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Cheng J, Zhou L, Wang H. Symbiotic microbial communities in various locations of the lung cancer respiratory tract along with potential host immunological processes affected. Front Cell Infect Microbiol 2024; 14:1296295. [PMID: 38371298 PMCID: PMC10873922 DOI: 10.3389/fcimb.2024.1296295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
Lung cancer has the highest mortality rate among all cancers worldwide. The 5-year overall survival rate for non-small cell lung cancer (NSCLC) is estimated at around 26%, whereas for small cell lung cancer (SCLC), the survival rate is only approximately 7%. This disease places a significant financial and psychological burden on individuals worldwide. The symbiotic microbiota in the human body has been significantly associated with the occurrence, progression, and prognosis of various diseases, such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. Studies have demonstrated that respiratory symbiotic microorganisms and their metabolites play a crucial role in modulating immune function and contributing to the pathophysiology of lung cancer through their interactions with the host. In this review, we provide a comprehensive overview of the microbial characteristics associated with lung cancer, with a focus on the respiratory tract microbiota from different locations, including saliva, sputum, bronchoalveolar lavage fluid (BALF), bronchial brush samples, and tissue. We describe the respiratory tract microbiota's biodiversity characteristics by anatomical region, elucidating distinct pathological features, staging, metastasis, host chromosomal mutations, immune therapies, and the differentiated symbiotic microbiota under the influence of environmental factors. Our exploration investigates the intrinsic mechanisms linking the microbiota and its host. Furthermore, we have also provided a comprehensive review of the immune mechanisms by which microbiota are implicated in the development of lung cancer. Dysbiosis of the respiratory microbiota can promote or inhibit tumor progression through various mechanisms, including DNA damage and genomic instability, activation and regulation of the innate and adaptive immune systems, and stimulation of epithelial cells leading to the upregulation of carcinogenesis-related pathways.
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Affiliation(s)
- Jiuling Cheng
- Respiratory Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lujia Zhou
- Henan Key Laboratory of Precision Diagnosis of Respiratory Infectious Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Zhengzhou Key Laboratory of Precision Diagnosis of Respiratory Infectious Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Huaqi Wang
- Respiratory Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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2
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Peters BA, Pass HI, Burk RD, Xue X, Goparaju C, Sollecito CC, Grassi E, Segal LN, Tsay JCJ, Hayes RB, Ahn J. The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer. Genome Med 2022; 14:121. [PMID: 36303210 PMCID: PMC9609265 DOI: 10.1186/s13073-022-01126-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cancer recurrence after tumor resection in early-stage non-small cell lung cancer (NSCLC) is common, yet difficult to predict. The lung microbiota and systemic immunity may be important modulators of risk for lung cancer recurrence, yet biomarkers from the lung microbiome and peripheral immune environment are understudied. Such markers may hold promise for prediction as well as improved etiologic understanding of lung cancer recurrence. METHODS In tumor and distant normal lung samples from 46 stage II NSCLC patients with curative resection (39 tumor samples, 41 normal lung samples), we conducted 16S rRNA gene sequencing. We also measured peripheral blood immune gene expression with nanoString®. We examined associations of lung microbiota and peripheral gene expression with recurrence-free survival (RFS) and disease-free survival (DFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression, and examined predictive accuracy using time-dependent receiver operating characteristic (ROC) curves. RESULTS Over a median of 4.8 years of follow-up (range 0.2-12.2 years), 43% of patients experienced a recurrence, and 50% died. In normal lung tissue, a higher abundance of classes Bacteroidia and Clostridia, and orders Bacteroidales and Clostridiales, were associated with worse RFS, while a higher abundance of classes Alphaproteobacteria and Betaproteobacteria, and orders Burkholderiales and Neisseriales, were associated with better RFS. In tumor tissue, a higher abundance of orders Actinomycetales and Pseudomonadales were associated with worse DFS. Among these taxa, normal lung Clostridiales and Bacteroidales were also related to worse survival in a previous small pilot study and an additional independent validation cohort. In peripheral blood, higher expression of genes TAP1, TAPBP, CSF2RB, and IFITM2 were associated with better DFS. Analysis of ROC curves revealed that lung microbiome and peripheral gene expression biomarkers provided significant additional recurrence risk discrimination over standard demographic and clinical covariates, with microbiome biomarkers contributing more to short-term (1-year) prediction and gene biomarkers contributing to longer-term (2-5-year) prediction. CONCLUSIONS We identified compelling biomarkers in under-explored data types, the lung microbiome, and peripheral blood gene expression, which may improve risk prediction of recurrence in early-stage NSCLC patients. These findings will require validation in a larger cohort.
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Affiliation(s)
- Brandilyn A Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, #1315AB, The Bronx, New York, NY, 10461, USA.
