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Castaldi P, Sauler M. Cigarette Smoking and the Airway Epithelium: Characterizing Changes in Gene Expression over Time. Am J Respir Crit Care Med 2023; 208:749-750. [PMID: 37610776 PMCID: PMC10563183 DOI: 10.1164/rccm.202308-1371ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/23/2023] [Indexed: 08/24/2023] Open
Affiliation(s)
- Peter Castaldi
- Channing Division of Network Medicine Brigham and Women's Hospital Boston, Massachusetts
- Division of General Medicine Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts
| | - Maor Sauler
- Division of Pulmonary, Critical Care, and Sleep Medicine Yale School of Medicine New Haven, Connecticut
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2
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Huang Z, Sun S, Lee M, Maslov AY, Shi M, Waldman S, Marsh A, Siddiqui T, Dong X, Peter Y, Sadoughi A, Shah C, Ye K, Spivack SD, Vijg J. Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking. Nat Genet 2022; 54:492-8. [PMID: 35410377 DOI: 10.1038/s41588-022-01035-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 02/16/2022] [Indexed: 01/19/2023]
Abstract
Although lung cancer risk among smokers is dependent on smoking dose, it remains unknown if this increased risk reflects an increased rate of somatic mutation accumulation in normal lung cells. Here, we applied single-cell whole-genome sequencing of proximal bronchial basal cells from 33 participants aged between 11 and 86 years with smoking histories varying from never-smoking to 116 pack-years. We found an increase in the frequency of single-nucleotide variants and small insertions and deletions with chronological age in never-smokers, with mutation frequencies significantly elevated among smokers. When plotted against smoking pack-years, mutations followed the linear increase in cancer risk until about 23 pack-years, after which no further increase in mutation frequency was observed, pointing toward individual selection for mutation avoidance. Known lung cancer-defined mutation signatures tracked with both age and smoking. No significant enrichment for somatic mutations in lung cancer driver genes was observed.
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3
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Khadirnaikar S, Chatterjee A, Kumar P, Shukla S. A Greedy Algorithm-Based Stem Cell LncRNA Signature Identifies a Novel Subgroup of Lung Adenocarcinoma Patients With Poor Prognosis. Front Oncol 2020; 10:1203. [PMID: 32850350 PMCID: PMC7431877 DOI: 10.3389/fonc.2020.01203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/12/2020] [Indexed: 12/26/2022] Open
Abstract
Cancer stem cells play an essential role in therapy response and aggressiveness of various cancers, including lung adenocarcinoma (LUAD). Interestingly it also shares many features of embryonic stem cells (ESCs). Recently, long non-coding RNAs (lncRNAs) have emerged as a critical regulator of cell physiology. Here, we used expression data of ESCs, LUAD, and normal lung to identify 198 long non-coding hESC-associated lncRNAs (hESC-lncRNAs). Intriguingly, K-means clustering of hESC-associated lncRNAs identified a subgroup of LUAD patients [undifferentiated LUAD (uLUAD)] with high stem cell-like characteristic, decreased differentiation genes expression, and poor survival. We also observed that the uLUAD patients had overexpression of proteins associated with cell proliferation. Interestingly, uLUAD patients were highly enriched with the stemness-related gene sets, and had higher mutation load. A notable result observed was high infiltration of T cells and a higher level of neopeptides in uLUAD patients, making these patients an optimal candidate for immunotherapy. Further, feature selection using greedy algorithm identified 17-hESC-lncRNAs signature, which showed significant consistency with 198 hESC-lncRNAs-based classification, and identified a group of patients with high stem cell-like characteristic in the 10 most common cancer types and CCLE cell lines. These results suggest the conventional role of hESC-lncRNAs in stem cell biology. In summary, we identified a novel subgroup of LUAD patients (uLUAD) using a set of hESC-lncRNAs. The uLUAD patients had high stem cell-like characteristic and reduced survival rate and may be referred for immunotherapy. Furthermore, our analysis also showed the importance of lncRNAs in cancer and cancer stem cells.
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Affiliation(s)
- Seema Khadirnaikar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India.,Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Annesha Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Pranjal Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
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4
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Chiodi I, Mondello C. Life style factors, tumor cell plasticity and cancer stem cells. Mutat Res Rev Mutat Res 2020; 784:108308. [PMID: 32430096 DOI: 10.1016/j.mrrev.2020.108308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022]
Abstract
Cancers are heterogeneous tissues and a layer of heterogeneity is determined by the presence of cells showing stemness traits, known as cancer stem cells (CSCs). Evidence indicates that CSCs are important players in tumor development, progression and relapse. Oncogenic transformation of normal stem cells can give rise to CSCs, but CSCs can also originate from de-differentiation of bulk tumor cells. Thus, factors promoting the increase of normal stem cell pools or stimulating the acquisition of stemness features by tumor cells can have serious consequences on cancer origin and progression. In this review, we will first give an overview of the CSC model of cancer development and we will then discuss the role of life style factors, such as high caloric diet, alcohol drinking and smoking, on the widening of stem cell pools and the induction of CSC features in tumors. Finally, we will discuss some healthy life style factors that can help to prevent cancer.
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Affiliation(s)
- Ilaria Chiodi
- Istituto di Genetica Molecolare L. L. Cavalli-Sforza, CNR, via Abbiategrasso 207, 27100, Pavia, Italy
| | - Chiara Mondello
- Istituto di Genetica Molecolare L. L. Cavalli-Sforza, CNR, via Abbiategrasso 207, 27100, Pavia, Italy.
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5
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Liu Y, Yin N, Wang X, Khoor A, Sambandam V, Ghosh AB, Fields ZA, Murray NR, Justilien V, Fields AP. Chromosome 3q26 Gain Is an Early Event Driving Coordinated Overexpression of the PRKCI, SOX2, and ECT2 Oncogenes in Lung Squamous Cell Carcinoma. Cell Rep 2020; 30:771-782.e6. [PMID: 31968252 PMCID: PMC7238436 DOI: 10.1016/j.celrep.2019.12.071] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/27/2019] [Accepted: 12/18/2019] [Indexed: 02/08/2023] Open
Abstract
Lung squamous cell carcinoma (LSCC) is a prevalent form of lung cancer exhibiting distinctive histological and genetic characteristics. Chromosome 3q26 copy number gain (CNG) is a genetic hallmark of LSCC present in >90% of tumors. We report that 3q26 CNGs occur early in LSCC tumorigenesis, persist during tumor progression, and drive coordinate overexpression of PRKCI, SOX2, and ECT2. Overexpression of PRKCI, SOX2, and ECT2 in the context of Trp53 loss is sufficient to transform mouse lung basal stem cells into tumors with histological and genomic features of LSCC. Functionally, PRKCI and SOX2 collaborate to activate an extensive transcriptional program that enforces a lineage-restricted LSCC phenotype, whereas PRKCI and ECT2 collaborate to promote oncogenic growth. Gene signatures indicative of PKCι-SOX2 and PKCι-ECT2 signaling activity are enriched in the classical subtype of human LSCC and predict distinct therapeutic vulnerabilities. Thus, the PRKCI, SOX2, and ECT2 oncogenes represent a multigenic driver of LSCC.
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MESH Headings
- Carcinogenesis/genetics
- Carcinogenesis/pathology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cell Proliferation/genetics
- Cell Transformation, Neoplastic
- Chromosomes, Human, Pair 3/genetics
- Gene Dosage
- Gene Expression Regulation, Neoplastic
- Gene Silencing
- Humans
- Isoenzymes/genetics
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Oncogenes
- Protein Kinase C/genetics
- Proto-Oncogene Proteins/genetics
- SOXB1 Transcription Factors/genetics
- Signal Transduction
- Transcription, Genetic
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Affiliation(s)
- Yi Liu
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Ning Yin
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Xue Wang
- Department of Health Sciences Research, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Andras Khoor
- Department of Pathology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Vaishnavi Sambandam
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Anwesha B Ghosh
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Zoe A Fields
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Nicole R Murray
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA
| | - Verline Justilien
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA.
| | - Alan P Fields
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL 32224, USA.
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6
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Gradin R, Lindstedt M, Johansson H. Batch adjustment by reference alignment (BARA): Improved prediction performance in biological test sets with batch effects. PLoS One 2019; 14:e0212669. [PMID: 30794641 PMCID: PMC6386283 DOI: 10.1371/journal.pone.0212669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022] Open
Abstract
Many biological data acquisition platforms suffer from inadvertent inclusion of biologically irrelevant variance in analyzed data, collectively termed batch effects. Batch effects can lead to difficulties in downstream analysis by lowering the power to detect biologically interesting differences and can in certain instances lead to false discoveries. They are especially troublesome in predictive modelling where samples in training sets and test sets are often completely correlated with batches. In this article, we present BARA, a normalization method for adjusting batch effects in predictive modelling. BARA utilizes a few reference samples to adjust for batch effects in a compressed data space spanned by the training set. We evaluate BARA using a collection of publicly available datasets and three different prediction models, and compare its performance to already existing methods developed for similar purposes. The results show that data normalized with BARA generates high and consistent prediction performances. Further, they suggest that BARA produces reliable performances independent of the examined classifiers. We therefore conclude that BARA has great potential to facilitate the development of predictive assays where test sets and training sets are correlated with batch.
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Affiliation(s)
| | - Malin Lindstedt
- Department of Immunotechnology, Lund University, Lund, Sweden
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7
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Nimmakayala RK, Seshacharyulu P, Lakshmanan I, Rachagani S, Chugh S, Karmakar S, Rauth S, Vengoji R, Atri P, Talmon GA, Lele SM, Smith LM, Thapa I, Bastola D, Ouellette MM, Batra SK, Ponnusamy MP. Cigarette Smoke Induces Stem Cell Features of Pancreatic Cancer Cells via PAF1. Gastroenterology 2018; 155:892-908.e6. [PMID: 29864419 PMCID: PMC6120776 DOI: 10.1053/j.gastro.2018.05.041] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 05/08/2018] [Accepted: 05/30/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Cigarette smoking is a major risk factor for pancreatic cancer. Aggressive pancreatic tumors contain cancer cells with stem cell features. We investigated whether cigarette smoke induces stem cell features in pancreatic cancer cells. METHODS KrasG12D; Pdx1-Cre mice were exposed to cigarette smoke or clean air (controls) for up to 20 weeks; pancreata were collected and analyzed by histology, quantitative reverse transcription polymerase chain reaction, and confocal immunofluorescence microscopy. HPNE and Capan1 cells were exposed to cigarette smoke extract (CSE), nicotine and nicotine-derived carcinogens (NNN or NNK), or clean air (controls) for 80 days and evaluated for stem cell markers and features using flow cytometry-based autofluorescence, sphere formation, and immunoblot assays. Proteins were knocked down in cells with small interfering RNAs. We performed RNA sequencing analyses of CSE-exposed cells. We used chromatin immunoprecipitation assays to confirm the binding of FOS-like 1, AP-1 transcription factor subunit (FOSL1) to RNA polymerase II-associated factor (PAF1) promoter. We obtained pancreatic ductal adenocarcinoma (PDAC) and matched nontumor tissues (n = 15) and performed immunohistochemical analyses. RESULTS Chronic exposure of HPNE and Capan1 cells to CSE caused them to increase markers of stem cells, including autofluorescence and sphere formation, compared with control cells. These cells increased expression of ABCG2, SOX9, and PAF1, via cholinergic receptor nicotinic alpha 7 subunit (CHRNA7) signaling to mitogen-activated protein kinase 1 and FOSL1. CSE-exposed pancreatic cells with knockdown of PAF1 did not show stem cell features. Exposure of cells to NNN and NNK led to increased expression of CHRNA7, FOSL1, and PAF1 along with stem cell features. Pancreata from KrasG12D; Pdx1-Cre mice exposed to cigarette smoke had increased levels of PAF1 mRNA and protein, compared with control mice, as well as increased expression of SOX9. Levels of PAF1 and FOSL1 were increased in PDAC tissues, especially those from smokers, compared with nontumor pancreatic tissue. CSE exposure increased expression of PHD-finger protein 5A, a pluripotent transcription factor and its interaction with PAF1. CONCLUSIONS Exposure to cigarette smoke activates stem cell features of pancreatic cells, via CHRNA7 signaling and FOSL1 activation of PAF1 expression. Levels of PAF1 are increased in pancreatic tumors of humans and mice with chronic cigarette smoke exposure.
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Affiliation(s)
- Rama Krishna Nimmakayala
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Parthasarathy Seshacharyulu
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Satyanarayana Rachagani
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Seema Chugh
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Saswati Karmakar
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Sanchita Rauth
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Pranita Atri
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Geoffrey A. Talmon
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Subodh M. Lele
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Lynette M. Smith
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, NE
| | - Dhundy Bastola
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, NE
| | - Michel M. Ouellette
- Department of Internal Medicine, College of Medicine, University of Nebraska medical Center, Omaha, NE
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE,Correspondence: Moorthy P. Ponnusamy and Surinder K. Batra, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5870, U.S.A., Phone: 402-559-1170, Fax: 402-559-6650, (M.P.P) and (S.K.B)
| | - Moorthy P. Ponnusamy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE,Correspondence: Moorthy P. Ponnusamy and Surinder K. Batra, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5870, U.S.A., Phone: 402-559-1170, Fax: 402-559-6650, (M.P.P) and (S.K.B)
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8
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De Santis MM, Bölükbas DA, Lindstedt S, Wagner DE. How to build a lung: latest advances and emerging themes in lung bioengineering. Eur Respir J 2018; 52:13993003.01355-2016. [PMID: 29903859 DOI: 10.1183/13993003.01355-2016] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/30/2018] [Indexed: 12/19/2022]
Abstract
Chronic respiratory diseases remain a major cause of morbidity and mortality worldwide. The only option at end-stage disease is lung transplantation, but there are not enough donor lungs to meet clinical demand. Alternative options to increase tissue availability for lung transplantation are urgently required to close the gap on this unmet clinical need. A growing number of tissue engineering approaches are exploring the potential to generate lung tissue ex vivo for transplantation. Both biologically derived and manufactured scaffolds seeded with cells and grown ex vivo have been explored in pre-clinical studies, with the eventual goal of generating functional pulmonary tissue for transplantation. Recently, there have been significant efforts to scale-up cell culture methods to generate adequate cell numbers for human-scale bioengineering approaches. Concomitantly, there have been exciting efforts in designing bioreactors that allow for appropriate cell seeding and development of functional lung tissue over time. This review aims to present the current state-of-the-art progress for each of these areas and to discuss promising new ideas within the field of lung bioengineering.
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Affiliation(s)
- Martina M De Santis
- Lung Bioengineering and Regeneration, Dept of Experimental Medical Sciences, Lund University, Lund, Sweden.,Lung Repair and Regeneration (LRR), Comprehensive Pneumology Center (CPC), Helmholtz Zentrum Munich, Member of the German Center for Lung Research (DZL), Munich, Germany.,Stem Cell Centre, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Deniz A Bölükbas
- Lung Bioengineering and Regeneration, Dept of Experimental Medical Sciences, Lund University, Lund, Sweden.,Stem Cell Centre, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Sandra Lindstedt
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden.,Dept of Cardiothoracic Surgery, Heart and Lung Transplantation, Lund University Hospital, Lund, Sweden
| | - Darcy E Wagner
- Lung Bioengineering and Regeneration, Dept of Experimental Medical Sciences, Lund University, Lund, Sweden .,Lung Repair and Regeneration (LRR), Comprehensive Pneumology Center (CPC), Helmholtz Zentrum Munich, Member of the German Center for Lung Research (DZL), Munich, Germany.,Stem Cell Centre, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
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9
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Staudt MR, Salit J, Kaner RJ, Hollmann C, Crystal RG. Altered lung biology of healthy never smokers following acute inhalation of E-cigarettes. Respir Res 2018; 19:78. [PMID: 29754582 PMCID: PMC5950177 DOI: 10.1186/s12931-018-0778-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 04/16/2018] [Indexed: 12/20/2022] Open
Abstract
Background Little is known about health risks associated with electronic cigarette (EC) use although EC are rising in popularity and have been advocated as a means to quit smoking cigarettes. Methods Ten never-smokers, without exposure history to tobacco products or EC, were assessed at baseline with questionnaire, chest X-ray, lung function, plasma levels of endothelial microparticles (EMP), and bronchoscopy to obtain small airway epithelium (SAE) and alveolar macrophages (AM). One week later, subjects inhaled 10 puffs of “Blu” brand EC, waited 30 min, then another 10 puff; n = 7 were randomized to EC with nicotine and n = 3 to EC without nicotine to assess biological responses in healthy, naive individuals. Results Two hr. post-EC exposure, subjects were again assessed as at baseline. No significant changes in clinical parameters were observed. Biological changes were observed compared to baseline, including altered transcriptomes of SAE and AM for all subjects and elevated plasma EMP levels following inhalation of EC with nicotine. Conclusions This study provides in vivo human data demonstrating that acute inhalation of EC aerosols dysregulates normal human lung homeostasis in a limited cohort of healthy naïve individuals. These observations have implications to new EC users, nonsmokers exposed to secondhand EC aerosols and cigarette smokers using EC to quit smoking. Trial registration ClinicalTrials.gov NCT01776398 (registered 10/12/12), NCT02188511 (registered 7/2/14). Electronic supplementary material The online version of this article (10.1186/s12931-018-0778-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michelle R Staudt
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, USA
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, USA
| | - Robert J Kaner
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, USA
| | - Charleen Hollmann
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, USA.
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10
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Wagner DE, Cardoso WV, Gilpin SE, Majka S, Ott H, Randell SH, Thébaud B, Waddell T, Weiss DJ; ATS Subcommittee on Stem Cells and Cell Therapies. An Official American Thoracic Society Workshop Report 2015. Stem Cells and Cell Therapies in Lung Biology and Diseases. Ann Am Thorac Soc 2016; 13:S259-78. [PMID: 27509163 DOI: 10.1513/AnnalsATS.201606-466ST] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The University of Vermont College of Medicine, in collaboration with the NHLBI, Alpha-1 Foundation, American Thoracic Society, Cystic Fibrosis Foundation, European Respiratory Society, International Society for Cellular Therapy, and the Pulmonary Fibrosis Foundation, convened a workshop, "Stem Cells and Cell Therapies in Lung Biology and Lung Diseases," held July 27 to 30, 2015, at the University of Vermont. The conference objectives were to review the current understanding of the role of stem and progenitor cells in lung repair after injury and to review the current status of cell therapy and ex vivo bioengineering approaches for lung diseases. These are all rapidly expanding areas of study that both provide further insight into and challenge traditional views of mechanisms of lung repair after injury and pathogenesis of several lung diseases. The goals of the conference were to summarize the current state of the field, discuss and debate current controversies, and identify future research directions and opportunities for both basic and translational research in cell-based therapies for lung diseases. This 10th anniversary conference was a follow up to five previous biennial conferences held at the University of Vermont in 2005, 2007, 2009, 2011, and 2013. Each of those conferences, also sponsored by the National Institutes of Health, American Thoracic Society, and respiratory disease foundations, has been important in helping guide research and funding priorities. The major conference recommendations are summarized at the end of the report and highlight both the significant progress and major challenges in these rapidly progressing fields.
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11
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Yang J, Zuo WL, Fukui T, Chao I, Gomi K, Lee B, Staudt MR, Kaner RJ, Strulovici-Barel Y, Salit J, Crystal RG, Shaykhiev R. Smoking-Dependent Distal-to-Proximal Repatterning of the Adult Human Small Airway Epithelium. Am J Respir Crit Care Med 2017; 196:340-352. [PMID: 28345955 DOI: 10.1164/rccm.201608-1672oc] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RATIONALE Small airways are the primary site of pathologic changes in chronic obstructive pulmonary disease (COPD), the major smoking-induced lung disorder. OBJECTIVES On the basis of the concept of proximal-distal patterning that determines regional specialization of the airway epithelium during lung development, we hypothesized that a similar program operates in the adult human lung being altered by smoking, leading to decreased regional identity of the small airway epithelium (SAE). METHODS The proximal and distal airway signatures were identified by comparing the transcriptomes of large and small airway epithelium samples obtained by bronchoscopy from healthy nonsmokers. The expression of these signatures was evaluated in the SAE of healthy smokers and smokers with COPD compared with that of healthy nonsmokers. The capacity of airway basal stem cells (BCs) to maintain region-associated phenotypes was evaluated using the air-liquid interface model. MEASUREMENTS AND MAIN RESULTS The distal and proximal airway signatures, containing 134 and 233 genes, respectively, were identified. These signatures included known developmental regulators of airway patterning, as well as novel regulators such as epidermal growth factor receptor, which was associated with the proximal airway phenotype. In the SAE of smokers with COPD, there was a dramatic smoking-dependent loss of the regional transcriptome identity with concomitant proximalization. This repatterning phenotype was reproduced by stimulating SAE BCs with epidermal growth factor, which was up-regulated in the SAE of smokers, during differentiation of SAE BCs in vitro. CONCLUSIONS Smoking-induced global distal-to-proximal reprogramming of the SAE represents a novel pathologic feature of COPD and is mediated by exaggerated epidermal growth factor/epidermal growth factor receptor signaling in SAE BCs.
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Affiliation(s)
- Jing Yang
- 1 Department of Genetic Medicine and.,2 Department of Respiratory Medicine, West China Hospital, Sichuan University, Sichuan, China
| | | | | | | | - Kazunori Gomi
- 3 Department of Medicine, Weill Cornell Medical College, New York, New York; and
| | - Busub Lee
- 3 Department of Medicine, Weill Cornell Medical College, New York, New York; and
| | | | - Robert J Kaner
- 1 Department of Genetic Medicine and.,3 Department of Medicine, Weill Cornell Medical College, New York, New York; and
| | | | | | - Ronald G Crystal
- 1 Department of Genetic Medicine and.,3 Department of Medicine, Weill Cornell Medical College, New York, New York; and
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12
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Riester M, Wu HJ, Zehir A, Gönen M, Moreira AL, Downey RJ, Michor F. Distance in cancer gene expression from stem cells predicts patient survival. PLoS One 2017; 12:e0173589. [PMID: 28333954 PMCID: PMC5363813 DOI: 10.1371/journal.pone.0173589] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/23/2017] [Indexed: 12/13/2022] Open
Abstract
The degree of histologic cellular differentiation of a cancer has been associated with prognosis but is subjectively assessed. We hypothesized that information about tumor differentiation of individual cancers could be derived objectively from cancer gene expression data, and would allow creation of a cancer phylogenetic framework that would correlate with clinical, histologic and molecular characteristics of the cancers, as well as predict prognosis. Here we utilized mRNA expression data from 4,413 patient samples with 7 diverse cancer histologies to explore the utility of ordering samples by their distance in gene expression from that of stem cells. A differentiation baseline was obtained by including expression data of human embryonic stem cells (hESC) and human mesenchymal stem cells (hMSC) for solid tumors, and of hESC and CD34+ cells for liquid tumors. We found that the correlation distance (the degree of similarity) between the gene expression profile of a tumor sample and that of stem cells orients cancers in a clinically coherent fashion. For all histologies analyzed (including carcinomas, sarcomas, and hematologic malignancies), patients with cancers with gene expression patterns most similar to that of stem cells had poorer overall survival. We also found that the genes in all undifferentiated cancers of diverse histologies that were most differentially expressed were associated with up-regulation of specific oncogenes and down-regulation of specific tumor suppressor genes. Thus, a stem cell-oriented phylogeny of cancers allows for the derivation of a novel cancer gene expression signature found in all undifferentiated forms of diverse cancer histologies, that is competitive in predicting overall survival in cancer patients compared to previously published prediction models, and is coherent in that gene expression was associated with up-regulation of specific oncogenes and down-regulation of specific tumor suppressor genes associated with regulation of the multicellular state.
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Affiliation(s)
- Markus Riester
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, United States of America
| | - Hua-Jun Wu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, United States of America
| | - Ahmet Zehir
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY United States of America
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY United States of America
| | - Andre L. Moreira
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY United States of America
| | - Robert J. Downey
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY United States of America
- * E-mail: (RJD); (FM)
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, United States of America
- * E-mail: (RJD); (FM)
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13
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Kadara H, Scheet P, Wistuba II, Spira AE. Early Events in the Molecular Pathogenesis of Lung Cancer. Cancer Prev Res (Phila) 2016; 9:518-27. [PMID: 27006378 DOI: 10.1158/1940-6207.capr-15-0400] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/01/2016] [Indexed: 11/16/2022]
Abstract
The majority of cancer-related deaths in the United States and worldwide are attributed to lung cancer. There are more than 90 million smokers in the United States who represent a significant population at elevated risk for lung malignancy. In other epithelial tumors, it has been shown that if neoplastic lesions can be detected and treated at their intraepithelial stage, patient prognosis is significantly improved. Thus, new strategies to detect and treat lung preinvasive lesions are urgently needed in order to decrease the overwhelming public health burden of lung cancer. Limiting these advances is a poor knowledge of the earliest events that underlie lung cancer development and that would constitute markers and targets for early detection and prevention. This review summarizes the state of knowledge of human lung cancer pathogenesis and the molecular pathology of premalignant lung lesions, with a focus on the molecular premalignant field that associates with lung cancer development. Lastly, we highlight new approaches and models to study genome-wide alterations in human lung premalignancy in order to facilitate the discovery of new markers for early detection and prevention of this fatal disease. Cancer Prev Res; 9(7); 518-27. ©2016 AACR.
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Affiliation(s)
- Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas. The University of Texas Graduate School of Biomedical Sciences, Houston, Texas.
| | - Paul Scheet
- The University of Texas Graduate School of Biomedical Sciences, Houston, Texas. Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Avrum E Spira
- Section of Computational Biomedicine, Boston University School of Medicine, Boston University, Boston, Massachusetts
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14
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Liu Y, Yang S, Li MY, Huang R, Ng CS, Wan IY, Long X, Wu J, Wu B, Du J, Mok TS, Underwood MJ, Chen GG. Tumorigenesis of smoking carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone is related to its ability to stimulate thromboxane synthase and enhance stemness of non-small cell lung cancer stem cells. Cancer Lett 2016; 370:198-206. [PMID: 26518146 DOI: 10.1016/j.canlet.2015.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/20/2015] [Accepted: 10/20/2015] [Indexed: 12/21/2022]
Abstract
Lung cancer stem cells (LCSCs) play a critical role in lung cancer development, however, it is unknown whether thromboxane synthase (TXS) plays a role in the maintenance of LCSCs stemness. This study aimed to determine the in vivo role of TXS in lung cancer induced by 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), a smoking carcinogen. Results showed that ozagrel, a TXS blocker, suppressed NNK-induced lung tumors in mice. The expressions of CD133 and ALDH1A1 were positively associated with TXS. Similar results were observed in human NSCLC tumor samples. NNK significantly stimulated TXS and enhanced the generation of LCSCs, evident by the upregulation of CD133 and ALDH1A1 expression, and the increase in the number and size of tumor spheres. NNK also promoted the expression of LCSC-related molecules including β-catenin and Nanog. All these NNK-mediated effects could be offset by ozagrel. In the colony formation assay, NNK increased whereas ozagrel decreased the number of colonies. Collectively, LCSCs and TXS participate in NNK-induced lung cancer. Our data suggest that TXS is a promising therapeutic target as it is a key molecular in NNK-mediated stemness of LCSCs.
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Abstract
In the past 2 years, lung cancer research and clinical care have advanced significantly. Advancements in the field have improved outcomes and promise to lead to further reductions in deaths from lung cancer, the leading cause of cancer death worldwide. These advances include identification of new molecular targets for personalized targeted therapy, validation of molecular signatures of lung cancer risk in smokers, progress in lung tumor immunotherapy, and implementation of population-based lung cancer screening with chest computed tomography in the United States. In this review, we highlight recent research in these areas and challenges for the future.
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Affiliation(s)
- Avrum Spira
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - Balazs Halmos
- Department of Medicine, Columbia University Medical Center, New York, New York; and
| | - Charles A. Powell
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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16
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Abstract
The earliest abnormality in the lung associated with smoking is hyperplasia of airway basal cells, the stem/progenitor cells of the ciliated and secretory cells that are central to pulmonary host defense. Using cell biology and 'omics technologies to assess basal cells isolated from bronchoscopic brushings of nonsmokers, smokers, and smokers with chronic obstructive pulmonary disease (COPD), compelling evidence has been provided in support of the concept that airway basal cells are central to the pathogenesis of smoking-associated lung diseases. When confronted by the chronic stress of smoking, airway basal cells become disorderly, regress to a more primitive state, behave as dictated by their inheritance, are susceptible to acquired changes in their genome, lose the capacity to regenerate the epithelium, are responsible for the major changes in the airway that characterize COPD, and, with persistent stress, can undergo malignant transformation. Together, these observations led to the conclusion that accelerated loss of lung function in susceptible individuals begins with disordered airway basal cell biology (i.e., that airway basal cells are the "smoking gun" of COPD, a potential target for the development of therapies to prevent smoking-related lung disorders).
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Affiliation(s)
- Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York
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17
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Shaykhiev R, Crystal RG. Early events in the pathogenesis of chronic obstructive pulmonary disease. Smoking-induced reprogramming of airway epithelial basal progenitor cells. Ann Am Thorac Soc 2014; 11 Suppl 5:S252-8. [PMID: 25525728 PMCID: PMC4298974 DOI: 10.1513/annalsats.201402-049aw] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 03/17/2014] [Indexed: 12/17/2022] Open
Abstract
The airway epithelium is the primary site of the earliest pathologic changes induced by smoking, contributing to the development of chronic obstructive pulmonary disease (COPD). The normal human airway epithelium is composed of several major cell types, including differentiated ciliated and secretory cells, intermediate undifferentiated cells, and basal cells (BC). BC contain the stem/progenitor cell population responsible for maintenance of the normally differentiated airway epithelium. Although inflammatory and immune processes play a significant role in the pathogenesis of COPD, the earliest lesions include hyperplasia of the BC population, suggesting that the disease may start with this cell type. Apart from BC hyperplasia, smoking induces a number of COPD-relevant airway epithelial remodeling phenotypes that are likely initiated in the BC population, including mucous cell hyperplasia, squamous cell metaplasia, epithelial-mesenchymal transition, altered ciliated and nonmucous secretory cell differentiation, and suppression of junctional barrier integrity. Significant progress has been recently made in understanding the biology of human airway BC, including gene expression features, stem/progenitor, and other functions, including interaction with other airway cell types. Accumulating evidence suggests that human airway BC function as both sensors and cellular sources of various cytokines and growth factors relevant to smoking-associated airway injury, as well as the origin of various molecular and histological phenotypes relevant to the pathogenesis of COPD. In the context of these considerations, we suggest that early BC-specific smoking-induced molecular changes are critical to the pathogenesis of COPD, and these represent a candidate target for novel therapeutic approaches to prevent COPD progression in susceptible individuals.
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Affiliation(s)
- Renat Shaykhiev
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York
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18
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Vlashi E, Pajonk F. Cancer stem cells, cancer cell plasticity and radiation therapy. Semin Cancer Biol 2014; 31:28-35. [PMID: 25025713 DOI: 10.1016/j.semcancer.2014.07.001] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/24/2014] [Accepted: 07/05/2014] [Indexed: 12/19/2022]
Abstract
Since the first prospective identification of cancer stem cells in solid cancers the cancer stem cell hypothesis has reemerged as a research topic of increasing interest. It postulates that solid cancers are organized hierarchically with a small number of cancer stem cells driving tumor growth, repopulation after injury and metastasis. They give rise to differentiated progeny, which lack these features. The model predicts that for any therapy to provide cure, all cancer stem cells have to be eliminated while the survival of differentiated progeny is less critical. In this review we discuss recent reports challenging the idea of a unidirectional differentiation of cancer cells. These reports provide evidence supporting the idea that non-stem cancer cells exhibit a remarkable degree of plasticity that allows them to re-acquire cancer stem cell traits, especially in the context of radiation therapy. We summarize conditions under which differentiation is reversed and discuss the current knowledge of the underlying mechanisms.
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Affiliation(s)
- Erina Vlashi
- Department of Radiation Oncology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Comprehensive Cancer Center at UCLA, Los Angeles, CA 90095, USA
| | - Frank Pajonk
- Department of Radiation Oncology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Comprehensive Cancer Center at UCLA, Los Angeles, CA 90095, USA.
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19
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Justilien V, Walsh MP, Ali SA, Thompson EA, Murray NR, Fields AP. The PRKCI and SOX2 oncogenes are coamplified and cooperate to activate Hedgehog signaling in lung squamous cell carcinoma. Cancer Cell 2014; 25:139-51. [PMID: 24525231 PMCID: PMC3949484 DOI: 10.1016/j.ccr.2014.01.008] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/20/2013] [Accepted: 01/13/2014] [Indexed: 12/20/2022]
Abstract
We report that two oncogenes coamplified on chromosome 3q26, PRKCI and SOX2, cooperate to drive a stem-like phenotype in lung squamous cell carcinoma (LSCC). Protein kinase Cι (PKCι) phosphorylates SOX2, a master transcriptional regulator of stemness, and recruits it to the promoter of Hedgehog (Hh) acyltransferase (HHAT) that catalyzes the rate-limiting step in Hh ligand production. PKCι-mediated SOX2 phosphorylation is required for HHAT promoter occupancy, HHAT expression, and maintenance of a stem-like phenotype. Primary LSCC tumors coordinately overexpress PKCι, SOX2, and HHAT and require PKCι-SOX2-HHAT signaling to maintain a stem-like phenotype. Thus, PKCι and SOX2 are genetically, biochemically, and functionally linked in LSCC, and together they drive tumorigenesis by establishing a cell-autonomous Hh signaling axis.
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MESH Headings
- Acyltransferases/antagonists & inhibitors
- Acyltransferases/genetics
- Acyltransferases/metabolism
- Animals
- Apoptosis
- Blotting, Western
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- High-Throughput Nucleotide Sequencing
- Humans
- Immunoenzyme Techniques
- Isoenzymes/antagonists & inhibitors
- Isoenzymes/genetics
- Isoenzymes/metabolism
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Promoter Regions, Genetic/genetics
- Protein Kinase C/antagonists & inhibitors
- Protein Kinase C/genetics
- Protein Kinase C/metabolism
- RNA, Messenger/genetics
- RNA, Small Interfering/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- SOXB1 Transcription Factors/antagonists & inhibitors
- SOXB1 Transcription Factors/genetics
- SOXB1 Transcription Factors/metabolism
- Signal Transduction
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tumor Cells, Cultured
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Affiliation(s)
- Verline Justilien
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, FL 32224, USA
| | - Michael P Walsh
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, FL 32224, USA
| | - Syed A Ali
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, FL 32224, USA
| | - E Aubrey Thompson
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, FL 32224, USA
| | - Nicole R Murray
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, FL 32224, USA
| | - Alan P Fields
- Department of Cancer Biology, Mayo Clinic Cancer Center, Jacksonville, FL 32224, USA.
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20
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Affiliation(s)
- Renat Shaykhiev
- Department of Genetic Medicine; Weill Cornell Medical College; New York, NY USA
| | - Ronald G Crystal
- Department of Genetic Medicine; Weill Cornell Medical College; New York, NY USA
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