1
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Sujit SJ, Aminu M, Karpinets TV, Chen P, Saad MB, Salehjahromi M, Boom JD, Qayati M, George JM, Allen H, Antonoff MB, Hong L, Hu X, Heeke S, Tran HT, Le X, Elamin YY, Altan M, Vokes NI, Sheshadri A, Lin J, Zhang J, Lu Y, Behrens C, Godoy MCB, Wu CC, Chang JY, Chung C, Jaffray DA, Wistuba II, Lee JJ, Vaporciyan AA, Gibbons DL, Heymach J, Zhang J, Cascone T, Wu J. Enhancing NSCLC recurrence prediction with PET/CT habitat imaging, ctDNA, and integrative radiogenomics-blood insights. Nat Commun 2024; 15:3152. [PMID: 38605064 PMCID: PMC11009351 DOI: 10.1038/s41467-024-47512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/27/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
While we recognize the prognostic importance of clinicopathological measures and circulating tumor DNA (ctDNA), the independent contribution of quantitative image markers to prognosis in non-small cell lung cancer (NSCLC) remains underexplored. In our multi-institutional study of 394 NSCLC patients, we utilize pre-treatment computed tomography (CT) and 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) to establish a habitat imaging framework for assessing regional heterogeneity within individual tumors. This framework identifies three PET/CT subtypes, which maintain prognostic value after adjusting for clinicopathologic risk factors including tumor volume. Additionally, these subtypes complement ctDNA in predicting disease recurrence. Radiogenomics analysis unveil the molecular underpinnings of these imaging subtypes, highlighting downregulation in interferon alpha and gamma pathways in the high-risk subtype. In summary, our study demonstrates that these habitat imaging subtypes effectively stratify NSCLC patients based on their risk levels for disease recurrence after initial curative surgery or radiotherapy, providing valuable insights for personalized treatment approaches.
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Affiliation(s)
- Sheeba J Sujit
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muhammad Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pingjun Chen
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maliazurina B Saad
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Morteza Salehjahromi
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Boom
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Mohamed Qayati
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James M George
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Haley Allen
- Natural Sciences, Rice University, Houston, TX, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lingzhi Hong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Hu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hai T Tran
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalie I Vokes
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ajay Sheshadri
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Julie Lin
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Myrna C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carol C Wu
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joe Y Chang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Chung
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute of Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David A Jaffray
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Institute of Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Lung Cancer Genomics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Lung Cancer Interception Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Institute of Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Salehjahromi M, Karpinets TV, Sujit SJ, Qayati M, Chen P, Aminu M, Saad MB, Bandyopadhyay R, Hong L, Sheshadri A, Lin J, Antonoff MB, Sepesi B, Ostrin EJ, Toumazis I, Huang P, Cheng C, Cascone T, Vokes NI, Behrens C, Siewerdsen JH, Hazle JD, Chang JY, Zhang J, Lu Y, Godoy MCB, Chung C, Jaffray D, Wistuba I, Lee JJ, Vaporciyan AA, Gibbons DL, Gladish G, Heymach JV, Wu CC, Zhang J, Wu J. Synthetic PET from CT improves diagnosis and prognosis for lung cancer: Proof of concept. Cell Rep Med 2024; 5:101463. [PMID: 38471502 PMCID: PMC10983039 DOI: 10.1016/j.xcrm.2024.101463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/07/2023] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
[18F]Fluorodeoxyglucose positron emission tomography (FDG-PET) and computed tomography (CT) are indispensable components in modern medicine. Although PET can provide additional diagnostic value, it is costly and not universally accessible, particularly in low-income countries. To bridge this gap, we have developed a conditional generative adversarial network pipeline that can produce FDG-PET from diagnostic CT scans based on multi-center multi-modal lung cancer datasets (n = 1,478). Synthetic PET images are validated across imaging, biological, and clinical aspects. Radiologists confirm comparable imaging quality and tumor contrast between synthetic and actual PET scans. Radiogenomics analysis further proves that the dysregulated cancer hallmark pathways of synthetic PET are consistent with actual PET. We also demonstrate the clinical values of synthetic PET in improving lung cancer diagnosis, staging, risk prediction, and prognosis. Taken together, this proof-of-concept study testifies to the feasibility of applying deep learning to obtain high-fidelity PET translated from CT.
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Affiliation(s)
| | | | - Sheeba J Sujit
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA
| | - Mohamed Qayati
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA
| | - Pingjun Chen
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA
| | - Muhammad Aminu
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA
| | - Maliazurina B Saad
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Lingzhi Hong
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA; Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ajay Sheshadri
- Department of Pulmonary Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - Julie Lin
- Department of Pulmonary Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin J Ostrin
- Department of General Internal Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Iakovos Toumazis
- Department of Health Services Research, MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Huang
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Chao Cheng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Natalie I Vokes
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey H Siewerdsen
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA; Institute for Data Science in Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - John D Hazle
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA
| | - Joe Y Chang
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Lu
- Department of Nuclear Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Myrna C B Godoy
- Department of Thoracic Imaging, MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Chung
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, TX, USA; Institute for Data Science in Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - David Jaffray
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA; Institute for Data Science in Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, MD Anderson Cancer Center, Houston, TX, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Gregory Gladish
- Department of Thoracic Imaging, MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Carol C Wu
- Department of Thoracic Imaging, MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA; Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA; Lung Cancer Genomics Program, MD Anderson Cancer Center, Houston, TX, USA; Lung Cancer Interception Program, MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Imaging Physics, MD Anderson Cancer Center, Houston, TX, USA; Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA; Institute for Data Science in Oncology, MD Anderson Cancer Center, Houston, TX, USA.
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3
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Tai MC, Bantis LE, Parhy G, Kato T, Tanaka I, Chow CW, Fujimoto J, Behrens C, Hase T, Kawaguchi K, Fahrmann JF, Ostrin EJ, Yokoi K, Chen-Yoshikawa TF, Hasegawa Y, Hanash SM, Wistuba II, Taguchi A. Circulating microRNA Panel for Prediction of Recurrence and Survival in Early-Stage Lung Adenocarcinoma. Int J Mol Sci 2024; 25:2331. [PMID: 38397007 PMCID: PMC10888571 DOI: 10.3390/ijms25042331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/04/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Early-stage lung adenocarcinoma (LUAD) patients remain at substantial risk for recurrence and disease-related death, highlighting the unmet need of biomarkers for the assessment and identification of those in an early stage who would likely benefit from adjuvant chemotherapy. To identify circulating miRNAs useful for predicting recurrence in early-stage LUAD, we performed miRNA microarray analysis with pools of pretreatment plasma samples from patients with stage I LUAD who developed recurrence or remained recurrence-free during the follow-up period. Subsequent validation in 85 patients with stage I LUAD resulted in the development of a circulating miRNA panel comprising miR-23a-3p, miR-320c, and miR-125b-5p and yielding an area under the curve (AUC) of 0.776 in predicting recurrence. Furthermore, the three-miRNA panel yielded an AUC of 0.804, with a sensitivity of 45.8% at 95% specificity in the independent test set of 57 stage I and II LUAD patients. The miRNA panel score was a significant and independent factor for predicting disease-free survival (p < 0.001, hazard ratio [HR] = 1.64, 95% confidence interval [CI] = 1.51-4.22) and overall survival (p = 0.001, HR = 1.51, 95% CI = 1.17-1.94). This circulating miRNA panel is a useful noninvasive tool to stratify early-stage LUAD patients and determine an appropriate treatment plan with maximal efficacy.
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Affiliation(s)
- Mei-Chee Tai
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (G.P.); (T.K.)
| | - Leonidas E. Bantis
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Gargy Parhy
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (G.P.); (T.K.)
| | - Taketo Kato
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (G.P.); (T.K.)
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (K.K.); (T.F.C.-Y.)
| | - Ichidai Tanaka
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan (T.H.); (Y.H.)
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (G.P.); (T.K.)
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (G.P.); (T.K.)
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tetsunari Hase
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan (T.H.); (Y.H.)
| | - Koji Kawaguchi
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (K.K.); (T.F.C.-Y.)
| | - Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.F.F.); (S.M.H.)
| | - Edwin J. Ostrin
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kohei Yokoi
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (K.K.); (T.F.C.-Y.)
| | - Toyofumi F. Chen-Yoshikawa
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (K.K.); (T.F.C.-Y.)
| | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan (T.H.); (Y.H.)
- National Hospital Organization Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Samir M. Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.F.F.); (S.M.H.)
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (G.P.); (T.K.)
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA (G.P.); (T.K.)
- Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya 464-8681, Japan
- Division of Advanced Cancer Diagnostics, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Aichi, Japan
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4
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Wen Z, Luo D, Wang S, Rong R, Evers BM, Jia L, Fang Y, Daoud EV, Yang S, Gu Z, Arner EN, Lewis CM, Solis Soto LM, Fujimoto J, Behrens C, Wistuba II, Yang DM, Brekken RA, O'Donnell KA, Xie Y, Xiao G. Deep Learning-Based H-Score Quantification of Immunohistochemistry-Stained Images. Mod Pathol 2024; 37:100398. [PMID: 38043788 DOI: 10.1016/j.modpat.2023.100398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/17/2023] [Revised: 11/14/2023] [Accepted: 11/21/2023] [Indexed: 12/05/2023]
Abstract
Immunohistochemistry (IHC) is a well-established and commonly used staining method for clinical diagnosis and biomedical research. In most IHC images, the target protein is conjugated with a specific antibody and stained using diaminobenzidine (DAB), resulting in a brown coloration, whereas hematoxylin serves as a blue counterstain for cell nuclei. The protein expression level is quantified through the H-score, calculated from DAB staining intensity within the target cell region. Traditionally, this process requires evaluation by 2 expert pathologists, which is both time consuming and subjective. To enhance the efficiency and accuracy of this process, we have developed an automatic algorithm for quantifying the H-score of IHC images. To characterize protein expression in specific cell regions, a deep learning model for region recognition was trained based on hematoxylin staining only, achieving pixel accuracy for each class ranging from 0.92 to 0.99. Within the desired area, the algorithm categorizes DAB intensity of each pixel as negative, weak, moderate, or strong staining and calculates the final H-score based on the percentage of each intensity category. Overall, this algorithm takes an IHC image as input and directly outputs the H-score within a few seconds, significantly enhancing the speed of IHC image analysis. This automated tool provides H-score quantification with precision and consistency comparable to experienced pathologists but at a significantly reduced cost during IHC diagnostic workups. It holds significant potential to advance biomedical research reliant on IHC staining for protein expression quantification.
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Affiliation(s)
- Zhuoyu Wen
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Danni Luo
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shidan Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ruichen Rong
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Bret M Evers
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Liwei Jia
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yisheng Fang
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Elena V Daoud
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shengjie Yang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Zifan Gu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Emily N Arner
- Department of Surgery, The University of Texas Southwestern Medical Center, Dallas, Texas; Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Cheryl M Lewis
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas; Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Luisa M Solis Soto
- Division of Pathology and Laboratory Medicine, Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fujimoto
- Division of Pathology and Laboratory Medicine, Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Division of Cancer Medicine, Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Division of Pathology and Laboratory Medicine, Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Donghan M Yang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Rolf A Brekken
- Department of Surgery, The University of Texas Southwestern Medical Center, Dallas, Texas; Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, Texas; Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Kathryn A O'Donnell
- Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, Texas; Hamon Center for Regenerative Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas; Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yang Xie
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas; Hamon Center for Regenerative Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas; Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Peter O'Donnell Jr School of Public Health, The University of Texas Southwestern Medical Center, Dallas, Texas; Hamon Center for Regenerative Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas; Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, Texas.
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5
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Barbasch TA, Behrens C, McLain M, Arredondo E, Bell AM. A distinct neurogenomic response to a trade-off between social challenge and opportunity in male sticklebacks ( Gasterosteus aculeatus). Biol Lett 2023; 19:20230253. [PMID: 37935370 PMCID: PMC10645126 DOI: 10.1098/rsbl.2023.0253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/07/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Animals frequently make adaptive decisions about what to prioritize when faced with multiple, competing demands simultaneously. However, the proximate mechanisms of decision-making in the face of competing demands are not well understood. We explored this question using brain transcriptomics in a classic model system: threespined sticklebacks, where males face conflict between courtship and territorial defence. We characterized the behaviour and brain gene expression profiles of males confronted by a trade-off between courtship and territorial defence by comparing them to males not confronted by this trade-off. When faced with the trade-off, males behaviourally prioritized defence over courtship, and this decision was reflected in their brain gene expression profiles. A distinct set of genes and biological processes was recruited in the brain when males faced a trade-off and these responses were largely non-overlapping across two brain regions. Combined, these results raise new questions about the interplay between the neural and molecular mechanisms involved in decision-making.
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Affiliation(s)
- T. A. Barbasch
- School of Integrative Biology, University of Illinois Urbana Champaign, 505 S. Goodwin Ave, Urbana, IL 61801, USA
| | - C. Behrens
- School of Integrative Biology, University of Illinois Urbana Champaign, 505 S. Goodwin Ave, Urbana, IL 61801, USA
| | - M. McLain
- School of Integrative Biology, University of Illinois Urbana Champaign, 505 S. Goodwin Ave, Urbana, IL 61801, USA
| | - E. Arredondo
- School of Integrative Biology, University of Illinois Urbana Champaign, 505 S. Goodwin Ave, Urbana, IL 61801, USA
| | - A. M. Bell
- School of Integrative Biology, University of Illinois Urbana Champaign, 505 S. Goodwin Ave, Urbana, IL 61801, USA
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6
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Diao S, Chen P, Showkatian E, Bandyopadhyay R, Rojas FR, Zhu B, Hong L, Aminu M, Saad MB, Salehjahromi M, Muneer A, Sujit SJ, Behrens C, Gibbons DL, Heymach JV, Kalhor N, Wistuba II, Solis Soto LM, Zhang J, Qin W, Wu J. Automated Cellular-Level Dual Global Fusion of Whole-Slide Imaging for Lung Adenocarcinoma Prognosis. Cancers (Basel) 2023; 15:4824. [PMID: 37835518 PMCID: PMC10571722 DOI: 10.3390/cancers15194824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/08/2023] [Revised: 09/24/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Histopathologic whole-slide images (WSI) are generally considered the gold standard for cancer diagnosis and prognosis. Survival prediction based on WSI has recently attracted substantial attention. Nevertheless, it remains a central challenge owing to the inherent difficulties of predicting patient prognosis and effectively extracting informative survival-specific representations from WSI with highly compounded gigapixels. In this study, we present a fully automated cellular-level dual global fusion pipeline for survival prediction. Specifically, the proposed method first describes the composition of different cell populations on WSI. Then, it generates dimension-reduced WSI-embedded maps, allowing for efficient investigation of the tumor microenvironment. In addition, we introduce a novel dual global fusion network to incorporate global and inter-patch features of cell distribution, which enables the sufficient fusion of different types and locations of cells. We further validate the proposed pipeline using The Cancer Genome Atlas lung adenocarcinoma dataset. Our model achieves a C-index of 0.675 (±0.05) in the five-fold cross-validation setting and surpasses comparable methods. Further, we extensively analyze embedded map features and survival probabilities. These experimental results manifest the potential of our proposed pipeline for applications using WSI in lung adenocarcinoma and other malignancies.
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Affiliation(s)
- Songhui Diao
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen College of Advanced Technology, University of Chinese Academy of Sciences, Shenzhen 518055, China
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pingjun Chen
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eman Showkatian
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rukhmini Bandyopadhyay
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Frank R. Rojas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bo Zhu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lingzhi Hong
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muhammad Aminu
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maliazurina B. Saad
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Morteza Salehjahromi
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amgad Muneer
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sheeba J. Sujit
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V. Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luisa M. Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wenjian Qin
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jia Wu
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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7
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Parra ER, Zhang J, Jiang M, Tamegnon A, Pandurengan RK, Behrens C, Solis L, Haymaker C, Heymach JV, Moran C, Lee JJ, Gibbons D, Wistuba II. Immune cellular patterns of distribution affect outcomes of patients with non-small cell lung cancer. Nat Commun 2023; 14:2364. [PMID: 37185575 PMCID: PMC10130161 DOI: 10.1038/s41467-023-37905-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Studying the cellular geographic distribution in non-small cell lung cancer is essential to understand the roles of cell populations in this type of tumor. In this study, we characterize the spatial cellular distribution of immune cell populations using 23 makers placed in five multiplex immunofluorescence panels and their associations with clinicopathologic variables and outcomes. Our results demonstrate two cellular distribution patterns-an unmixed pattern mostly related to immunoprotective cells and a mixed pattern mostly related to immunosuppressive cells. Distance analysis shows that T-cells expressing immune checkpoints are closer to malignant cells than other cells. Combining the cellular distribution patterns with cellular distances, we can identify four groups related to inflamed and not-inflamed tumors. Cellular distribution patterns and distance are associated with survival in univariate and multivariable analyses. Spatial distribution is a tool to better understand the tumor microenvironment, predict outcomes, and may can help select therapeutic interventions.
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Affiliation(s)
- Edwin Roger Parra
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Jiexin Zhang
- Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mei Jiang
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Auriole Tamegnon
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Carmen Behrens
- Departments of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa Solis
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cara Haymaker
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Victor Heymach
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cesar Moran
- Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jack J Lee
- Departments of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Departments of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio Ivan Wistuba
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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8
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Tai MC, Bantis LE, Parhy G, Kato T, Tanaka I, Chow CW, Fujimoto J, Behrens C, Hase T, Kawaguchi K, Fahrmann JF, Ostrin E, Yokoi K, Chen-Yoshikawa TF, Hasegawa Y, Hanash SM, Wistuba II, Taguchi A. Abstract 3744: A circulating microRNA panel predicts recurrence and survival in early-stage lung adenocarcinoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Early-stage lung adenocarcinoma (LUAD) patients have substantial risk for recurrence and disease-related death. Cisplatin-based adjuvant chemotherapy remains the standard for care of LUAD patients who have undergone surgical resection with a high risk of recurrence. However, adjuvant chemotherapy is associated with increased risk of toxicity including chemotherapy-related death, with only a modest survival benefit. Therefore, there is an unmet need of biomarkers for assessment and identification of those in an early stage who would likely benefit from adjuvant chemotherapy. Circulating miRNAs are stably present in blood and potentially reflect different expressions in cancerous and non-cancerous tissues, making them attractive biomarkers. The purpose of this study was to identify circulating miRNAs useful for predicting recurrence in early-stage LUAD.
Materials and Methods: miRNA microarray analysis was performed with pooled pretreatment plasma samples from stage I LUAD patients who developed recurrence within two years after curative surgery or remained recurrence free over a six-year follow-up period, as well as from healthy controls. miRNA biomarker candidates were assayed in two independent plasma sample sets from 85 stage I LUAD (validation set) and from 57 stage I and II LUAD (test set) patients.
Results: Based on miRNA microarray data and previous reports, predictive performance of miR-23a-3p, miR-23b-3p, miR-191-5p, miR-185-5p, miR-151a-3p, miR-320c, miR-21-5p, miR-125b-5p, miR-30d-5p, and miR-197-3p was evaluated in the validation set. Plasma levels of miR-23a-3p, miR-185-5p, miR-320c, miR-21-5p, miR-125b-5p, miR-30d-5p, and miR-197-3p were significantly higher in those with recurrence as compared to those without. A miRNA panel comprised of miR-23a-3p, miR-320c, and miR-125b-5p was developed based on a logistic regression, with yielding an AUC of 0.776 (95% confidence interval [CI] = 0.660 to 0.893). The three-miRNA panel with fixed coefficients yielded an AUC of 0.804 (95% CI = 0.688 to 0.920) with a sensitivity of 45.8% at 95% specificity in the test set. The miRNA panel score was a significant and independent factor for predicting disease-free survival (DFS; P < 0.001, HR = 1.64, 95% CI = 1.51-4.22) and overall survival (OS; P = 0.001, HR = 1.51, 95% CI = 1.17-1.94).
Conclusion: This circulating miRNA panel may serve as a noninvasive blood test for predicting DFS and OS in early-stage LUAD patients. Our findings provide rationale for further investigation to stratify early-stage LUAD patients using blood-based biomarkers to increase the ability to provide more personalized care.
Citation Format: Mei-Chee Tai, Leonidas E. Bantis, Gargy Parhy, Taketo Kato, Ichidai Tanaka, Chi-Wan Chow, Junya Fujimoto, Carmen Behrens, Tetsunari Hase, Koji Kawaguchi, Johannes F. Fahrmann, Edwin Ostrin, Kohei Yokoi, Toyofumi F. Chen-Yoshikawa, Yoshinori Hasegawa, Samir M. Hanash, Ignacio I. Wistuba, Ayumu Taguchi. A circulating microRNA panel predicts recurrence and survival in early-stage lung adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3744.
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Affiliation(s)
- Mei-Chee Tai
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Gargy Parhy
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Taketo Kato
- 3Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ichidai Tanaka
- 3Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chi-Wan Chow
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Junya Fujimoto
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carmen Behrens
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tetsunari Hase
- 3Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | | | - Edwin Ostrin
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kohei Yokoi
- 3Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | | | - Samir M. Hanash
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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9
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Hernandez SD, Lu W, Serrano AG, Arrechedera CJ, Sanchez-Espiridion B, Ozirmak N, Molina M, Kostousov L, Barnes S, Khan K, Tang X, Fujimoto J, Parra ER, Raso G, Schmidt ST, Behrens C, Heymach J, Zhang J, Chen K, Sepesi B, Cascone T, Gibbons D, Wistuba II, Haymaker C, Solis LM. Abstract 4460: Spatial profiling of immune biomarkers in resected treatment-naïve early stage lung adenocarcinoma. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Recently, neoadjuvant immunotherapy plus chemotherapy has been approved for treatment of resectable non-small cell lung carcinoma (NSCLC). Defining the immune landscape of these tumors and its spatial distribution will help to understand lung cancer biology. Here, we analyzed the distribution of immune-related biomarkers in tumor-defined regions and its associations with clinicopathological variables in resected lung adenocarcinomas using high-plex profiling approaches.
Methodology: Thirty-three FFPE tumor tissues from surgically resected treatment-naïve lung adenocarcinoma stage I/II were used to construct a tissue microarray from the MD Anderson ICON cohort. We used three 1-mm core per patient [2 from central tumor (CT), and 1 from invasive margin (IM)] and performed the GeoMx Digital Spatial Profiling protein protocol to assess 49 immune biomarkers. Pancytokeratin (panCK; epithelial), CD45 (immune) and SYTO 13 (nuclear) were utilized as morphology biomarkers. Regions of interests were placed in cores containing tumor, and segmented in ‘”Tumor (Tu)” (PanCK+) and the “tumor microenvironment (TME)” (PanCK-). Digital counts were normalized using background correction. Statistical analysis was performed using linear mixed model. A p value equal or less than 0.05 was considered significant.
Results: We first compared the relative counts of immune biomarkers in the TME in CT and IM. IM had higher CD3, CD8, CD45RO, as well as CD163 and STING (P ranges 0.006 to 0.035), while CT had higher PD1 (P 0.025). Then we analyzed differential biomarker expression by sex and smoking status. Females had higher counts of Immune related biomarkers: CD45, CD3, CD20, immune checkpoints: PD-L1, VISTA, CTLA4, LAG3, and ICOS, and myeloid: CD68, CD11c, CD163, and B2M (P ranges 0.0005 to 0.046). Smokers had higher counts of CD66b (P 0.007) and B2M (P 0.039) while never smokers had higher counts of HLA-DR, CD34, FoxP3, OX40L, Tim-3, and B7-H3 (P ranges 0.001 to 0.049). Finally, we analyzed Tu segments. IM had higher CD66b, VISTA, CD163, OX40L, HLA-DR, GZMB, STING, and CD8 (P ranges 0.007 to 0.045) than CT. Female patients had higher CD45, CD68, CD11c and CD163 (P ranges 0.008 to 0.045), and males had higher SMA (P 0.005). Smokers had higher CD66b (P 0.007), B2-microglobulin (P 0.043), and never smokers had higher HLA-DR, STING, CD34, CD44, FoxP3 and CD25 (P ranges 0.006 to 0.043).
Conclusions: In this study, biomarker analysis of treatment-naïve adenocarcinoma in CT areas and IM indicates a higher immune response in the IM and presence of inhibitory signaling inside the tumor. Our data also showed that tumors from females have higher immune response than tumors from males, which is concordant with previous studies. Distinct profiling by smoking status was also observed. Further analysis of gene expression analysis of this set is ongoing.
Citation Format: Sharia D. Hernandez, Wei Lu, Alejandra G. Serrano, Claudio J. Arrechedera, Beatriz Sanchez-Espiridion, Nejla Ozirmak, Max Molina, Larisa Kostousov, Sean Barnes, Khaja Khan, Ximing Tang, Junya Fujimoto, Edwin R. Parra, Gabriela Raso, Stephanie T. Schmidt, Carmen Behrens, John Heymach, Jianjun Zhang, Ken Chen, Boris Sepesi, Tina Cascone, Don Gibbons, Ignacio I. Wistuba, Cara Haymaker, Luisa M. Solis. Spatial profiling of immune biomarkers in resected treatment-naïve early stage lung adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4460.
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Affiliation(s)
- Sharia D. Hernandez
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Wei Lu
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Alejandra G. Serrano
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | | | | | - Nejla Ozirmak
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Max Molina
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Larisa Kostousov
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Sean Barnes
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Khaja Khan
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Ximing Tang
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Junya Fujimoto
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Edwin R. Parra
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Gabriela Raso
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Stephanie T. Schmidt
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Carmen Behrens
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - John Heymach
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Jianjun Zhang
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Ken Chen
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Boris Sepesi
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Tina Cascone
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Don Gibbons
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Ignacio I. Wistuba
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Cara Haymaker
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
| | - Luisa M. Solis
- 1The University of Texas MD Anderson Cancer Center, MD Anderson Cancer Center, TX
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10
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Wang S, Rong R, Yang DM, Fujimoto J, Bishop JA, Yan S, Cai L, Behrens C, Berry LD, Wilhelm C, Aisner D, Sholl L, Johnson BE, Kwiatkowski DJ, Wistuba II, Bunn PA, Minna J, Xiao G, Kris MG, Xie Y. Features of tumor-microenvironment images predict targeted therapy survival benefit in patients with EGFR-mutant lung cancer. J Clin Invest 2023; 133:e160330. [PMID: 36647832 PMCID: PMC9843059 DOI: 10.1172/jci160330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/08/2022] [Indexed: 01/18/2023] Open
Abstract
Tyrosine kinase inhibitors (TKIs) targeting epidermal growth factor receptor (EGFR) are effective for many patients with lung cancer with EGFR mutations. However, not all patients are responsive to EGFR TKIs, including even those harboring EGFR-sensitizing mutations. In this study, we quantified the cells and cellular interaction features of the tumor microenvironment (TME) using routine H&E-stained biopsy sections. These TME features were used to develop a prediction model for survival benefit from EGFR TKI therapy in patients with lung adenocarcinoma and EGFR-sensitizing mutations in the Lung Cancer Mutation Consortium 1 (LCMC1) and validated in an independent LCMC2 cohort. In the validation data set, EGFR TKI treatment prolonged survival in the predicted-to-benefit group but not in the predicted-not-to-benefit group. Among patients treated with EGFR TKIs, the predicted-to-benefit group had prolonged survival outcomes compared with the predicted not-to-benefit group. The EGFR TKI survival benefit positively correlated with tumor-tumor interaction image features and negatively correlated with tumor-stroma interaction. Moreover, the tumor-stroma interaction was associated with higher activation of the hepatocyte growth factor/MET-mediated PI3K/AKT signaling pathway and epithelial-mesenchymal transition process, supporting the hypothesis of fibroblast-involved resistance to EGFR TKI treatment.
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Affiliation(s)
- Shidan Wang
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ruichen Rong
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Donghan M. Yang
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Justin A. Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shirley Yan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ling Cai
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Carmen Behrens
- Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lynne D. Berry
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Clare Wilhelm
- Department of Thoracic Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dara Aisner
- Department of Pathology, University of Colorado, Denver, Colorado, USA
| | - Lynette Sholl
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, Massachusetts, USA
| | - Bruce E. Johnson
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - David J. Kwiatkowski
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard University, Boston, Massachusetts, USA
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Paul A. Bunn
- Division of Medical Oncology, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - John Minna
- Hamon Center for Therapeutic Oncology Research
- Departments of Internal Medicine and Pharmacology
- Simmons Comprehensive Cancer Center, and
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Simmons Comprehensive Cancer Center, and
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Mark G. Kris
- Department of Thoracic Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, The Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Simmons Comprehensive Cancer Center, and
- Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA
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11
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Chen R, Li J, Fujimoto J, Hong L, Hu X, Quek K, Tang M, Mitra A, Behrens C, Chow CW, Jiang P, Little LD, Gumbs C, Song X, Zhang J, Tan D, Heymach JV, Wistuba I, Futreal PA, Gibbons DL, Byers LA, Zhang J, Reuben A. Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma. J Exp Clin Cancer Res 2022; 41:172. [PMID: 35546239 PMCID: PMC9092788 DOI: 10.1186/s13046-022-02361-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/10/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Lung cancer is the leading cause of cancer death, partially owing to its extensive heterogeneity. The analysis of intertumor heterogeneity has been limited by an inability to concurrently obtain tissue from synchronous metastases unaltered by multiple prior lines of therapy.
Methods
In order to study the relationship between genomic, epigenomic and T cell repertoire heterogeneity in a rare autopsy case from a 32-year-old female never-smoker with left lung primary late-stage lung adenocarcinoma (LUAD), we did whole-exome sequencing (WES), DNA methylation and T cell receptor (TCR) sequencing to characterize the immunogenomic landscape of one primary and 19 synchronous metastatic tumors.
Results
We observed heterogeneous mutation, methylation, and T cell patterns across distinct metastases. Only TP53 mutation was detected in all tumors suggesting an early event while other cancer gene mutations were later events which may have followed subclonal diversification. A set of prevalent T cell clonotypes were completely excluded from left-side thoracic tumors indicating distinct T cell repertoire profiles between left-side and non left-side thoracic tumors. Though a limited number of predicted neoantigens were shared, these were associated with homology of the T cell repertoire across metastases. Lastly, ratio of methylated neoantigen coding mutations was negatively associated with T-cell density, richness and clonality, suggesting neoantigen methylation may partially drive immunosuppression.
Conclusions
Our study demonstrates heterogeneous genomic and T cell profiles across synchronous metastases and how restriction of unique T cell clonotypes within an individual may differentially shape the genomic and epigenomic landscapes of synchronous lung metastases.
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12
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Akhave N, Zhang J, Bayley E, Frank M, Chiou SH, Behrens C, Chen R, Hu X, Parra ER, Lee WC, Swisher S, Solis L, Weissferdt A, Moran C, Kalhor N, Zhang J, Scheet P, Vaporciyan AA, Sepesi B, Gibbons DL, Heymach JV, Lee JJ, Wistuba II, Andrew Futreal P, Zhang J, Fujimoto J, Reuben A. Immunogenomic profiling of lung adenocarcinoma reveals poorly differentiated tumors are associated with an immunogenic tumor microenvironment. Lung Cancer 2022; 172:19-28. [PMID: 35973335 DOI: 10.1016/j.lungcan.2022.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 04/13/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 10/15/2022]
Abstract
OBJECTIVES Pathologists have routinely observed distinct histologic patterns of growth in early-stage lung adenocarcinoma (LUAD), which have been suggested to be associated with prognosis. Herein, we investigated the relationship between LUAD patterns of growth, as defined by the updated international association for the study of lung cancer (IASLC) grading criteria, and differences in the tumor immune microenvironment to identify predictors of response to immunotherapy. METHODS 174 resected stage I-III LUAD tumors were classified by histologic pattern of growth (i.e. solid, micropapillary, acinar, papillary, and lepidic) and then grouped as well differentiated, moderately differentiated, and poorly differentiated. Comprehensive multiplatform analysis including whole exome sequencing, gene expression profiling, immunohistochemistry, CIBERSORT, and T-cell receptor sequencing was performed and groups were compared for differences in genomic drivers, immune cell infiltrate, clonality, and survival. Finally, multivariate analysis was performed adjusting for pathologic stage and smoking status. RESULTS Poorly differentiated tumors demonstrated a strong association with smoking relative to moderately differentiated or well differentiated tumors. However, unlike in prior reports, poorly differentiated tumors were not associated with a worse survival after curative-intent resection. Genomic analysis revealed that poorly differentiated tumors are associated with high tumor mutation burden but showed no association with oncogenic drivers. Immune analyses revealed that poorly differentiated tumors are associated with increased T-cell clonality, expression of PD-L1, and infiltration by cytotoxic CD8 T-cells, activated CD4 T-cells, and pro-inflammatory (M1) macrophages. Finally, multivariate analysis controlling for stage and smoking status confirmed independence of immune differences between IASLC grade groups. CONCLUSIONS Poorly differentiated tumors, as defined by the updated IASLC grading criteria, are associated with a distinct immunogenic tumor microenvironment that predicts for therapeutic response to immune agents, including checkpoint inhibitors, and should be included in the clinical trial design of immunotherapy studies in early-stage lung adenocarcinoma.
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Affiliation(s)
- Neal Akhave
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Erin Bayley
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Meredith Frank
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Shin-Heng Chiou
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, 195 Little Albany St, New Brunswick, NJ 08901, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Runzhe Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Won-Chul Lee
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Luisa Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Annikka Weissferdt
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Cesar Moran
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Neda Kalhor
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Jack J Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA.
| | - Junya Fujimoto
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA.
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe, Houston, TX 77030, USA.
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13
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Bartolacci C, Andreani C, Vale G, Berto S, Melegari M, Crouch AC, Baluya DL, Kemble G, Hodges K, Starrett J, Politi K, Starnes SL, Lorenzini D, Raso MG, Solis Soto LM, Behrens C, Kadara H, Gao B, Wistuba II, Minna JD, McDonald JG, Scaglioni PP. Targeting de novo lipogenesis and the Lands cycle induces ferroptosis in KRAS-mutant lung cancer. Nat Commun 2022; 13:4327. [PMID: 35882862 PMCID: PMC9325712 DOI: 10.1038/s41467-022-31963-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/06/2022] [Indexed: 12/22/2022] Open
Abstract
Mutant KRAS (KM), the most common oncogene in lung cancer (LC), regulates fatty acid (FA) metabolism. However, the role of FA in LC tumorigenesis is still not sufficiently characterized. Here, we show that KMLC has a specific lipid profile, with high triacylglycerides and phosphatidylcholines (PC). We demonstrate that FASN, the rate-limiting enzyme in FA synthesis, while being dispensable in EGFR-mutant or wild-type KRAS LC, is required for the viability of KMLC cells. Integrating lipidomic, transcriptomic and functional analyses, we demonstrate that FASN provides saturated and monounsaturated FA to the Lands cycle, the process remodeling oxidized phospholipids, such as PC. Accordingly, blocking either FASN or the Lands cycle in KMLC, promotes ferroptosis, a reactive oxygen species (ROS)- and iron-dependent cell death, characterized by the intracellular accumulation of oxidation-prone PC. Our work indicates that KM dictates a dependency on newly synthesized FA to escape ferroptosis, establishing a targetable vulnerability in KMLC.
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Affiliation(s)
- Caterina Bartolacci
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Cristina Andreani
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Gonçalo Vale
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Stefano Berto
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Margherita Melegari
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Anna Colleen Crouch
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dodge L Baluya
- Tissue Imaging and Proteomics Laboratory, Washington State University, Pullman, WA, 99164, USA
| | | | - Kurt Hodges
- Department of Pathology, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | | | - Katerina Politi
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Sandra L Starnes
- Department of Surgery, Division of Thoracic Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Daniele Lorenzini
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, via Venezian 1, 20133, Milan, Italy
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic H&N Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boning Gao
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jeffrey G McDonald
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Pier Paolo Scaglioni
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA.
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14
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Schmidt ST, Akhave N, Knightly RE, Reuben A, Vokes N, Zhang J, Li J, Fujimoto J, Byers LA, Sanchez-Espiridion B, Diao L, Wang J, Federico L, Forget MA, McGrail DJ, Weissferdt A, Lin SY, Lee Y, Suzuki E, Kovacs JJ, Behrens C, Wistuba II, Futreal A, Vaporciyan A, Sepesi B, Heymach JV, Bernatchez C, Haymaker C, Cascone T, Zhang J, Bristow CA, Heffernan TP, Negrao MV, Gibbons DL. Shared Nearest Neighbors Approach and Interactive Browser for Network Analysis of a Comprehensive Non-Small-Cell Lung Cancer Data Set. JCO Clin Cancer Inform 2022; 6:e2200040. [PMID: 35944232 PMCID: PMC9470146 DOI: 10.1200/cci.22.00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Advances in biological measurement technologies are enabling large-scale studies of patient cohorts across multiple omics platforms. Holistic analysis of these data can generate actionable insights for translational research and necessitate new approaches for data integration and mining. METHODS We present a novel approach for integrating data across platforms on the basis of the shared nearest neighbors algorithm and use it to create a network of multiplatform data from the immunogenomic profiling of non-small-cell lung cancer project. RESULTS Benchmarking demonstrates that the shared nearest neighbors-based network approach outperforms a traditional gene-gene network in capturing established interactions while providing new ones on the basis of the interplay between measurements from different platforms. When used to examine patient characteristics of interest, our approach provided signatures associated with and new leads related to recurrence and TP53 oncogenotype. CONCLUSION The network developed offers an unprecedented, holistic view into immunogenomic profiling of non-small-cell lung cancer, which can be explored through the accompanying interactive browser that we built.
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Affiliation(s)
- Stephanie T. Schmidt
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Neal Akhave
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan E. Knightly
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Natalie Vokes
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lauren A. Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marie-Andree Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel J. McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Annikka Weissferdt
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Younghee Lee
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Erika Suzuki
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jeffrey J. Kovacs
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ara Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John V. Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chantale Bernatchez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christopher A. Bristow
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy P. Heffernan
- TRACTION Platform, Division of Therapeutics Discovery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Marcelo V. Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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15
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Rocha P, Zhang J, Laza-Briviesca R, Cruz-Bermúdez A, Yoshimura K, Behrens C, Pataer A, Parra-Cuentas E, Haymaker C, Fujimoto J, Swisher S, Heymach J, Gibbons DL, Lee JJ, Sepesi B, Cascone T, Solis LM, Provencio M, Wistuba II, Kadara H. Abstract 6152: Distinct immune gene programs associated with host tumor immunity, neoadjuvant chemotherapy and chemoimmunotherapy in resectable NSCLC. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Our understanding of the immunopathology of early-stage NSCLC is still limited. While neoadjuvant immunotherapeutic strategies have recently shown anti-tumor effects in resectable NSCLC, their mechanisms remain inadequately understood. Here, we explore immune programs that inform of tumor immunity and response to neoadjuvant chemotherapy and chemoimmunotherapy in localized NSCLC.
Methods: Targeted immune gene sequencing using the HTG Precision Immuno-Oncology panel was performed in localized NSCLCs from three cohorts based on treatment: naïve (n=190), neoadjuvant chemotherapy (n=38) and neoadjuvant chemoimmunotherapy (n=21). Three tumor immune microenvironment (TIME) phenotypes (inflamed, cold, excluded) were derived based on CD8+ T cell infiltration. Signatures of immune cell abundance and immune genes were statistically compared based on tumoral PD-L1 expression, immune phenotypes, associated with pathological response, and were cross-compared across the three cohorts.
Results: PD-L1 positive tumors exhibited increased signature scores for various lymphoid and myeloid cell subsets (both, p<0.05). TIME phenotypes exhibited disparate frequencies by stage, PD-L1 expression, and mutational burden. Inflamed NSCLCs displayed overall significantly heightened levels of immune signatures with the excluded group representing an intermediate state. A signature of cytotoxic T cells was associated with favorable survival in neoadjuvant chemotherapy-treated NSCLCs (p<0.05). Major pathological response to chemoimmunotherapy was positively associated with CD8 T cells (p<0.05) and Th1 cells were significantly reduced post-chemoimmunotherapy (p<0.001). Among the three cohorts, chemoimmunotherapy-treated NSCLCs exhibited highest scores for various immune cell subsets including T effector and B cells (both, p<0.05).
Conclusions: Our findings highlight immune gene programs that may underlie host tumor immunity and response to neoadjuvant chemotherapy and chemoimmunotherapy in early-stage NSCLC.
Citation Format: Pedro Rocha, Jiexin Zhang, Raquel Laza-Briviesca, Alberto Cruz-Bermúdez, Katsuhiro Yoshimura, Carmen Behrens, Apar Pataer, Edwin Parra-Cuentas, Cara Haymaker, Junya Fujimoto, Stephen Swisher, John Heymach, Don L. Gibbons, J Jack Lee, Boris Sepesi, Tina Cascone, Luisa M. Solis, Mariano Provencio, Ignacio I. Wistuba, Humam Kadara. Distinct immune gene programs associated with host tumor immunity, neoadjuvant chemotherapy and chemoimmunotherapy in resectable NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6152.
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Affiliation(s)
- Pedro Rocha
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
| | - Jiexin Zhang
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
| | | | | | | | | | - Apar Pataer
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
| | | | - Cara Haymaker
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
| | | | | | - John Heymach
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
| | | | - J Jack Lee
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
| | - Boris Sepesi
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
| | - Tina Cascone
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
| | | | | | | | - Humam Kadara
- 1MD Anderson Cancer Center, Houston, Texas, Houston, TX
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16
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Fahrmann JF, Tanaka I, Irajizad E, Mao X, Dennison JB, Murage E, Casabar J, Mayo J, Peng Q, Celiktas M, Vykoukal JV, Park S, Taguchi A, Delgado O, Tripathi SC, Katayama H, Soto LMS, Rodriguez-Canales J, Behrens C, Wistuba I, Hanash S, Ostrin EJ. Mutational Activation of the NRF2 Pathway Upregulates Kynureninase Resulting in Tumor Immunosuppression and Poor Outcome in Lung Adenocarcinoma. Cancers (Basel) 2022; 14:2543. [PMID: 35626147 PMCID: PMC9139317 DOI: 10.3390/cancers14102543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
Activation of the NRF2 pathway through gain-of-function mutations or loss-of-function of its suppressor KEAP1 is a frequent finding in lung cancer. NRF2 activation has been reported to alter the tumor microenvironment. Here, we demonstrated that NRF2 alters tryptophan metabolism through the kynurenine pathway that is associated with a tumor-promoting, immune suppressed microenvironment. Specifically, proteomic profiles of 47 lung adenocarcinoma (LUAD) cell lines (11 KEAP1 mutant and 36 KEAP1 wild-type) revealed the tryptophan-kynurenine enzyme kynureninase (KYNU) as a top overexpressed protein associated with activated NRF2. The siRNA-mediated knockdown of NFE2L2, the gene encoding for NRF2, or activation of the NRF2 pathway through siRNA-mediated knockdown of KEAP1 or via chemical induction with the NRF2-activator CDDO-Me confirmed that NRF2 is a regulator of KYNU expression in LUAD. Metabolomic analyses confirmed KYNU to be enzymatically functional. Analysis of multiple independent gene expression datasets of LUAD, as well as a LUAD tumor microarray demonstrated that elevated KYNU was associated with immunosuppression, including potent induction of T-regulatory cells, increased levels of PD1 and PD-L1, and resulted in poorer survival. Our findings indicate a novel mechanism of NRF2 tumoral immunosuppression through upregulation of KYNU.
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Affiliation(s)
- Johannes F. Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Ichidai Tanaka
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya 464-8601, Japan;
| | - Ehsan Irajizad
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA;
| | - Xiangying Mao
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Jennifer B. Dennison
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Eunice Murage
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Julian Casabar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Jeffrey Mayo
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.M.); (Q.P.)
| | - Qian Peng
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.M.); (Q.P.)
| | - Muge Celiktas
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Jody V. Vykoukal
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Soyoung Park
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Ayumu Taguchi
- Division of Molecular Diagnostics, Aichi Cancer Center, Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan;
| | - Oliver Delgado
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | | | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Luisa Maren Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (L.M.S.S.); (J.R.-C.); (C.B.); (I.W.)
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (L.M.S.S.); (J.R.-C.); (C.B.); (I.W.)
| | - Carmen Behrens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (L.M.S.S.); (J.R.-C.); (C.B.); (I.W.)
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (L.M.S.S.); (J.R.-C.); (C.B.); (I.W.)
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.F.F.); (X.M.); (J.B.D.); (E.M.); (J.C.); (M.C.); (J.V.V.); (S.P.); (O.D.); (H.K.); (S.H.)
| | - Edwin J. Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA; (J.M.); (Q.P.)
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17
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Spindler N, Felter M, Hansen O, Nielsen T, Suppli M, Josipovic M, Poulsen L, Gaard-Petersen F, Sand H, Abramova T, Johansen M, Kornerup J, Alsaker M, Serup-Hansen E, Geertsen P, Vogelius I, Behrens C, Persson G. OC-0604 Early toxicity after SABR of oligometastatic bony metastases in the BONY M phase II trial. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)02626-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Mann Nielsen A, Storm Smedegaard K, Dreyer Teller M, Behrens C, Sibolt P, Riise Pedersen M, Pappot H, Vogelius I, Suppli M, Persson G. PO-1460 Phase III trial of esophagus-sparing palliative spine irradiation - QA of dosimetric parameters. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)03424-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Bekke S, Andersen K, Behrens C, Sjöström D, Sibolt P, Damkjær S. PO-1674 Going from planar kV-MV to kV-kV setup images in image-guided radiotherapy of breast cancer. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)03638-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Rocha P, Zhang J, Laza-Briviesca R, Cruz-Bermúdez A, Bota-Rabassedas N, Sanchez-Espiridion B, Yoshimura K, Behrens C, Lu W, Tang X, Pataer A, Parra ER, Haymaker C, Fujimoto J, Swisher SG, Heymach JV, Gibbons DL, Lee JJ, Sepesi B, Cascone T, Solis LM, Provencio M, Wistuba II, Kadara H. Distinct immune gene programs associated with host tumor immunity, neoadjuvant chemotherapy and chemoimmunotherapy in resectable NSCLC. Clin Cancer Res 2022; 28:2461-2473. [PMID: 35394499 DOI: 10.1158/1078-0432.ccr-21-3207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 02/12/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Our understanding of the immunopathology of resectable NSCLC is still limited. Here, we explore immune programs that inform of tumor immunity and response to neoadjuvant chemotherapy and chemoimmunotherapy in localized NSCLC. EXPERIMENTAL DESIGN Targeted immune gene sequencing using the HTG Precision Immuno-Oncology panel was performed in localized NSCLCs from three cohorts based on treatment: naïve (n=190), neoadjuvant chemotherapy (n=38) and neoadjuvant chemoimmunotherapy (n=21). Tumor immune microenvironment (TIME) phenotypes based on the location of CD8+ T cells (inflamed, cold, excluded), tumoral PD-L1 expression (<1% and {greater than or equal to}1%), and tumor infiltrating lymphocytes (TILs). Immune programs and signatures were statistically analyzed based on tumoral PD-L1 expression, immune phenotypes, pathological response and were cross-compared across the three cohorts. RESULTS PD-L1 positive tumors exhibited increased signature scores for various lymphoid and myeloid cell subsets (p<0.05). TIME phenotypes exhibited disparate frequencies by stage, PD-L1 expression, and mutational burden. Inflamed and PD-L1+/TILs+ NSCLCs displayed overall significantly heightened levels of immune signatures, with the excluded group representing an intermediate state. A cytotoxic T cell signature was associated with favorable survival in neoadjuvant chemotherapy-treated NSCLCs (p<0.05). Pathological response to chemoimmunotherapy was positively associated with higher expression of genes involved in immune activation, chemotaxis, as well as T and NK cells (p<0.05 for all). Among the three cohorts, chemoimmunotherapy-treated NSCLCs exhibited highest scores for various immune cell subsets including T effector and B cells (p<0.05). CONCLUSIONS Our findings highlight immune gene programs that may underlie host tumor immunity and response to neoadjuvant chemotherapy and chemoimmunotherapy in resectable NSCLC.
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Affiliation(s)
- Pedro Rocha
- The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Jiexin Zhang
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | | | - Alberto Cruz-Bermúdez
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain., Madrid, Spain
| | | | | | - Katsuhiro Yoshimura
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Carmen Behrens
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wei Lu
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ximing Tang
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Apar Pataer
- The University of Texas MD Anderson Cancer Center, houston, Texas, United States
| | - Edwin R Parra
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Cara Haymaker
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Junya Fujimoto
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Stephen G Swisher
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John V Heymach
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Don L Gibbons
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - J Jack Lee
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Boris Sepesi
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Tina Cascone
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Luisa M Solis
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Mariano Provencio
- Medical Oncology Department, Hospital Universitario Puerta de Hierro Majadahonda, Madrid, Spain., Majadahonda, Madrid, Spain
| | - Ignacio I Wistuba
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Humam Kadara
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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21
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Alhalabi O, Chen J, Zhang Y, Lu Y, Wang Q, Ramachandran S, Tidwell RS, Han G, Yan X, Meng J, Wang R, Hoang AG, Wang WL, Song J, Lopez L, Andreev-Drakhlin A, Siefker-Radtke A, Zhang X, Benedict WF, Shah AY, Wang J, Msaouel P, Zhang M, Guo CC, Czerniak B, Behrens C, Soto L, Papadimitrakopoulou V, Lewis J, Rinsurongkawong W, Rinsurongkawong V, Lee J, Roth J, Swisher S, Wistuba I, Heymach J, Wang J, Campbell MT, Efstathiou E, Titus M, Logothetis CJ, Ho TH, Zhang J, Wang L, Gao J. MTAP deficiency creates an exploitable target for antifolate therapy in 9p21-loss cancers. Nat Commun 2022; 13:1797. [PMID: 35379845 PMCID: PMC8980015 DOI: 10.1038/s41467-022-29397-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/10/2022] [Indexed: 12/14/2022] Open
Abstract
Methylthioadenosine phosphorylase, an essential enzyme for the adenine salvage pathway, is often deficient (MTAPdef) in tumors with 9p21 loss and hypothetically renders tumors susceptible to synthetic lethality by antifolates targeting de novo purine synthesis. Here we report our single arm phase II trial (NCT02693717) that assesses pemetrexed in MTAPdef urothelial carcinoma (UC) with the primary endpoint of overall response rate (ORR). Three of 7 enrolled MTAPdef patients show response to pemetrexed (ORR 43%). Furthermore, a historic cohort shows 4 of 4 MTAPdef patients respond to pemetrexed as compared to 1 of 10 MTAP-proficient patients. In vitro and in vivo preclinical data using UC cell lines demonstrate increased sensitivity to pemetrexed by inducing DNA damage, and distorting nucleotide pools. In addition, MTAP-knockdown increases sensitivity to pemetrexed. Furthermore, in a lung adenocarcinoma retrospective cohort (N = 72) from the published BATTLE2 clinical trial (NCT01248247), MTAPdef associates with an improved response rate to pemetrexed. Our data demonstrate a synthetic lethal interaction between MTAPdef and de novo purine inhibition, which represents a promising therapeutic strategy for larger prospective trials.
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Affiliation(s)
- Omar Alhalabi
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianfeng Chen
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yuxue Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sumankalai Ramachandran
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Rebecca Slack Tidwell
- Department of Biostatistics,, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xinmiao Yan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jieru Meng
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Anh G Hoang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Wei-Lien Wang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jian Song
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lidia Lopez
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alex Andreev-Drakhlin
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Arlene Siefker-Radtke
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xinqiao Zhang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - William F Benedict
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Amishi Y Shah
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jennifer Wang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Miao Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Charles C Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carmen Behrens
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Luisa Soto
- Department of Translational molecular pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vassiliki Papadimitrakopoulou
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jeff Lewis
- Department of Biostatistics,, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Waree Rinsurongkawong
- Department of Biostatistics,, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vadeerat Rinsurongkawong
- Department of Biostatistics,, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jack Lee
- Department of Biostatistics,, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jack Roth
- Department of Thoracic and Cardiovascular surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio Wistuba
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John Heymach
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Matthew T Campbell
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Eleni Efstathiou
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark Titus
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Christopher J Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Thai H Ho
- Division of Medical Oncology, Mayo Clinic, Phoenix, AZ, USA
| | - Jianjun Zhang
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (GSBS), Houston, TX, USA.
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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22
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Li H, Liu Z, Liu L, Zhang H, Han C, Girard L, Park H, Zhang A, Dong C, Ye J, Rayford A, Peyton M, Li X, Avila K, Cao X, Hu S, Alam MM, Akbay EA, Solis LM, Behrens C, Hernandez-Ruiz S, Lu W, Wistuba I, Heymach JV, Chisamore M, Micklem D, Gabra H, Gausdal G, Lorens JB, Li B, Fu YX, Minna JD, Brekken RA. AXL targeting restores PD-1 blockade sensitivity of STK11/LKB1 mutant NSCLC through expansion of TCF1 + CD8 T cells. Cell Rep Med 2022; 3:100554. [PMID: 35492873 PMCID: PMC9040166 DOI: 10.1016/j.xcrm.2022.100554] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 10/22/2021] [Accepted: 02/08/2022] [Indexed: 12/14/2022]
Abstract
Mutations in STK11/LKB1 in non-small cell lung cancer (NSCLC) are associated with poor patient responses to immune checkpoint blockade (ICB), and introduction of a Stk11/Lkb1 (L) mutation into murine lung adenocarcinomas driven by mutant Kras and Trp53 loss (KP) resulted in an ICB refractory syngeneic KPL tumor. Mechanistically this occurred because KPL mutant NSCLCs lacked TCF1-expressing CD8 T cells, a phenotype recapitulated in human STK11/LKB1 mutant NSCLCs. Systemic inhibition of Axl results in increased type I interferon secretion from dendritic cells that expanded tumor-associated TCF1+PD-1+CD8 T cells, restoring therapeutic response to PD-1 ICB in KPL tumors. This was observed in syngeneic immunocompetent mouse models and in humanized mice bearing STK11/LKB1 mutant NSCLC human tumor xenografts. NSCLC-affected individuals with identified STK11/LKB1 mutations receiving bemcentinib and pembrolizumab demonstrated objective clinical response to combination therapy. We conclude that AXL is a critical targetable driver of immune suppression in STK11/LKB1 mutant NSCLC.
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Affiliation(s)
- Huiyu Li
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA
- Cancer Biology Graduate Program, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhida Liu
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Longchao Liu
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Hongyi Zhang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chuanhui Han
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hyunsil Park
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA
| | - Anli Zhang
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Chunbo Dong
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Jianfeng Ye
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Austin Rayford
- BerGenBio ASA, Bergen, Norway
- Department of Biomedicine, Centre for Cancer Biomarkers, Norwegian Centre of Excellence, University of Bergen, Bergen, Norway
| | - Michael Peyton
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA
| | - Xiaoguang Li
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Kimberley Avila
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA
| | - Xuezhi Cao
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Shuiqing Hu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Md Maksudul Alam
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Esra A. Akbay
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sharia Hernandez-Ruiz
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V. Heymach
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | | | | | | | - James B. Lorens
- Department of Biomedicine, Centre for Cancer Biomarkers, Norwegian Centre of Excellence, University of Bergen, Bergen, Norway
| | - Bo Li
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-9072, USA
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA
- Cancer Biology Graduate Program, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rolf A. Brekken
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA
- Cancer Biology Graduate Program, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
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23
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Tang M, Abbas HA, Negrao MV, Ramineni M, Hu X, Hubert SM, Fujimoto J, Reuben A, Varghese S, Zhang J, Li J, Chow CW, Mao X, Song X, Lee WC, Wu J, Little L, Gumbs C, Behrens C, Moran C, Weissferdt A, Lee JJ, Sepesi B, Swisher S, Cheng C, Kurie J, Gibbons D, Heymach JV, Wistuba II, Futreal PA, Kalhor N, Zhang J. The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics. Nat Commun 2021; 12:7081. [PMID: 34873156 PMCID: PMC8648877 DOI: 10.1038/s41467-021-27341-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 11/16/2021] [Indexed: 12/31/2022] Open
Abstract
Histology plays an essential role in therapeutic decision-making for lung cancer patients. However, the molecular determinants of lung cancer histology are largely unknown. We conduct whole-exome sequencing and microarray profiling on 19 micro-dissected tumor regions of different histologic subtypes from 9 patients with lung cancers of mixed histology. A median of 68.9% of point mutations and 83% of copy number aberrations are shared between different histologic components within the same tumors. Furthermore, different histologic components within the tumors demonstrate similar subclonal architecture. On the other hand, transcriptomic profiling reveals shared pathways between the same histologic subtypes from different patients, which is supported by the analyses of the transcriptomic data from 141 cell lines and 343 lung cancers of different histologic subtypes. These data derived from mixed histologic subtypes in the setting of identical genetic background and exposure history support that the histologic fate of lung cancer cells is associated with transcriptomic features rather than the genomic profiles in most tumors. The molecular determinants of lung cancer histologic subtypes are not well understood. Here the authors analyze lung cancers of mixed histology and find that histologic subtypes are associated with transcriptomic features rather than genomic profiles in most tumors.
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Affiliation(s)
- Ming Tang
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hussein A Abbas
- Medical Oncology Fellowship, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maheshwari Ramineni
- Department of Pathology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xin Hu
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shawna Marie Hubert
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Susan Varghese
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jun Li
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xizeng Mao
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Won-Chul Lee
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jia Wu
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Latasha Little
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cesar Moran
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Annikka Weissferdt
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - J Jack Lee
- Department of Biostatistics, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Boris Sepesi
- Department of Thoracic Surgery, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Stephen Swisher
- Department of Thoracic Surgery, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chao Cheng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jonathan Kurie
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Don Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Neda Kalhor
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Jianjun Zhang
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Thoracic/Head and Neck Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Schmidt ST, Akhave N, Reuben A, Cascone T, Zhang J, Li J, Fujimoto J, Byers LA, Sanchez-Espiridion B, Diao L, Wang J, Federico L, Forget MA, McGrail DJ, Weissferdt A, Lin SY, Lee Y, Vokes N, Behrens C, Wistuba II, Futreal A, Vaporciyan A, Sepesi B, Heymach JV, Bernatchez C, Haymaker C, Zhang J, Bristow CA, Heffernan TP, Negrao MV, Gibbons DL. Abstract P009: A shared nearest neighbors approach for integrated, multi-platform networks and its application to the exploration of multiomics data from early-stage non-small cell lung cancers. Mol Cancer Ther 2021. [DOI: 10.1158/1535-7163.targ-21-p009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The ImmunogenomiC prOfiling of Non-small cell lung cancer (NSCLC) Project (ICON) represents an ambitious undertaking to comprehensively characterize immuno-genomic diversity in NSCLC across diverse platforms. The depth and breadth of this cohort presented a unique opportunity to develop a specialized method for multi-platform data integration and exploration, which can be broadly applied to forthcoming large-scale patient profiling studies. Such a holistic approach can unlock insights for therapeutic targets, biomarkers, and treatment plans by providing a more complete view of phenomena driving disease pathogenesis and evolution. Purpose: We developed a novel shared nearest neighbors (SNN) approach to create an integrated network of ICON’s multi-platform data and identified collections of closely related measurements within the resulting network tied to noteworthy patient characteristics, including recurrence and oncogenotype. Methods: The ICON dataset is derived from tumor and normal lung tissue samples collected from 150 patients at time of resection as well as blood samples collected then and at intervals during the year following. Tissue samples underwent RNA-sequencing (RNA-seq), whole exome sequencing, T-cell receptor sequencing, multiplex immunofluorescence for immune cells, and reverse phase protein array profiling; flow cytometry for immune cells was performed on tissue and blood samples. From these data, the ICON data network was built using an integrative approach based on the SNN algorithm in which genes were linked on the basis of their shared top correlates in orthogonal datasets. Results: The ICON data network currently includes over 20,000 genes linked by over 500,000 connections derived from correlations between RNA-seq and orthogonal platforms. We captured established associations between cancer-related genes and examined these along with new ones in the network. To do so, we used the InfoMap algorithm to extract more interpretable sub-networks, termed modules, from the ICON data network. Single sample gene set enrichment scores for each module were used in multivariate analysis to highlight modules linked to clinical characteristics of interest. As an example, we found modules significantly tied to disease recurrence. The most notable of these was strongly associated with metabolic pathways, and other modules associated with platelets and ion channels were also identified. The metabolic pathway module is being explored as a prognostic biomarker, underscoring the opportunites enabled by mining the network. Conclusions: Through the framework developed, we identified modules in the ICON data network significantly associated with important patient characteristics like recurrence and oncogenotype. We are validating the gene sets identified as potential biomarkers and are developing an interactive application to facilitate further mining of the network. Taken together, our SNN network-building approach enables the integration and exploration of patient data from diverse platforms.
Citation Format: Stephanie T. Schmidt, Neal Akhave, Alexandre Reuben, Tina Cascone, Jianhua Zhang, Jun Li, Junya Fujimoto, Lauren A. Byers, Beatriz Sanchez-Espiridion, Lixia Diao, Jing Wang, Lorenzo Federico, Marie-Andree Forget, Daniel J McGrail, Annikka Weissferdt, Shiaw-Yih Lin, Younghee Lee, Natalie Vokes, Carmen Behrens, Ignacio I. Wistuba, Andrew Futreal, Ara Vaporciyan, Boris Sepesi, John V. Heymach, Chantale Bernatchez, Cara Haymaker, Jianjun Zhang, Christopher A. Bristow, Timothy P. Heffernan, Marcelo V. Negrao, Don L. Gibbons. A shared nearest neighbors approach for integrated, multi-platform networks and its application to the exploration of multiomics data from early-stage non-small cell lung cancers [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P009.
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Affiliation(s)
| | - Neal Akhave
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Tina Cascone
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jun Li
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Junya Fujimoto
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lauren A. Byers
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lixia Diao
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jing Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Shiaw-Yih Lin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Younghee Lee
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Natalie Vokes
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Carmen Behrens
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ara Vaporciyan
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John V. Heymach
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Cara Haymaker
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Don L. Gibbons
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Rocha P, Zhang J, Laza-Briviesca R, Cruz-Bermúdez A, Yoshimura K, Behrens C, Pataer A, Parra E, Haymaker C, Fujimoto J, Swisher S, Heymach J, Gibbons D, Lee J, Sepesi B, Cascone T, Solis L, Provencio M, Kadara H, Wistuba I. 7P Distinct immune gene programs associated with host tumor immunity, neoadjuvant chemotherapy and chemoimmunotherapy in resectable NSCLC. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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26
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Chen M, Chen R, Jin Y, Li J, Hu X, Zhang J, Fujimoto J, Hubert SM, Gay CM, Zhu B, Tian Y, McGranahan N, Lee WC, George J, Hu X, Chen Y, Wu M, Behrens C, Chow CW, Pham HHN, Fukuoka J, Wu J, Parra ER, Little LD, Gumbs C, Song X, Wu CJ, Diao L, Wang Q, Cardnell R, Zhang J, Wang J, Le X, Gibbons DL, Heymach JV, Jack Lee J, William WN, Cheng C, Glisson B, Wistuba I, Andrew Futreal P, Thomas RK, Reuben A, Byers LA, Zhang J. Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer. Nat Commun 2021; 12:6655. [PMID: 34789716 PMCID: PMC8599854 DOI: 10.1038/s41467-021-26821-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/10/2020] [Accepted: 10/25/2021] [Indexed: 02/03/2023] Open
Abstract
Small-cell lung cancer (SCLC) is speculated to harbor complex genomic intratumor heterogeneity (ITH) associated with high recurrence rate and suboptimal response to immunotherapy. Here, using multi-region whole exome/T cell receptor (TCR) sequencing as well as immunohistochemistry, we reveal a rather homogeneous mutational landscape but extremely cold and heterogeneous TCR repertoire in limited-stage SCLC tumors (LS-SCLCs). Compared to localized non-small cell lung cancers, LS-SCLCs have similar predicted neoantigen burden and genomic ITH, but significantly colder and more heterogeneous TCR repertoire associated with higher chromosomal copy number aberration (CNA) burden. Furthermore, copy number loss of IFN-γ pathway genes is frequently observed and positively correlates with CNA burden. Higher mutational burden, higher T cell infiltration and positive PD-L1 expression are associated with longer overall survival (OS), while higher CNA burden is associated with shorter OS in patients with LS-SCLC.
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Affiliation(s)
- Ming Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China. .,The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China. .,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China. .,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, 310022, China.
| | - Runzhe Chen
- grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510060 China ,grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Ying Jin
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Jun Li
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xin Hu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jiexin Zhang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Junya Fujimoto
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Shawna M. Hubert
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Carl M. Gay
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Bo Zhu
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Yanhua Tian
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Nicholas McGranahan
- grid.11485.390000 0004 0422 0975Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, WC1E6BT UK
| | - Won-Chul Lee
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Julie George
- grid.6190.e0000 0000 8580 3777Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50931 Germany ,grid.411097.a0000 0000 8852 305XDepartment of Otorhinolaryngology, Head and Neck Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Xiao Hu
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Yamei Chen
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Meijuan Wu
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Carmen Behrens
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chi-Wan Chow
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Hoa H. N. Pham
- grid.174567.60000 0000 8902 2273Department of Pathology, Nagasaki University Graduate school of Biomedical Sciences, Nagasaki, Japan
| | - Junya Fukuoka
- grid.174567.60000 0000 8902 2273Department of Pathology, Nagasaki University Graduate school of Biomedical Sciences, Nagasaki, Japan
| | - Jia Wu
- grid.240145.60000 0001 2291 4776Department of Image Physics, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Edwin Roger Parra
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Latasha D. Little
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Curtis Gumbs
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xingzhi Song
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chang-Jiun Wu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Lixia Diao
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Qi Wang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Robert Cardnell
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jianhua Zhang
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jing Wang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xiuning Le
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Don L. Gibbons
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - John V. Heymach
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - J. Jack Lee
- grid.240145.60000 0001 2291 4776Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - William N. William
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chao Cheng
- grid.39382.330000 0001 2160 926XInstitute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Bonnie Glisson
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Ignacio Wistuba
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - P. Andrew Futreal
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Roman K. Thomas
- grid.6190.e0000 0000 8580 3777Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, 50931 Germany ,grid.411097.a0000 0000 8852 305XDepartment of Pathology, Medical Faculty, University Hospital Cologne, Cologne, 50931 Germany ,grid.7497.d0000 0004 0492 0584DKFZ, German Cancer Research Center and German Cancer Consortium (DKTK), Heidelberg, 69115 Germany
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
| | - Lauren A. Byers
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA. .,Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
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Li H, Liu Z, Liu L, Zhang H, Han C, Girard L, Park H, Zhang A, Dong C, Ye J, Rayford A, Peyton M, Li X, Avila K, Cao X, Hu S, Akbay E, Solis L, Behrens C, Hernandez-Ruiz S, Wei L, Wistuba I, Heymach J, Chisamore M, Micklem D, Gabra H, Gausdal G, Lorens J, Li B, Fu YX, Minna J, Brekken R. 602 AXL targeting with bemcentinb restores PD-1 blockade sensitivity of STK11/LKB1 mutant NSCLC through innate immune cell mediated expansion of TCF1+ CD8 T cells. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BackgroundMutations in tumor suppressor STK11/LKB1 are associated with negative predictive and prognostic impact in NSCLC patients receiving immune checkpoint inhibitors (CPI) in several published cohorts, although there have been some conflicting reports on the association of such mutations with patient outcomes in this setting [1–9]. STK11/LKB1 tumors are characterized by a suppressive tumor micro-environment devoid of cytotoxic T cells, and we hypothesized that targeting the receptor tyrosine kinase AXL, a known driver of an innate immune suppressive microenvironment, would restore sensitivity to PD-1 in syngeneic pre-clinical models as well as in patients harboring STK11/LKB1 mutated NSCLC.MethodsStk11/Lkb1 (L) mutation was introduced by CRISPR technology into murine lung adenocarcinomas driven by mutant Kras and Trp53 loss (KP). Sensitivity towards anti-PD-1 was evaluated in the absence and presence of the small molecule AXL inhibitor bemcentinib in the KPL model and in a human NSCLC xenograft model carrying a STK11/LKB1 mutation. The immune tumor landscape was mapped following introduction of the Stk11/Lkb1 mutation and therapeutic intervention with anti-PD-1/pembrolizumab and bemcentinib. FFPE fine-needle aspirate biopsies of target lesions were acquired from patients at screening immediately prior to enrollment in BGBC008, a PhII single-arm, 2-stage study with bemcentinib (200mg/d) and pembrolizumab (200 mg/q3wk) for previously-treated stage IV lung adenocarcinoma patients who were CPI naïve or CPI refractory. Patients were assessed for response according to RECIST1.1 criteria at scheduled scan intervals.ResultsIntroduction of a STK11/LKB1 mutation into murine lung adenocarcinomas driven by mutant Kras and Trp53 loss resulted in a PD-1 refractory syngeneic KPL tumor. Mechanistically this occurred because KPL mutant NSCLCs lacked TCF1-expressing CD8 T cells, a phenotype that was recapitulated in human STK11/LKB1 mutant NSCLCs. Systemic inhibition of AXL with bemcentinib resulted in increased type I interferon secretion from dendritic cells resulting in expansion of tumor-associated TCF1+PD-1+CD8 T cells and restored therapeutic response to PD-1. This effect was observed in a syngeneic immunocompetent mouse model and in humanized mice bearing STK11/LKB1 mutant NSCLC human tumor xenografts.In an ongoing clinical trial (NCT03184571), 3 evaluable NSCLC patients with identified STK11/LKB1 mutations demonstrated objective clinical response/clinical benefit to the combination of AXL inhibitor bemcentinib and pembrolizumabConclusionsIn these models, AXL is a critical targetable driver of immune suppression in STK11/LKB1 mutant NSCLC contributing to CPI resistance. Our results show that inhibition of AXL rescues this deficit and represents a new clinical strategy in combination with anti-PD-1 therapy in NSCLC patients carrying a STK11/LKB1 mutationAcknowledgementsThe authors would like to thank all patients and their caretakers for participating in this trial.Trial RegistrationPatients treated with bemcentinib and pembrolizumab combination therapy were enrolled in the BGBC008 clinical trial (BerGenBio ASA and Merck & Co., Inc., Kenilworth NJ, USA, NCT03184571)ReferencesGu M, Xu T, Chang P. KRAS/LKB1 and KRAS/TP53 co-mutations create divergent immune signatures in lung adenocarcinomas. Ther Adv Med Oncol. 2021;13:17588359211006950.Cho BC, Lopes G, Kowalski DM. Relationship between STK11 and KEAP1 mutational status and efficacy in KEYNOTE-042: pembrolizumab monotherapy as first-line therapy for PD-L1 positive advanced NSCLC. Cancer Res. 2020;80(16 Supplement):CT084.Aredo JV, Padda SK, Kunder CA. Impact of KRAS mutation subtype and concurrent pathogenic mutations on non-small cell lung cancer outcomes. Lung Cancer. 2019;133:144–150.Kwack WG, Shin SY, Lee SH. Primary Resistance to Immune Checkpoint Blockade in an STK11/TP53/KRAS-Mutant Lung Adenocarcinoma with High PD-L1 Expression. Oncol Targets Ther. 2020;13:8901–8905.Shire NJ, Klein AB, Golozar A. STK11 (LKB1) mutations in metastatic NSCLC: Prognostic value in the real world. PLoS One. 2020;15(9):e0238358. 6. Skoulidis F, Goldberg ME, Greenawalt DM. STK11/LKB1 Mutations and PD-1 Inhibitor Resistance in KRAS-Mutant Lung Adenocarcinoma. Cancer Discov. 2018;8(7):822–835. 7. Wang H, Guo J, Shang X. Less immune cell infiltration and worse prognosis after immunotherapy for patients with lung adenocarcinoma who harbored STK11 mutation. Int. Immunopharmacol. 2020;84:106574. 8. Kitajima S, Ivanova E, Gou S. Suppression of STING Associated with LKB1 Loss in KRAS-Driven Lung Cancer. Cancer Discov. 2019;9(1):34–45. 9. Mograbi B, Heeke S, Hofman P. The Importance of STK11/LKB1 Assessment in Non-Small Cell Lung Carcinomas. Diagnostics (Basel). 2021;11(2):196.Ethics ApprovalThis study was approved by the following ethical committees: Use of human cord blood: UT Southwestern (UTSW) Parkland Hospital, STU 112010-047Animal studies: UTSW Medical Center, Institutional Animal Care and Use Committee, APN 2015-100921Clinical study: London Bridge Research Ethics Committee (UK): 17/LO/0418; REC-South East (Norway): 2017/473; Drug Research Ethics Committee of the University Hospital Clinic of Barcelona (Spain): BGBC008/MK-3475_PN-531; Medical College of Wisconsin Institutional Review Board #4 (USA): PRO00029453
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Sinjab A, Han G, Treekitkarnmongkol W, Hara K, Brennan PM, Dang M, Hao D, Wang R, Dai E, Dejima H, Zhang J, Bogatenkova E, Sanchez-Espiridion B, Chang K, Little DR, Bazzi S, Tran LM, Krysan K, Behrens C, Duose DY, Parra ER, Raso MG, Solis LM, Fukuoka J, Zhang J, Sepesi B, Cascone T, Byers LA, Gibbons DL, Chen J, Moghaddam SJ, Ostrin EJ, Rosen D, Heymach JV, Scheet P, Dubinett SM, Fujimoto J, Wistuba II, Stevenson CS, Spira A, Wang L, Kadara H. Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing. Cancer Discov 2021; 11:2506-2523. [PMID: 33972311 PMCID: PMC8487926 DOI: 10.1158/2159-8290.cd-20-1285] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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: 09/03/2020] [Revised: 02/26/2021] [Accepted: 04/30/2021] [Indexed: 11/16/2022]
Abstract
Little is known of the geospatial architecture of individual cell populations in lung adenocarcinoma (LUAD) evolution. Here, we perform single-cell RNA sequencing of 186,916 cells from five early-stage LUADs and 14 multiregion normal lung tissues of defined spatial proximities from the tumors. We show that cellular lineages, states, and transcriptomic features geospatially evolve across normal regions to LUADs. LUADs also exhibit pronounced intratumor cell heterogeneity within single sites and transcriptional lineage-plasticity programs. T regulatory cell phenotypes are increased in normal tissues with proximity to LUAD, in contrast to diminished signatures and fractions of cytotoxic CD8+ T cells, antigen-presenting macrophages, and inflammatory dendritic cells. We further find that the LUAD ligand-receptor interactome harbors increased expression of epithelial CD24, which mediates protumor phenotypes. These data provide a spatial atlas of LUAD evolution, and a resource for identification of targets for its treatment. SIGNIFICANCE: The geospatial ecosystem of the peripheral lung and early-stage LUAD is not known. Our multiregion single-cell sequencing analyses unravel cell populations, states, and phenotypes in the spatial and ecologic evolution of LUAD from the lung that comprise high-potential targets for early interception.This article is highlighted in the In This Issue feature, p. 2355.
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Affiliation(s)
- Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Warapen Treekitkarnmongkol
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kieko Hara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick M Brennan
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dapeng Hao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hitoshi Dejima
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elena Bogatenkova
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Danielle R Little
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Samer Bazzi
- Faculty of Arts and Sciences, University of Balamand, Koura, Lebanon
| | - Linh M Tran
- Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Kostyantyn Krysan
- Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Carmen Behrens
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Jianjun Zhang
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Cardiovascular and Thoracic Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tina Cascone
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lauren Averett Byers
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jichao Chen
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin J Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel Rosen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - John V Heymach
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Scheet
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Steven M Dubinett
- Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, 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 Spira
- Lung Cancer Initiative at Johnson and Johnson, Boston, Massachusetts
- Section of Computational Biomedicine, Boston University, Boston, Massachusetts
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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29
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Tanaka I, Dayde D, Tai MC, Mori H, Solis LM, Tripathi SC, Fahrmann JF, Unver N, Parhy G, Jain R, Parra ER, Murakami Y, Aguilar-Bonavides C, Mino B, Celiktas M, Dhillon D, Casabar JP, Nakatochi M, Stingo F, Baladandayuthapani V, Wang H, Katayama H, Dennison JB, Lorenzi PL, Do KA, Fujimoto J, Behrens C, Ostrin EJ, Rodriguez-Canales J, Hase T, Fukui T, Kajino T, Kato S, Yatabe Y, Hosoda W, Kawaguchi K, Yokoi K, Chen-Yoshikawa TF, Hasegawa Y, Gazdar AF, Wistuba II, Hanash S, Taguchi A. SRGN-Triggered Aggressive and Immunosuppressive Phenotype in a Subset of TTF-1-Negative Lung Adenocarcinomas. J Natl Cancer Inst 2021; 114:290-301. [PMID: 34524427 DOI: 10.1093/jnci/djab183] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 05/25/2021] [Revised: 07/27/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND About 20% of lung adenocarcinoma (LUAD) is negative for the lineage-specific oncogene Thyroid transcription factor 1 (TTF-1) and exhibits worse clinical outcome with a low frequency of actionable genomic alterations. To identify molecular features associated with TTF-1-negative LUAD, we compared the transcriptomic and proteomic profiles of LUAD cell lines. SRGN, a chondroitin sulfate proteoglycan Serglycin, was identified as a markedly overexpressed gene in TTF-1-negative LUAD. We therefore investigated the roles and regulation of SRGN in TTF-1-negative LUAD. METHODS Proteomic and metabolomic analyses of 41 LUAD cell lines were done using mass spectrometry. The function of SRGN was investigated in 3 TTF-1-negative and 4 TTF-1-positive LUAD cell lines and in a syngeneic mouse model (n = 5 to 8 mice per group). Expression of SRGN in was evaluated in 94 and 105 surgically resected LUAD tumor specimens using immunohistochemistry. All statistical tests were two-sided. RESULTS SRGN was markedly overexpressed at mRNA and protein levels in TTF-1-negative LUAD cell lines (P < .001 for both mRNA and protein levels). Expression of SRGN in LUAD tumor tissue was associated with poor outcome (hazard ratio = 4.22, 95% confidential interval = 1.12 to 15.86; likelihood ratio test, P = .03), and with higher expression of Programmed cell death 1 ligand 1 (PD-L1) in tumor cells and higher infiltration of Programmed cell death protein 1 (PD-1)-positive lymphocytes. SRGN regulated expression of PD-L1, as well as proinflammatory cytokines including Interleukin-6 (IL-6), Interleukin-8 (IL-8), and C-X-C motif chemokine 1 (CXCL1) in LUAD cell lines, and increased migratory and invasive properties of LUAD cells and fibroblasts, and enhanced angiogenesis. SRGN was induced by DNA de-methylation resulting from Nicotinamide N-methyltransferase (NNMT)-mediated impairment of methionine metabolism. CONCLUSION Our findings suggest that SRGN plays a pivotal role in tumor-stromal interaction and reprogramming into an aggressive and immunosuppressive tumor microenvironment in TTF-1-negative LUAD.
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Affiliation(s)
- Ichidai Tanaka
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Delphine Dayde
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mei Chee Tai
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Haruki Mori
- Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Luisa M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Satyendra C Tripathi
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Johannes F Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nese Unver
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gargy Parhy
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rekha Jain
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yoshiko Murakami
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | | | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Muge Celiktas
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dilsher Dhillon
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Julian Phillip Casabar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Francesco Stingo
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Veera Baladandayuthapani
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hong Wang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer B Dennison
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kim-Anh Do
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Edwin J Ostrin
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tetsunari Hase
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takayuki Fukui
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taisuke Kajino
- Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan
| | - Seiichi Kato
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasushi Yatabe
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Waki Hosoda
- Department of Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Koji Kawaguchi
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kohei Yokoi
- Department of Thoracic Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Yoshinori Hasegawa
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology, Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Division of Molecular Diagnostics, Aichi Cancer Center, Nagoya, Japan.,Division of Advanced Cancer Diagnostics, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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30
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Sinjab A, Han G, Treekitkarnmongkol W, Hara K, Brennan P, Dang M, Hao D, Wang R, Dai E, Dejima H, Zhang J, Bogatenkova E, Sanchez-Espiridion B, Chang K, Little DR, Bazzi S, Tran L, Krysan K, Behrens C, Duose D, Parra ER, Raso MG, Solis LM, Fukuoka J, Zhang J, Sepesi B, Cascone T, Byers LA, Gibbons DL, Chen J, Moghaddam SJ, Ostrin EJ, Rosen DG, Heymach JV, Scheet P, Dubinett S, Wistuba II, Fujimoto J, Stevenson CS, Spira AE, Wang L, Kadara H. Abstract 130: Resolving the spatial and cellular architecture of lung adenocarcinoma by multi-region single-cell sequencing. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lung adenocarcinoma (LUAD) is the most commonly diagnosed histological subtype of lung cancer. While earlier work has underscored genomic and immune alterations in LUAD, the roles of individual cell populations in early-stage human LUAD evolution in space remain unknown. Here, we provide a detailed cellular atlas of early-stage LUAD and its spatial ecosystem along the peripheral lung. We performed single-cell RNA sequencing of 186,916 cells including enriched epithelial fractions from five early-stage LUADs with fourteen multi-region normal lung tissues of defined spatial proximities from the primary LUADs. We show that major epithelial and immune cellular lineages, states, and transcriptomic features geospatially and progressively evolve across normal regions and with increasing LUAD proximity. Analysis of 70,030 lung epithelial cells unraveled diverse lineage trajectories, transcriptional lineage plasticity programs underlying KRAS-mutant cells, and intratumoral heterogeneity within single sites. T regulatory cell programs including multiple immune checkpoints increased in tissues with closer proximity to LUADs, in sharp contrast to signatures of CD8+ cytotoxic T cells, antigen presentation by macrophages, and inflammatory dendritic cells. We found that some spatial signatures (e.g. a B cell signature score) were increased along the pathologic spectrum of normal lung, preneoplastic lesions, and matched invasive LUADs. LUAD cell-cell communication networks were enriched with ligand-receptor interactions involving CD24, LGALS9 and TIM3 immune checkpoints, including crosstalk between CD24 antigen in LUAD epithelial cells and SIGLEC10 in myeloid subsets. CD24 was markedly increased in preneoplasias relative to normal lung and further in LUAD, and its expression was highly positively correlated with immunosuppressive phenotypes. These data provide an atlas of cellular states and phenotypes underlying early-stage LUAD evolution in space, and a scalable resource for identification of targets for early treatment.
Citation Format: Ansam Sinjab, Guangchun Han, Warapen Treekitkarnmongkol, Kieko Hara, Patrick Brennan, Minghao Dang, Dapeng Hao, Ruiping Wang, Enyu Dai, Hitoshi Dejima, Jiexin Zhang, Elena Bogatenkova, Beatriz Sanchez-Espiridion, Kyle Chang, Danielle R. Little, Samer Bazzi, Linh Tran, Kostyantyn Krysan, Carmen Behrens, Dzifa Duose, Edwin R. Parra, Maria Gabriela Raso, Luisa M. Solis, Junya Fukuoka, Jianjun Zhang, Boris Sepesi, Tina Cascone, Lauren A. Byers, Don L. Gibbons, Jichao Chen, Seyed Javad Moghaddam, Edwin J. Ostrin, Daniel G. Rosen, John V. Heymach, Paul Scheet, Steven Dubinett, Ignacio I. Wistuba, Junya Fujimoto, Christopher S. Stevenson, Avrum E. Spira, Linghua Wang, Humam Kadara. Resolving the spatial and cellular architecture of lung adenocarcinoma by multi-region single-cell sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 130.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Enyu Dai
- 1MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | - Linh Tran
- 3The University of California Los Angeles, Los Angeles, CA
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31
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Han G, Sinjab A, Hara K, Treekitkarnmongkol W, Brennan P, Chang K, Bokatenkova E, Sanchez-Espiridion B, Behrens C, Solis LM, Gao B, Girard L, Zhang J, Sepesi B, Cascone T, Byers LA, Gibbons DL, Chen J, Moghaddam SJ, Ostrin EJ, Scheet P, Fujimoto J, Shay J, Heymach JV, Minna JD, Dubinett S, Wistuba II, Stevenson CS, Spira AE, Wang L, Kadara H. Abstract 702: Single-cell expression landscape of SARS-CoV-2 receptor ACE2 and host proteases in human lung adenocarcinoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Severely symptomatic COVID-19 is associated with lung inflammation, pneumonia, and respiratory failure, thereby raising concerns of elevated risk of COVID-19-asociated mortality among lung cancer patients. Angiotensin converting enzyme 2 (ACE2) is the major receptor for SARS-CoV-2 entry into lung cells. Yet, the single-cell expression landscape of ACE2 and other SARS-CoV-2-related genes in pulmonary tissues of lung cancer patients remains unknown. To fill these voids, we leveraged our ongoing efforts in single-cell transcriptomic analysis of 186,916 cells including a large number of epithelial cells (n=70,030) derived from 5 LUADs and 14 matching uninvolved normal lung tissues, to delineate expression levels and cellular distribution of ACE2 and SARS-CoV-2 priming proteases TMPRSS2 and TMPRSS4. Single-cell RNA sequencing of 186,916 cells revealed epithelial-specific expression of ACE2, TMPRSS2 and TMPRSS4. Analysis of 70,030 LUAD- and normal-derived epithelial cells showed that ACE2 levels were highest in normal alveolar type 2 (AT2) cells and that TMPRSS2 was expressed in 65% of normal AT2 cells. Conversely, expression of TMPRSS4 was highest and most frequently detected (75%) in malignant lung cells. ACE2-positive cells co-expressed genes implicated in lung pathobiology, including COPD-associated HHIP, and the scavengers CD36 and DMBT1. Notably, the viral scavenger DMBT1 was significantly positively correlated with ACE2 expression in AT2 cells. In conclusion, we describe normal and tumor lung epithelial populations that express SARS-CoV-2 receptor and proteases, as well as major host defense genes, and that thus comprise potential treatment targets for COVID-19 particularly among lung cancer patients.
Citation Format: Guangchun Han, Ansam Sinjab, Kieko Hara, Warapen Treekitkarnmongkol, Patrick Brennan, Kyle Chang, Elena Bokatenkova, Beatriz Sanchez-Espiridion, Carmen Behrens, Luisa M. Solis, Boning Gao, Luc Girard, Jianjun Zhang, Boris Sepesi, Tina Cascone, Lauren A. Byers, Don L. Gibbons, Jichao Chen, Seyed Javad Moghaddam, Edwin J. Ostrin, Paul Scheet, Junya Fujimoto, Jerry Shay, John V. Heymach, John D. Minna, Steven Dubinett, Ignacio I. Wistuba, Christopher S. Stevenson, Avrum E. Spira, Linghua Wang, Humam Kadara. Single-cell expression landscape of SARS-CoV-2 receptor ACE2 and host proteases in human lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 702.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Boning Gao
- 2University of Texas Southwestern, Dallas, TX
| | - Luc Girard
- 2University of Texas Southwestern, Dallas, TX
| | | | | | | | | | | | | | | | | | | | | | - Jerry Shay
- 2University of Texas Southwestern, Dallas, TX
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32
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Hu X, Fujimoto J, Ying L, Fukuoka J, Ashizawa K, Sun W, Reuben A, Chow CW, McGranahan N, Chen R, Hu J, Godoy MC, Tabata K, Kuroda K, Shi L, Li J, Behrens C, Parra ER, Little LD, Gumbs C, Mao X, Song X, Tippen S, Thornton RL, Kadara H, Scheet P, Roarty E, Ostrin EJ, Wang X, Carter BW, Antonoff MB, Zhang J, Vaporciyan AA, Pass H, Swisher SG, Heymach JV, Lee JJ, Wistuba II, Hong WK, Futreal PA, Su D, Zhang J. Author Correction: Multi-region exome sequencing reveals genomic evolution from preneoplasia to lung adenocarcinoma. Nat Commun 2021; 12:2888. [PMID: 33980839 PMCID: PMC8116337 DOI: 10.1038/s41467-021-23163-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lisha Ying
- Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital & Key Laboratory Diagnosis and Treatment Technology on Thoracic Oncology of Zhejiang Province, 310022, Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, 8528523, Nagasaki, Japan
| | - Kazuto Ashizawa
- Department of Clinical Oncology, Nagasaki University Graduate School of Biomedical Sciences, 8528523, Nagasaki, Japan
| | - Wenyong Sun
- Department of Pathology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, 310022, Hangzhou, China
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Nicholas McGranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, WC1E6BT, UK
| | - Runzhe Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jinlin Hu
- Department of Pathology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, 310022, Hangzhou, China
| | - Myrna C Godoy
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kazuhiro Tabata
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, 8528523, Nagasaki, Japan
| | - Kishio Kuroda
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, 8528523, Nagasaki, Japan
| | - Lei Shi
- Department of Radiology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, 310022, Hangzhou, China
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Latasha D Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xizeng Mao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samantha Tippen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Rebecca L Thornton
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paul Scheet
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Emily Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Edwin Justin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xu Wang
- Department of Radiology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, 310022, Hangzhou, China
| | - Brett W Carter
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Harvey Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Waun Ki Hong
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Dan Su
- Department of Pathology, Institute of Cancer Research and Basic Medical Sciences of Chinese Academy of Sciences, Cancer Hospital of University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, 310022, Hangzhou, China.
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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Dejima H, Hu X, Chen R, Zhang J, Fujimoto J, Parra ER, Haymaker C, Hubert SM, Duose D, Solis LM, Su D, Fukuoka J, Tabata K, Pham HHN, Mcgranahan N, Zhang B, Ye J, Ying L, Little L, Gumbs C, Chow CW, Estecio MR, Godoy MCB, Antonoff MB, Sepesi B, Pass HI, Behrens C, Zhang J, Vaporciyan AA, Heymach JV, Scheet P, Lee JJ, Wu J, Futreal PA, Reuben A, Kadara H, Wistuba II, Zhang J. Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features. Nat Commun 2021; 12:2722. [PMID: 33976164 PMCID: PMC8113327 DOI: 10.1038/s41467-021-22890-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown. In this study, we characterize the immune contexture of invasive lung ADC and its precursors by transcriptomic immune profiling, T cell receptor (TCR) sequencing and multiplex immunofluorescence (mIF). Our results demonstrate that anti-tumor immunity evolved as a continuum from lung preneoplasia, to preinvasive ADC, minimally-invasive ADC and frankly invasive lung ADC with a gradually less effective and more intensively regulated immune response including down-regulation of immune-activation pathways, up-regulation of immunosuppressive pathways, lower infiltration of cytotoxic T cells (CTLs) and anti-tumor helper T cells (Th), higher infiltration of regulatory T cells (Tregs), decreased T cell clonality, and lower frequencies of top T cell clones in later-stages. Driver mutations, chromosomal copy number aberrations (CNAs) and aberrant DNA methylation may collectively impinge host immune responses and facilitate immune evasion, promoting the outgrowth of fit subclones in preneoplasia into dominant clones in invasive ADC.
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Affiliation(s)
- Hitoshi Dejima
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Hu
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Runzhe Chen
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiexin Zhang
- Department of Bioinformatics & Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin R Parra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shawna M Hubert
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dzifa Duose
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M Solis
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Su
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Nicholas Mcgranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, UK
| | - Baili Zhang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie Ye
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lisha Ying
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Zhejiang Cancer Research Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Latasha Little
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcos Roberto Estecio
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center of Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Myrna C B Godoy
- Department of Thoracic Imaging, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Humam Kadara
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Jianjun Zhang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Behrens C, Rocha P, Parra ER, Feng L, Rodriguez-Canales J, Solis LM, Mino B, Zhang J, Gibbons DL, Sepesi B, Rice D, Heymach JV, Moran C, Creighton CJ, Lee JJ, Kadara H, Wistuba II. Female Gender Predicts Augmented Immune Infiltration in Lung Adenocarcinoma. Clin Lung Cancer 2021; 22:e415-e424. [PMID: 32763065 DOI: 10.1016/j.cllc.2020.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 03/16/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Immune infiltration in lung adenocarcinomas (LUADs) has been associated with response to immune checkpoint inhibitors. Clinical features underlying differential responses of patients with LUADs to immunotherapy are not well understood. Here, we analyzed the association between LUAD immune infiltration and clinicopathologic variables. MATERIALS AND METHODS Intratumoral CD3, CD8, and CD68 cell densities (tumor-associated immune cells [TAICs]) were immunohistochemically assessed in 146 surgically resected LUADs. LUADs were classified into 2 groups, low and high TAICs, based on the median values of cell densities for CD3, CD8, and CD68. Somatic mutation burden and driver gene mutation status were analyzed in a subset of the cases (n = 92). We statistically analyzed the association between the TAIC groups and various clinicopathologic and molecular variables by using the χ2/Fisher and Wilcoxon sum tests and multivariable logistic regression models. RESULTS Patient gender, tumor size, and STK11 mutations were significantly associated with TAIC levels in LUAD. Female patients exhibited significantly elevated TAIC levels (P = .005) compared with male patients. Tumor size was inversely associated with TAIC levels (P = .012). STK11 mutated tumors were associated with lower TAICs (P = .008). Higher TAICs were consistently observed in female patients with LUADs after adjusting for stage, tumor size, and age. Multivariable regression models confirmed female gender as an independent variable associated with TAIC levels in LUAD (P = .0141). CONCLUSION Immune infiltration in LUADs was significantly higher in female patients, warranting further exploration into the association between this clinical variable and immunotherapeutic response in LUAD.
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Affiliation(s)
- Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX.
| | - Pedro Rocha
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lei Feng
- Department of Bioinformatics and Computational Biology Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luisa M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David Rice
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cesar Moran
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chad J Creighton
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics and Informatics, Dan L. Duncan Comprehensive Cancer Center, Houston, TX; Department of Medicine, Baylor College of Medicine, Houston, TX
| | - J Jack Lee
- Department of Bioinformatics and Computational Biology Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX
| | - Ignacio I Wistuba
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
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Le X, Negrao MV, Reuben A, Federico L, Diao L, McGrail D, Nilsson M, Robichaux J, Munoz IG, Patel S, Elamin Y, Fan YH, Lee WC, Parra E, Solis Soto LM, Chen R, Li J, Karpinets T, Khairullah R, Kadara H, Behrens C, Sepesi B, Wang R, Zhu M, Wang L, Vaporciyan A, Roth J, Swisher S, Haymaker C, Zhang J, Wang J, Wong KK, Byers LA, Bernatchez C, Zhang J, Wistuba II, Gibbons DL, Akbay EA, Heymach JV. Characterization of the Immune Landscape of EGFR-Mutant NSCLC Identifies CD73/Adenosine Pathway as a Potential Therapeutic Target. J Thorac Oncol 2021; 16:583-600. [PMID: 33388477 DOI: 10.1016/j.jtho.2020.12.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [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: 08/21/2020] [Revised: 11/22/2020] [Accepted: 12/19/2020] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Lung adenocarcinomas harboring EGFR mutations do not respond to immune checkpoint blockade therapy and their EGFR wildtype counterpart. The mechanisms underlying this lack of clinical response have been investigated but remain incompletely understood. METHODS We analyzed three cohorts of resected lung adenocarcinomas (Profiling of Resistance Patterns of Oncogenic Signaling Pathways in Evaluation of Cancer of Thorax, Immune Genomic Profiling of NSCLC, and The Cancer Genome Atlas) and compared tumor immune microenvironment of EGFR-mutant tumors to EGFR wildtype tumors, to identify actionable regulators to target and potentially enhance the treatment response. RESULTS EGFR-mutant NSCLC exhibited low programmed death-ligand 1, low tumor mutational burden, decreased number of cytotoxic T cells, and low T cell receptor clonality, consistent with an immune-inert phenotype, though T cell expansion ex vivo was preserved. In an analysis of 75 immune checkpoint genes, the top up-regulated genes in the EGFR-mutant tumors (NT5E and ADORA1) belonged to the CD73/adenosine pathway. Single-cell analysis revealed that the tumor cell population expressed CD73, both in the treatment-naive and resistant tumors. Using coculture systems with EGFR-mutant NSCLC cells, T regulatory cell proportion was decreased with CD73 knockdown. In an immune-competent mouse model of EGFR-mutant lung cancer, the CD73/adenosine pathway was markedly up-regulated and CD73 blockade significantly inhibited tumor growth. CONCLUSIONS Our work revealed that EGFR-mutant NSCLC has an immune-inert phenotype. We identified the CD73/adenosine pathway as a potential therapeutic target for EGFR-mutant NSCLC.
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Affiliation(s)
- Xiuning Le
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marcelo V Negrao
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel McGrail
- Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Monique Nilsson
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jacqulyne Robichaux
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Irene Guijarro Munoz
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sonia Patel
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yasir Elamin
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - You-Hong Fan
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Won-Chul Lee
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin Parra
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa Maren Solis Soto
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Runzhe Chen
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roohussaba Khairullah
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Humam Kadara
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mingrui Zhu
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ara Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jack Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kwok-Kin Wong
- Division of Hematology and Medical Oncology, NYU Perlmutter Cancer Center, New York, New York; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Lauren A Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Esra A Akbay
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Han G, Sinjab A, Hara K, Treekitkarnmongkol W, Brennan P, Chang K, Bogatenkova E, Sanchez-Espiridion B, Behrens C, Solis LM, Gao B, Girard L, Zhang J, Sepesi B, Cascone T, Byers LA, Gibbons DL, Chen J, Moghaddam SJ, Ostrin EJ, Scheet P, Fujimoto J, Shay J, Heymach JV, Minna JD, Dubinett S, Wistuba II, Stevenson CS, Spira AE, Wang L, Kadara H. Single-Cell Expression Landscape of SARS-CoV-2 Receptor ACE2 and Host Proteases in Normal and Malignant Lung Tissues from Pulmonary Adenocarcinoma Patients. Cancers (Basel) 2021; 13:cancers13061250. [PMID: 33809063 PMCID: PMC7998226 DOI: 10.3390/cancers13061250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary The coronavirus disease 2019 (COVID-19) pandemic continues to spread rapidly on a global scale. When presenting with severe respiratory complications, COVID-19 results in markedly high death rates, particularly among patients with comorbidities such as cancer. Motivated by the ongoing global health crisis, we leveraged a growing in-house cohort of pulmonary tissues from lung cancer patients to analyze, at high resolution, the expression of host proteins implicated in the entryway of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into lung epithelial cells. Our results identify key pathways in lung pathobiology and inflammation that offer the potential to identify novel markers and therapeutic targets that can be repurposed for clinical management of COVID-19, particularly among lung cancer patients, a population that represents over half a million individuals in the United States alone. Abstract The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Severely symptomatic COVID-19 is associated with lung inflammation, pneumonia, and respiratory failure, thereby raising concerns of elevated risk of COVID-19-associated mortality among lung cancer patients. Angiotensin-converting enzyme 2 (ACE2) is the major receptor for SARS-CoV-2 entry into lung cells. The single-cell expression landscape of ACE2 and other SARS-CoV-2-related genes in pulmonary tissues of lung cancer patients remains unknown. We sought to delineate single-cell expression profiles of ACE2 and other SARS-CoV-2-related genes in pulmonary tissues of lung adenocarcinoma (LUAD) patients. We examined the expression levels and cellular distribution of ACE2 and SARS-CoV-2-priming proteases TMPRSS2 and TMPRSS4 in 5 LUADs and 14 matched normal tissues by single-cell RNA-sequencing (scRNA-seq) analysis. scRNA-seq of 186,916 cells revealed epithelial-specific expression of ACE2, TMPRSS2, and TMPRSS4. Analysis of 70,030 LUAD- and normal-derived epithelial cells showed that ACE2 levels were highest in normal alveolar type 2 (AT2) cells and that TMPRSS2 was expressed in 65% of normal AT2 cells. Conversely, the expression of TMPRSS4 was highest and most frequently detected (75%) in lung cells with malignant features. ACE2-positive cells co-expressed genes implicated in lung pathobiology, including COPD-associated HHIP, and the scavengers CD36 and DMBT1. Notably, the viral scavenger DMBT1 was significantly positively correlated with ACE2 expression in AT2 cells. We describe normal and tumor lung epithelial populations that express SARS-CoV-2 receptor and proteases, as well as major host defense genes, thus comprising potential treatment targets for COVID-19 particularly among lung cancer patients.
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Affiliation(s)
- Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (K.H.); (W.T.); (B.S.-E.); (L.M.S.); (J.F.); (I.I.W.)
| | - Kieko Hara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (K.H.); (W.T.); (B.S.-E.); (L.M.S.); (J.F.); (I.I.W.)
| | - Warapen Treekitkarnmongkol
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (K.H.); (W.T.); (B.S.-E.); (L.M.S.); (J.F.); (I.I.W.)
| | - Patrick Brennan
- Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (P.B.); (E.B.)
| | - Kyle Chang
- Guardant Health, Redwood City, CA 94063, USA;
| | - Elena Bogatenkova
- Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (P.B.); (E.B.)
| | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (K.H.); (W.T.); (B.S.-E.); (L.M.S.); (J.F.); (I.I.W.)
| | - Carmen Behrens
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.B.); (J.Z.); (T.C.); (L.A.B.); (D.L.G.); (J.V.H.)
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (K.H.); (W.T.); (B.S.-E.); (L.M.S.); (J.F.); (I.I.W.)
| | - Boning Gao
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern, Dallas, TX 75390, USA; (B.G.); (L.G.); (J.D.M.)
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern, Dallas, TX 75390, USA; (B.G.); (L.G.); (J.D.M.)
| | - Jianjun Zhang
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.B.); (J.Z.); (T.C.); (L.A.B.); (D.L.G.); (J.V.H.)
| | - Boris Sepesi
- Department of Cardiovascular and Thoracic Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77005, USA;
| | - Tina Cascone
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.B.); (J.Z.); (T.C.); (L.A.B.); (D.L.G.); (J.V.H.)
| | - Lauren A. Byers
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.B.); (J.Z.); (T.C.); (L.A.B.); (D.L.G.); (J.V.H.)
| | - Don L. Gibbons
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.B.); (J.Z.); (T.C.); (L.A.B.); (D.L.G.); (J.V.H.)
| | - Jichao Chen
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.C.); (S.J.M.)
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (J.C.); (S.J.M.)
| | - Edwin J. Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA;
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (K.H.); (W.T.); (B.S.-E.); (L.M.S.); (J.F.); (I.I.W.)
| | - Jerry Shay
- Department of Cell Biology, University of Texas Southwestern, Dallas, TX 75390, USA;
| | - John V. Heymach
- Department of Thoracic, Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (C.B.); (J.Z.); (T.C.); (L.A.B.); (D.L.G.); (J.V.H.)
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern, Dallas, TX 75390, USA; (B.G.); (L.G.); (J.D.M.)
| | - Steven Dubinett
- Department of Medicine, The University of California Los Angeles, Los Angeles, CA 90095, USA;
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (K.H.); (W.T.); (B.S.-E.); (L.M.S.); (J.F.); (I.I.W.)
| | | | - Avrum E. Spira
- Lung Cancer Initiative at Johnson and Johnson, Cambridge, MA 02142, USA; (C.S.S.); (A.E.S.)
- Section of Computational Biomedicine, Boston University, Boston, MA 02215, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Correspondence: (L.W.); (H.K.)
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (A.S.); (K.H.); (W.T.); (B.S.-E.); (L.M.S.); (J.F.); (I.I.W.)
- Correspondence: (L.W.); (H.K.)
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Tan X, Banerjee P, Pham EA, Rutaganira FUN, Basu K, Bota-Rabassedas N, Guo HF, Grzeskowiak CL, Liu X, Yu J, Shi L, Peng DH, Rodriguez BL, Zhang J, Zheng V, Duose DY, Solis LM, Mino B, Raso MG, Behrens C, Wistuba II, Scott KL, Smith M, Nguyen K, Lam G, Choong I, Mazumdar A, Hill JL, Gibbons DL, Brown PH, Russell WK, Shokat K, Creighton CJ, Glenn JS, Kurie JM. PI4KIIIβ is a therapeutic target in chromosome 1q-amplified lung adenocarcinoma. