R, Shan B, Naing A, Hong D, Tsimberidou AM, Karp D, Lu C, Papadimitrakopoulou V, Heymach J, Meric-Bernstam F, Fu S. Outcome analysis of Phase I trial patients with metastatic KRAS and/or TP53 mutant non-small cell lung cancer. Oncotarget 2018; 9:33258-33270. [PMID: 30279957 PMCID: PMC6161801 DOI: 10.18632/oncotarget.25947] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/18/2018] [Indexed: 01/26/2023] Open
Abstract
KRAS and TP53 mutations, which are the most common genetic drivers of tumorigenesis, are still considered undruggable targets. Therefore, we analyzed these genetic aberrations in metastatic non-small cell lung cancer (NSCLC) for the development of potential therapeutics. One hundred eighty-five consecutive patients with metastatic NSCLC in a phase 1 trial center were included. Their genomic aberrations, clinical characteristics, survivals, and phase 1 trial therapies were analyzed. About 10%, 18%, 36%, and 36% of the patients had metastatic KRAS+/TP53+, KRAS+/TP53-,KRAS-/TP53+, and KRAS-/TP53- NSCLC, respectively. The most common concurrent genetic aberrations beside KRAS and/or TP53 (>5%) were KIT, epidermal growth factor receptor, PIK3CA, c-MET, BRAF, STK11, ATM, CDKN2A, and APC. KRAS+/TP53+ NSCLC did not respond well to the phase 1 trial therapy and was associated with markedly worse progression-free (PFS) and overall (OS) survivals than the other three groups together. KRAS hotspot mutations at locations other than codon G12 were associated with considerably worse OS than those at this codon. Gene aberration-matched therapy produced prolonged PFS and so was anti-angiogenesis in patients with TP53 mutations. Introduction of the evolutionary action score system of TP53 missense mutations enabled us to identify a subgroup of NSCLC patients with low-risk mutant p53 proteins having a median OS duration of 64.5 months after initial diagnosis of metastasis. These data suggested that patients with metastatic dual KRAS+/TP53+ hotspot-mutant NSCLC had poor clinical outcomes. Further analysis identified remarkably prolonged survival in patients with low-risk mutant p53 proteins, which warrants confirmatory studies.
Collapse
Affiliation(s)
- Yudong Wang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, People’s Republic of China
| | - Zhijie Wang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Medical Oncology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Sarina Piha-Paul
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naiyi Shi
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kenneth Hess
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Russell Broaddus
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Baoen Shan
- Department of Cancer Research, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, People’s Republic of China
| | - Aung Naing
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Apostolia M. Tsimberidou
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel Karp
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Lu
- Department of Thoracic Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vali Papadimitrakopoulou
- Department of Thoracic Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Heymach
- Department of Thoracic Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
69
|
Yu KH, Berry GJ, Rubin DL, Ré C, Altman RB, Snyder M. Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma. Cell Syst 2017; 5:620-627.e3. [PMID: 29153840 PMCID: PMC5746468 DOI: 10.1016/j.cels.2017.10.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 07/30/2017] [Accepted: 10/19/2017] [Indexed: 12/16/2022]
Abstract
Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA sequencing, and proteomics data of 538 lung adenocarcinoma patients from The Cancer Genome Atlas and used these to identify molecular pathways associated with histopathology patterns. We report cell-cycle regulation and nucleotide binding pathways underpinning tumor cell dedifferentiation, and we predicted histology grade using transcriptomics and proteomics signatures (area under curve >0.80). We built an integrative histopathology-transcriptomics model to generate better prognostic predictions for stage I patients (p = 0.0182 ± 0.0021) compared with gene expression or histopathology studies alone, and the results were replicated in an independent cohort (p = 0.0220 ± 0.0070). These results motivate the integration of histopathology and omics data to investigate molecular mechanisms of pathology findings and enhance clinical prognostic prediction.
Collapse
Affiliation(s)
- Kun-Hsing Yu
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305-5479, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Daniel L Rubin
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305-5479, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Radiology, Stanford University, Stanford, CA 94305-5105, USA; Department of Medicine (Biomedical Informatics Research), Stanford University, Stanford, CA 94305-5479, USA
| | - Christopher Ré
- Department of Computer Science, Stanford University, Stanford, CA 94305-9025, USA
| | - Russ B Altman
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305-5479, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA; Department of Computer Science, Stanford University, Stanford, CA 94305-9025, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305-4125, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
| |
Collapse
|
70
|
Bartels S, Persing S, Hasemeier B, Schipper E, Kreipe H, Lehmann U. Molecular Analysis of Circulating Cell-Free DNA from Lung Cancer Patients in Routine Laboratory Practice. J Mol Diagn 2017; 19:722-732. [DOI: 10.1016/j.jmoldx.2017.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/18/2017] [Indexed: 01/30/2023] Open
|
71
|
Qasrawi A, Tolentino A, Abu Ghanimeh M, Abughanimeh O, Albadarin S. BRAF V600Q-mutated lung adenocarcinoma with duodenal metastasis and extreme leukocytosis. World J Clin Oncol 2017; 8:360-365. [PMID: 28848703 PMCID: PMC5554880 DOI: 10.5306/wjco.v8.i4.360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 06/11/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Driver mutations in patients with non-small cell lung cancer (NSCLC) can lead to distinct behaviors and patterns of metastasis. Mutations in the proto-oncogene B-raf (BRAF) occur in approximately 3% of NSCLC cases. In the literature, reports of patients with lung adenocarcinomas metastasizing to the duodenum are rare, and most of the only 21 cases reported were from before the advent of next-generation sequencing. We present here a case involving a 57-year-old female who had a lytic lesion in her lesser trochanter. Biopsy showed metastatic adenocarcinoma of lung origin. Chest X-ray showed a large left upper lobe mass. Next-generation sequencing analysis confirmed the presence of BRAF V600Q mutation. The patient presented with persistent anemia and melena. Esophagogastroduodenoscopy confirmed the presence of duodenal metastasis. She also had suspected paraneoplastic leukemoid reaction. To our knowledge, this is only the second well-documented case of gastrointestinal metastasis from BRAF-mutated lung cancer.
Collapse
|
72
|
Ciabatti E, Valetto A, Bertini V, Ferreri MI, Guazzelli A, Grassi S, Guerrini F, Petrini I, Metelli MR, Caligo MA, Rossi S, Galimberti S. Myelodysplastic syndromes: advantages of a combined cytogenetic and molecular diagnostic workup. Oncotarget 2017; 8:79188-79200. [PMID: 29108298 PMCID: PMC5668031 DOI: 10.18632/oncotarget.16578] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/14/2017] [Indexed: 12/26/2022] Open
Abstract
In this study we present a new diagnostic workup for the myelodysplastic syndromes (MDS) including FISH, aCGH, and somatic mutation assays in addition to the conventional cytogenetics (CC). We analyzed 61 patients by CC, FISH for chromosome 5, 7, 8 and PDGFR rearrangements, aCGH, and PCR for ASXL1, EZH2, TP53, TET2, RUNX1, DNMT3A, SF3B1 somatic mutations. Moreover, we quantified WT1 and RPS14 gene expression levels, in order to find their possible adjunctive value and their possible clinical impact. CC analysis showed 32% of patients with at least one aberration. FISH analysis detected chromosomal aberrations in 24% of patients and recovered 5 cases (13.5%) at normal karyotype (two 5q- syndromes, one del(7) case, two cases with PDGFR rearrangement). The aGCH detected 10 "new" unbalanced cases in respect of the CC, including one with alteration of the ETV6 gene. After mutational analysis, 33 patients (54%) presented at least one mutation and represented the only marker of clonality in 36% of all patients. The statistical analysis confirmed the prognostic role of CC either on overall or on progression-free-survival. In addition, deletions detected by aCGH and WT1 over-expression negatively conditioned survival. In conclusion, our work showed that 1) the addition of FISH (at least for chr. 5 and 7) can improve the definition of the risk score; 2) mutational analysis, especially for the TP53 and SF3B1, could better define the type of MDS and represent a "clinical warning"; 3) the aCGH use could be probably applied to selected cases (with suboptimal response or failure).
Collapse
Affiliation(s)
- Elena Ciabatti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy.,GenOMec, University of Siena, Siena, Italy
| | - Angelo Valetto
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Veronica Bertini
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Maria Immacolata Ferreri
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Alice Guazzelli
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Susanna Grassi
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy.,GenOMec, University of Siena, Siena, Italy
| | - Francesca Guerrini
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Iacopo Petrini
- Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Maria Rita Metelli
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Maria Adelaide Caligo
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Simona Rossi
- Laboratory of Medical Genetics, Azienda Ospedaliero-Universitaria Pisana, S. Chiara Hospital, Pisa, Italy
| | - Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| |
Collapse
|