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, NYU Langone Health, New York, NY, USA
- NYU Perlmutter Cancer Center, New York, NY, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, #1315AB, The Bronx, New York, NY, 10461, USA
- Department of Pediatrics, Albert Einstein College of Medicine, The Bronx, New York, NY, USA
- Department of Microbiology & Immunology, and Obstetrics & Gynecology & Women's Health, Albert Einstein College of Medicine, The Bronx, New York, NY, USA
| | - Xiaonan Xue
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, #1315AB, The Bronx, New York, NY, 10461, USA
| | - Chandra Goparaju
- Department of Cardiothoracic Surgery, NYU Langone Health, New York, NY, USA
| | | | - Evan Grassi
- Department of Pediatrics, Albert Einstein College of Medicine, The Bronx, New York, NY, USA
| | | | | | - Richard B Hayes
- NYU Perlmutter Cancer Center, New York, NY, USA
- Department of Population Health, NYU Langone Health, New York, NY, USA
| | - Jiyoung Ahn
- NYU Perlmutter Cancer Center, New York, NY, USA
- Department of Population Health, NYU Langone Health, New York, NY, USA
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3
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Bjaanæs MM, Nilsen G, Halvorsen AR, Russnes HG, Solberg S, Jørgensen L, Brustugun OT, Lingjærde OC, Helland Å. Whole genome copy number analyses reveal a highly aberrant genome in TP53 mutant lung adenocarcinoma tumors. BMC Cancer 2021; 21:1089. [PMID: 34625038 PMCID: PMC8501630 DOI: 10.1186/s12885-021-08811-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/23/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genetic alterations are common in non-small cell lung cancer (NSCLC), and DNA mutations and translocations are targets for therapy. Copy number aberrations occur frequently in NSCLC tumors and may influence gene expression and further alter signaling pathways. In this study we aimed to characterize the genomic architecture of NSCLC tumors and to identify genomic differences between tumors stratified by histology and mutation status. Furthermore, we sought to integrate DNA copy number data with mRNA expression to find genes with expression putatively regulated by copy number aberrations and the oncogenic pathways associated with these affected genes. METHODS Copy number data were obtained from 190 resected early-stage NSCLC tumors and gene expression data were available from 113 of the adenocarcinomas. Clinical and histopathological data were known, and EGFR-, KRAS- and TP53 mutation status was determined. Allele-specific copy number profiles were calculated using ASCAT, and regional copy number aberration were subsequently obtained and analyzed jointly with the gene expression data. RESULTS The NSCLC tumors tissue displayed overall complex DNA copy number profiles with numerous recurrent aberrations. Despite histological differences, tissue samples from squamous cell carcinomas and adenocarcinomas had remarkably similar copy number patterns. The TP53-mutated lung adenocarcinomas displayed a highly aberrant genome, with significantly altered copy number profiles including gains, losses and focal complex events. The EGFR-mutant lung adenocarcinomas had specific arm-wise aberrations particularly at chromosome7p and 9q. A large number of genes displayed correlation between copy number and expression level, and the PI(3)K-mTOR pathway was highly enriched for such genes. CONCLUSIONS The genomic architecture in NSCLC tumors is complex, and particularly TP53-mutated lung adenocarcinomas displayed highly aberrant copy number profiles. We suggest to always include TP53-mutation status when studying copy number aberrations in NSCLC tumors. Copy number may further impact gene expression and alter cellular signaling pathways.
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MESH Headings
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/pathology
- Alleles
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Chromosomes, Human, Pair 7
- Chromosomes, Human, Pair 9
- Class I Phosphatidylinositol 3-Kinases/genetics
- DNA Copy Number Variations
- Ex-Smokers
- Female
- Gene Dosage
- Gene Expression
- Genes, erbB-1/genetics
- Genes, p53
- Genes, ras/genetics
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Non-Smokers
- Polymorphism, Single Nucleotide
- Signal Transduction/genetics
- Smokers
- TOR Serine-Threonine Kinases/genetics
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Affiliation(s)
- Maria Moksnes Bjaanæs
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, 4950 Nydalen Oslo, Norway
| | - Gro Nilsen
- Department of Computer Science, University of Oslo, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ann Rita Halvorsen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
| | - Hege G. Russnes
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Steinar Solberg
- Department of Cardiothoracic Surgery, Oslo University Hospital, Oslo, Norway
| | - Lars Jørgensen
- Department of Cardiothoracic Surgery, Oslo University Hospital, Oslo, Norway
| | - Odd Terje Brustugun
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Section of Oncology, Vestre Viken Hospital, Drammen, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Department of Computer Science, University of Oslo, Oslo, Norway
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Åslaug Helland
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, Oslo, Norway
- Department of Oncology, Oslo University Hospital, 4950 Nydalen Oslo, Norway
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4
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Hijazo-Pechero S, Alay A, Marín R, Vilariño N, Muñoz-Pinedo C, Villanueva A, Santamaría D, Nadal E, Solé X. Gene Expression Profiling as a Potential Tool for Precision Oncology in Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:4734. [PMID: 34638221 PMCID: PMC8507534 DOI: 10.3390/cancers13194734] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/20/2023] Open
Abstract
Recent technological advances and the application of high-throughput mutation and transcriptome analyses have improved our understanding of cancer diseases, including non-small cell lung cancer. For instance, genomic profiling has allowed the identification of mutational events which can be treated with specific agents. However, detection of DNA alterations does not fully recapitulate the complexity of the disease and it does not allow selection of patients that benefit from chemo- or immunotherapy. In this context, transcriptional profiling has emerged as a promising tool for patient stratification and treatment guidance. For instance, transcriptional profiling has proven to be especially useful in the context of acquired resistance to targeted therapies and patients lacking targetable genomic alterations. Moreover, the comprehensive characterization of the expression level of the different pathways and genes involved in tumor progression is likely to better predict clinical benefit from different treatments than single biomarkers such as PD-L1 or tumor mutational burden in the case of immunotherapy. However, intrinsic technical and analytical limitations have hindered the use of these expression signatures in the clinical setting. In this review, we will focus on the data reported on molecular classification of non-small cell lung cancer and discuss the potential of transcriptional profiling as a predictor of survival and as a patient stratification tool to further personalize treatments.
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Affiliation(s)
- Sara Hijazo-Pechero
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Ania Alay
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Raúl Marín
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Noelia Vilariño
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
- Neuro-Oncology Unit, Hospital Universitari de Bellvitge-ICO L’Hospitalet (IDIBELL), 08908 Barcelona, Spain
| | - Cristina Muñoz-Pinedo
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
| | - Alberto Villanueva
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain;
| | - David Santamaría
- INSERM U1218, ACTION Laboratory, Institut Européen de Chimie et Biologie (IECB), Université de Bordeaux, F-33607 Pessac, France;
| | - Ernest Nadal
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain
| | - Xavier Solé
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (S.H.-P.); (A.A.); (R.M.)
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08908 Barcelona, Spain; (N.V.); (C.M.-P.)
- CIBER (Consorcio de Investigación Biomédica en Red) Epidemiologia y Salud Pública (CIBERESP), 28029 Madrid, Spain
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5
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Liljedahl H, Karlsson A, Oskarsdottir GN, Salomonsson A, Brunnström H, Erlingsdottir G, Jönsson M, Isaksson S, Arbajian E, Ortiz-Villalón C, Hussein A, Bergman B, Vikström A, Monsef N, Branden E, Koyi H, de Petris L, Patthey A, Behndig AF, Johansson M, Planck M, Staaf J. A gene expression-based single sample predictor of lung adenocarcinoma molecular subtype and prognosis. Int J Cancer 2020; 148:238-251. [PMID: 32745259 PMCID: PMC7689824 DOI: 10.1002/ijc.33242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/14/2022]
Abstract
Disease recurrence in surgically treated lung adenocarcinoma (AC) remains high. New approaches for risk stratification beyond tumor stage are needed. Gene expression-based AC subtypes such as the Cancer Genome Atlas Network (TCGA) terminal-respiratory unit (TRU), proximal-inflammatory (PI) and proximal-proliferative (PP) subtypes have been associated with prognosis, but show methodological limitations for robust clinical use. We aimed to derive a platform independent single sample predictor (SSP) for molecular subtype assignment and risk stratification that could function in a clinical setting. Two-class (TRU/nonTRU=SSP2) and three-class (TRU/PP/PI=SSP3) SSPs using the AIMS algorithm were trained in 1655 ACs (n = 9659 genes) from public repositories vs TCGA centroid subtypes. Validation and survival analysis were performed in 977 patients using overall survival (OS) and distant metastasis-free survival (DMFS) as endpoints. In the validation cohort, SSP2 and SSP3 showed accuracies of 0.85 and 0.81, respectively. SSPs captured relevant biology previously associated with the TCGA subtypes and were associated with prognosis. In survival analysis, OS and DMFS for cases discordantly classified between TCGA and SSP2 favored the SSP2 classification. In resected Stage I patients, SSP2 identified TRU-cases with better OS (hazard ratio [HR] = 0.30; 95% confidence interval [CI] = 0.18-0.49) and DMFS (TRU HR = 0.52; 95% CI = 0.33-0.83) independent of age, Stage IA/IB and gender. SSP2 was transformed into a NanoString nCounter assay and tested in 44 Stage I patients using RNA from formalin-fixed tissue, providing prognostic stratification (relapse-free interval, HR = 3.2; 95% CI = 1.2-8.8). In conclusion, gene expression-based SSPs can provide molecular subtype and independent prognostic information in early-stage lung ACs. SSPs may overcome critical limitations in the applicability of gene signatures in lung cancer.
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Affiliation(s)
- Helena Liljedahl
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Gudrun N Oskarsdottir
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Annette Salomonsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Hans Brunnström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Gigja Erlingsdottir
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland.,Department of Laboratory Medicine, Department of Pathology, Skåne University Hospital, Malmö, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Sofi Isaksson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | - Elsa Arbajian
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
| | | | - Aziz Hussein
- Department of Pathology and Cytology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bengt Bergman
- Department of Respiratory Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anders Vikström
- Department of Pulmonary Medicine, University Hospital Linköping, Linköping, Sweden
| | - Nastaran Monsef
- Department of Pathology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Eva Branden
- Respiratory Medicine Unit, Department of Medicine Solna and CMM, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden.,Centre for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Hirsh Koyi
- Respiratory Medicine Unit, Department of Medicine Solna and CMM, Karolinska Institute and Karolinska University Hospital Solna, Stockholm, Sweden.,Centre for Research and Development, Uppsala University/Region Gävleborg, Gävle, Sweden
| | - Luigi de Petris
- Thoracic Oncology Unit, Karolinska University Hospital and Department Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Annika Patthey
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Annelie F Behndig
- Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden
| | - Mikael Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden.,Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, Lund, Sweden
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6
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Salomonsson A, Micke P, Mattsson JSM, La Fleur L, Isaksson J, Jönsson M, Nodin B, Botling J, Uhlén M, Jirström K, Staaf J, Planck M, Brunnström H. Comprehensive analysis of RNA binding motif protein 3 (RBM3) in non-small cell lung cancer. Cancer Med 2020; 9:5609-5619. [PMID: 32491279 PMCID: PMC7402820 DOI: 10.1002/cam4.3149] [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: 01/02/2020] [Revised: 04/11/2020] [Accepted: 05/05/2020] [Indexed: 01/05/2023] Open
Abstract
AIMS High expression of the RNA-binding motif protein 3 (RBM3) correlates with improved prognosis in several major types of cancer. The aim of the present study was to examine the prognostic value of RBM3 protein and mRNA expression in non-small cell lung cancer (NSCLC). METHODS AND RESULTS Immunohistochemical expression of RBM3 was evaluated in surgically treated NSCLC from two independent patient populations (n = 213 and n = 306). Staining patterns were correlated with clinicopathological parameters, overall survival (OS), and recurrence-free interval (RFI). Cases with high nuclear RBM3 protein expression had a prolonged 5-year OS in both cohorts when analyzing adenocarcinomas separately (P = .02 and P = .01). RBM3 remained an independent prognostic factor for OS in multivariable analysis of cohort I (HR 0.44, 95% CI 0.21-0.90) and for RFI in cohort II (HR 0.38, 95% CI 0.22-0.74). In squamous cell carcinoma, there was instead an insignificant association to poor prognosis. Also, the expression levels of RBM3 mRNA were investigated in 2087 lung adenocarcinomas and 899 squamous cell carcinomas assembled from 13 and 8 public gene expression microarray datasets, respectively. The RBM3 mRNA levels were not clearly associated with patient outcome in either adenocarcinomas or squamous cell carcinomas. CONCLUSIONS The results from this study support that high protein expression of RBM3 is linked to improved outcome in lung adenocarcinoma.
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Affiliation(s)
- Annette Salomonsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Johanna S M Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Linnea La Fleur
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Johan Isaksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden.,Department of Respiratory Medicine, Gävle Hospital, Gävle, Sweden.,Centre for Research and Development, Uppsala university/County Council of Gävleborg, Gävle, Sweden
| | - Mats Jönsson
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Björn Nodin
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden.,School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Karin Jirström
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Maria Planck
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Respiratory medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Hans Brunnström
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden.,Department of Genetics and Pathology, Laboratory Medicine Region Skåne, Lund, Sweden
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7
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Modulation of proliferation factors in lung adenocarcinoma with an analysis of the transcriptional consequences of genomic EGFR activation. Oncotarget 2019; 10:6913-6933. [PMID: 31857847 PMCID: PMC6916753 DOI: 10.18632/oncotarget.27316] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 10/26/2019] [Indexed: 11/25/2022] Open
Abstract
Genes of the pre-replication, pre-initiation and replisome complexes duplicate the genome from many sites once in a normal cell cycle. This study examines complex components in lung adenocarcinoma (LUAD) closely, correlating changes in the genome and transcriptome with proliferation and overall survival. Molecular subtypes (The Cancer Genome Atlas (TCGA), 2014) based on copy number, DNA methylation, and mRNA expression had variable proliferation levels, the highest correlating with decreased survival. A pattern of increased expression typified by POLE2 and POLQ was found for multiple replication factors over thirty-seven tumor types. EGFR altered cases unanticipatedly inversely correlated with proliferation factor expression in LUAD, Colon adenocarcinoma, and Cancer Cell Line Encyclopedia cell lines, but not in glioblastoma or breast cancer. Activation mutations did not uniformly correlate with proliferation, most cases were pre-metastatic. A gene expression profile was identified, and pathway involvement considered. Significantly, results suggest EGFR over expression and activation are early alterations that likely stall the replication complex through PCNA phosphorylation creating replication stress responsible for DNA damage response and further mutation, but does not promote increased proliferation itself. An argument is presented that the mechanism driving lethality in this tumor cohort could differ from over proliferation seen in other LUAD.
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8
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Wang F, Diao XY, Zhang X, Shao Q, Feng YF, An X, Wang HY. Identification of genetic alterations associated with primary resistance to EGFR-TKIs in advanced non-small-cell lung cancer patients with EGFR sensitive mutations. Cancer Commun (Lond) 2019; 39:7. [PMID: 30823937 PMCID: PMC6397445 DOI: 10.1186/s40880-019-0354-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/26/2019] [Indexed: 01/21/2023] Open
Abstract
Background Identification of activated epidermal growth factor receptor (EGFR) mutations and application of EGFR-tyrosine kinase inhibitors (EGFR-TKIs) have greatly changed the therapeutic strategies of non-small-cell lung cancer (NSCLC). However, the long-term efficacy of EGFR-TKI therapy is limited due to the development of drug resistance. The aim of this study was to investigate the correlation between the aberrant alterations of 8 driver genes and the primary resistance to EGFR-TKIs in advanced NSCLC patients with activated EGFR mutations. Methods We retrospectively reviewed the clinical data from 416 patients with stage III/IV or recurrent NSCLC who received an initial EGFR-TKI treatment, from April 2004 and March 2011, at the Sun Yat-sen University Cancer Center. Several genetic alterations associated with the efficacy of EGFR-TKIs, including the alterations in BIM, ALK, KRAS, PIK3CA, PTEN, MET, IGF1R, and ROS1, were detected by the routine clinical technologies. The progression-free survival (PFS) and overall survival (OS) were compared between different groups using Kaplan–Meier survival analysis with the log-rank test. A Cox regression model was used to estimate multivariable-adjusted hazard ratios (HRs) and their 95% confidence intervals (95% CIs) associated with the PFS and OS. Results Among the investigated patients, 169 NSCLC patients harbored EGFR-sensitive mutations. EGFR-mutant patients having PTEN deletion had a shorter PFS and OS than those with intact PTEN (P = 0.003 for PFS, and P = 0.034 for OS). In the combined molecular analysis of EGFR signaling pathway and resistance genes, we found that EGFR-mutant patients coexisted with aberrant alterations in EGFR signaling pathway and those having resistant genes had a statistically poorer PFS than those without such alterations (P < 0.001). A Cox proportional regression model determined that PTEN deletion (HR = 4.29,95% CI = 1.72–10.70) and low PTEN expression (HR = 1.96, 95% CI = 1.22–3.13), MET FISH + (HR = 2.83,95% CI = 1.37–5.86) were independent predictors for PFS in patients with EGFR-TKI treatment after adjustment for multiple factor. Conclusions We determined that the coexistence of genetic alterations in cancer genes may explain primary resistance to EGFR-TKIs. Electronic supplementary material The online version of this article (10.1186/s40880-019-0354-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P.R. China. .,Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, No. 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China.
| | - Xia-Yao Diao
- Department of Urology, Sun Yat-sen Memorial Hospital, Guangzhou, 510120, Guangdong, P.R. China
| | - Xiao Zhang
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, No. 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Qiong Shao
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, No. 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China
| | - Yan-Fen Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P.R. China.,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P.R. China
| | - Xin An
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P.R. China
| | - Hai-Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong, P.R. China. .,Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, No. 651 Dongfeng Road East, Guangzhou, 510060, Guangdong, P.R. China.
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Parimbelli E, Marini S, Sacchi L, Bellazzi R. Patient similarity for precision medicine: A systematic review. J Biomed Inform 2018; 83:87-96. [PMID: 29864490 DOI: 10.1016/j.jbi.2018.06.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/16/2018] [Accepted: 06/01/2018] [Indexed: 12/19/2022]
Abstract
Evidence-based medicine is the most prevalent paradigm adopted by physicians. Clinical practice guidelines typically define a set of recommendations together with eligibility criteria that restrict their applicability to a specific group of patients. The ever-growing size and availability of health-related data is currently challenging the broad definitions of guideline-defined patient groups. Precision medicine leverages on genetic, phenotypic, or psychosocial characteristics to provide precise identification of patient subsets for treatment targeting. Defining a patient similarity measure is thus an essential step to allow stratification of patients into clinically-meaningful subgroups. The present review investigates the use of patient similarity as a tool to enable precision medicine. 279 articles were analyzed along four dimensions: data types considered, clinical domains of application, data analysis methods, and translational stage of findings. Cancer-related research employing molecular profiling and standard data analysis techniques such as clustering constitute the majority of the retrieved studies. Chronic and psychiatric diseases follow as the second most represented clinical domains. Interestingly, almost one quarter of the studies analyzed presented a novel methodology, with the most advanced employing data integration strategies and being portable to different clinical domains. Integration of such techniques into decision support systems constitutes and interesting trend for future research.
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Affiliation(s)
- E Parimbelli
- Telfer School of Management, University of Ottawa, Ottawa, Canada; Interdepartmental Centre for Health Technologies, University of Pavia, Italy.
| | - S Marini
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA; Interdepartmental Centre for Health Technologies, University of Pavia, Italy
| | - L Sacchi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Italy; Interdepartmental Centre for Health Technologies, University of Pavia, Italy
| | - R Bellazzi
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Italy; Interdepartmental Centre for Health Technologies, University of Pavia, Italy; RCCS ICS Maugeri, Pavia, Italy
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An 8-gene signature for prediction of prognosis and chemoresponse in non-small cell lung cancer. Oncotarget 2018; 7:86561-86572. [PMID: 27863408 PMCID: PMC5349935 DOI: 10.18632/oncotarget.13357] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 10/29/2016] [Indexed: 12/26/2022] Open
Abstract
Identification of a potential gene signature for improved diagnosis in non-small cell lung cancer (NSCLC) patient is necessary. Here, we aim to establish and validate the prognostic efficacy of a gene set that can predict prognosis and benefits of adjuvant chemotherapy (ACT) in NSCLC patients from various ethnicities. An 8-gene signature was calculated from the gene expression of 181 patients using univariate Cox proportional hazard regression analysis. The prognostic value of the signature was robustly validated in 1,477 patients from five microarray independent data sets and one RNA-seq data set. The 8-gene signature was identified as an independent predictor of patient survival in the presence of clinical parameters in univariate and multivariate analyses [hazard ratio (HR): 2.84, 95% confidence interval CI (1.74-4.65), p=3.06e-05, [HR] 2.62, 95% CI (1.51-4.53), p=0.001], respectively. Subset analysis demonstrated that the 8-gene signature could identify high-risk patients in stage II-III with improved survival from ACT [(HR) 1.47, 95% CI (1.01-2.14), p=0.044]. The 8-gene signature also stratified risk groups in EGFR-mutated and wild-type patients. In conclusion, the 8-gene signature is a strong and independent predictor that can significantly stratify patients into low- and high-risk groups. Our gene signature also has the potential to predict patients in stage II-III that are likely to benefit from ACT.
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Ringnér M, Staaf J. Consensus of gene expression phenotypes and prognostic risk predictors in primary lung adenocarcinoma. Oncotarget 2018; 7:52957-52973. [PMID: 27437773 PMCID: PMC5288161 DOI: 10.18632/oncotarget.10641] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 11/25/2022] Open
Abstract
Transcriptional profiling of lung adenocarcinomas has identified numerous gene expression phenotype (GEP) and risk prediction (RP) signatures associated with patient outcome. However, classification agreement between signatures, underlying transcriptional programs, and independent signature validation are less studied. We classified 2395 transcriptional adenocarcinoma profiles, assembled from 17 public cohorts, using 11 GEP and seven RP signatures, finding that 16 signatures were associated with patient survival in the total cohort and in multiple individual cohorts. For significant signatures, total cohort hazard ratios were ~2 in univariate analyses (mean=1.95, range=1.4-2.6). Strong classification agreement between signatures was observed, especially for predicted low-risk patients by adenocarcinoma-derived signatures. Expression of proliferation-related genes correlated strongly with GEP subtype classifications and RP scores, driving the gene signature association with prognosis. A three-group consensus definition of samples across 10 GEP classifiers demonstrated aggregation of samples with specific smoking patterns, gender, and EGFR/KRAS mutations, while survival differences were only significant when patients were divided into low- or high-risk. In summary, our study demonstrates a consensus between GEPs and RPs in lung adenocarcinoma through a common underlying transcriptional program. This consensus generalizes reported problems with current signatures in a clinical context, stressing development of new adenocarcinoma-specific single sample predictors for clinical use.
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Affiliation(s)
- Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Medicon Village, SE 22381, Lund, Sweden
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12
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Feldman R, Kim ES. Prognostic and predictive biomarkers post curative intent therapy. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:374. [PMID: 29057234 DOI: 10.21037/atm.2017.07.34] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Large-scale screening trials have demonstrated that early diagnosis of lung cancer results in a significant reduction in lung cancer mortality. Despite improvements in detecting more lung cancers at early stages, the 5-year survival rates of lung cancers diagnosed before widespread disease is only 30-50%. High rates of recurrence, despite early diagnosis, suggest the need to improve treatment strategies based on the likelihood of recurrence in patient subsets, as well as explore the role of predictive markers for therapy selection in the adjuvant setting. In the era of personalized medicine, there have been a wide array of molecular alterations and signatures studied for their potential prognostic and predictive utility, however most have failed to translate into clinical tools. This review will discuss progress made in clinical management of lung cancer, and recent progress in the development of patient selection tools for the refinement of early stage lung cancers.
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Affiliation(s)
- Rebecca Feldman
- Department of Solid Tumor Oncology, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
| | - Edward S Kim
- Department of Solid Tumor Oncology and Investigational Therapeutics, Levine Cancer Institute, Carolinas HealthCare System, Charlotte, NC, USA
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Karlsson A, Brunnström H, Micke P, Veerla S, Mattsson J, La Fleur L, Botling J, Jönsson M, Reuterswärd C, Planck M, Staaf J. Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification. J Thorac Oncol 2017; 12:1257-1267. [PMID: 28535939 DOI: 10.1016/j.jtho.2017.05.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/26/2017] [Accepted: 05/12/2017] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Large cell lung cancer (LCLC) and large cell neuroendocrine carcinoma (LCNEC) constitute a small proportion of NSCLC. The WHO 2015 classification guidelines changed the definition of the debated histological subtype LCLC to be based on immunomarkers for adenocarcinoma and squamous cancer. We sought to determine whether these new guidelines also translate into the transcriptional landscape of lung cancer, and LCLC specifically. METHODS Gene expression profiling was performed by using Illumina V4 HT12 microarrays (Illumina, San Diego, CA) on samples from 159 cases (comprising all histological subtypes, including 10 classified as LCLC WHO 2015 and 14 classified as LCNEC according to the WHO 2015 guidelines), with complimentary mutational and immunohistochemical data. Derived transcriptional phenotypes were validated in 199 independent tumors, including six WHO 2015 LCLCs and five LCNECs. RESULTS Unsupervised analysis of gene expression data identified a phenotype comprising 90% of WHO 2015 LCLC tumors, with characteristics of poorly differentiated proliferative cancer, a 90% tumor protein p53 gene (TP53) mutation rate, and lack of well-known NSCLC oncogene driver alterations. Validation in independent data confirmed aggregation of WHO 2015 LCLCs in the specific phenotype. For LCNEC tumors, the unsupervised gene expression analysis suggested two different transcriptional patterns corresponding to a proposed genetic division of LCNEC tumors into SCLC-like and NSCLC-like cancer on the basis of TP53 and retinoblastoma 1 gene (RB1) alteration patterns. CONCLUSIONS Refined classification of LCLC has implications for diagnosis, prognostics, and therapy decisions. Our molecular analyses support the WHO 2015 classification of LCLC and LCNEC tumors, which herein follow different tumorigenic paths and can accordingly be stratified into different transcriptional subgroups, thus linking diagnostic immunohistochemical staining-driven classification with the transcriptional landscape of lung cancer.
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Affiliation(s)
- Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Hans Brunnström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Department of Pathology, Regional Laboratories Region Skåne, Lund, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Srinivas Veerla
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johanna Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Linnea La Fleur
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Christel Reuterswärd
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden; Department of Respiratory Medicine and Allergology, Skåne University Hospital, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden.
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Ringnér M, Jönsson G, Staaf J. Prognostic and Chemotherapy Predictive Value of Gene-Expression Phenotypes in Primary Lung Adenocarcinoma. Clin Cancer Res 2015; 22:218-29. [DOI: 10.1158/1078-0432.ccr-15-0529] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/03/2015] [Indexed: 11/16/2022]
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15
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Santos C, Sanz-Pamplona R, Nadal E, Grasselli J, Pernas S, Dienstmann R, Moreno V, Tabernero J, Salazar R. Intrinsic cancer subtypes--next steps into personalized medicine. Cell Oncol (Dordr) 2015; 38:3-16. [PMID: 25586691 DOI: 10.1007/s13402-014-0203-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2014] [Indexed: 02/08/2023] Open
Abstract
Recent technological advances have significantly improved our understanding of tumor biology by means of high-throughput mutation and transcriptome analyses. The application of genomics has revealed the mutational landscape and the specific deregulated pathways in different tumor types. At a transcriptional level, multiple gene expression signatures have been developed to identify biologically distinct subgroups of tumors. By supervised analysis, several prognostic signatures have been generated, some of them being commercially available. However, an unsupervised approach is required to discover a priori unknown molecular subtypes, the so-called intrinsic subtypes. Moreover, an integrative analysis of the molecular events associated with tumor biology has been translated into a better tumor classification. This molecular characterization confers new opportunities for therapeutic strategies in the management of cancer patients. However, the applicability of these new molecular classifications is limited because of several issues such as technological validation and cost. Further comparison with well-established clinical and pathological features is expected to accelerate clinical translation. In this review, we will focus on the data reported on molecular classification in the most common tumor types such as breast, colorectal and lung carcinoma, with special emphasis on recent data regarding tumor intrinsic subtypes. Likewise, we will review the potential applicability of these new classifications in the clinical routine.
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Affiliation(s)
- Cristina Santos
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat, Av. Gran Via 199-203, 08907, Barcelona, Spain
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Zhang D, Huang Y, Wang H. [Advances of driver gene and targeted therapy of non-small cell lung cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2014; 17:750-4. [PMID: 25342042 PMCID: PMC6000403 DOI: 10.3779/j.issn.1009-3419.2014.10.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Lung cancer is the leading cause of cancer-related mortality in the worldwide. The discovery of drive gene makes tumor treatment is no longer "one-size-fits-all". Targeted therapy to change the present situation of cancer drugs become "bullet" with eyes, the effect is visible and bring a revolution in the treatment of lung cancer. The diver gene and targeted therapy have became the new cedule of non-small cell lung cancer (NSCLC). Society of Clinical Oncology (ASCO) has showed 11 kinds of diver genes. Here, we review the functional and structural characteristics and the targeted therapy in the 11 kinds of driver gene mutations.
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Affiliation(s)
- Dan Zhang
- Department of Postgraduate, Hebei United University, Tangshan 063009, China
| | - Yan Huang
- Department of Respiratory Medicine, the Affiliated Hospital of Hebei United University, Tangshan 063000, China
| | - Hongyang Wang
- Department of Respiratory Medicine, the Affiliated Hospital of Hebei United University, Tangshan 063000, China
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Karlsson A, Ringnér M, Lauss M, Botling J, Micke P, Planck M, Staaf J. Genomic and transcriptional alterations in lung adenocarcinoma in relation to smoking history. Clin Cancer Res 2014; 20:4912-24. [PMID: 25037737 DOI: 10.1158/1078-0432.ccr-14-0246] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Cigarette smoking is the major pathogenic factor for lung cancer. The precise mechanisms of tobacco-related carcinogenesis and its effect on the genomic and transcriptional landscape in lung cancer are not fully understood. EXPERIMENTAL DESIGN A total of 1,398 (277 never-smokers and 1,121 smokers) genomic and 1,449 (370 never-smokers and 1,079 smokers) transcriptional profiles were assembled from public lung adenocarcinoma cohorts, including matched next-generation DNA-sequencing data (n = 423). Unsupervised and supervised methods were used to identify smoking-related copy-number alterations (CNAs), predictors of smoking status, and molecular subgroups. RESULTS Genomic meta-analyses showed that never-smokers and smokers harbored a similar frequency of total CNAs, although specific regions (5q, 8q, 16p, 19p, and 22q) displayed a 20% to 30% frequency difference between the two groups. Importantly, supervised classification analyses based on CNAs or gene expression could not accurately predict smoking status (balanced accuracies ∼60% to 80%). However, unsupervised multicohort transcriptional profiling stratified adenocarcinomas into distinct molecular subgroups with specific patterns of CNAs, oncogenic mutations, and mutation transversion frequencies that were independent of the smoking status. One subgroup included approximately 55% to 90% of never-smokers and approximately 20% to 40% of smokers (both current and former) with molecular and clinical features of a less aggressive and smoking-unrelated disease. Given the considerable intragroup heterogeneity in smoking-defined subgroups, especially among former smokers, our results emphasize the clinical importance of accurate molecular characterization of lung adenocarcinoma. CONCLUSIONS The landscape of smoking-related CNAs and transcriptional alterations in adenocarcinomas is complex, heterogeneous, and with moderate differences. Our results support a molecularly distinct less aggressive adenocarcinoma entity, arising in never-smokers and a subset of smokers.
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Affiliation(s)
- Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Markus Ringnér
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Martin Lauss
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden.
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Planck M, Edlund K, Botling J, Micke P, Isaksson S, Staaf J. Genomic and transcriptional alterations in lung adenocarcinoma in relation to EGFR and KRAS mutation status. PLoS One 2013; 8:e78614. [PMID: 24205279 PMCID: PMC3812039 DOI: 10.1371/journal.pone.0078614] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
Introduction In lung adenocarcinoma, the mutational spectrum is dominated by EGFR and KRAS mutations. Improved knowledge about genomic and transcriptional alterations in and between mutation-defined subgroups may identify genes involved in disease development or progression. Methods Genomic profiles from 457 adenocarcinomas, including 113 EGFR-mutated, 134 KRAS-mutated and 210 EGFR and KRAS-wild type tumors (EGFRwt/KRASwt), and gene expression profiles from 914 adenocarcinomas, including 309 EGFR-mutated, 192 KRAS-mutated, and 413 EGFRwt/KRASwt tumors, were assembled from different repositories. Genomic and transcriptional differences between the three mutational groups were analyzed by both supervised and unsupervised methods. Results EGFR-mutated adenocarcinomas displayed a larger number of copy number alterations and recurrent amplifications, a higher fraction of total loss-of-heterozygosity, higher genomic complexity, and a more distinct expression pattern than EGFR-wild type adenocarcinomas. Several of these differences were also consistent when the three mutational groups were stratified by stage, gender and smoking status. Specific copy number alterations were associated with mutation status, predominantly including regions of gain with the highest frequency in EGFR-mutated tumors. Differential regions included both large and small regions of gain on 1p, 5q34-q35.3, 7p, 7q11.21, 12p12.1, 16p, and 21q, and losses on 6q16.3-q21, 8p, and 9p, with 20-40% frequency differences between the mutational groups. Supervised gene expression analyses identified 96 consistently differentially expressed genes between the mutational groups, and together with unsupervised analyses these analyses highlighted the difficulty in broadly resolving the three mutational groups into distinct transcriptional entities. Conclusions We provide a comprehensive overview of the genomic and transcriptional landscape in lung adenocarcinoma stratified by EGFR and KRAS mutations. Our analyses suggest that the overall genomic and transcriptional landscape of lung adenocarcinoma is affected, but only to a minor extent, by EGFR and KRAS mutation status.
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Affiliation(s)
- Maria Planck
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Medicon Village, Lund, Sweden
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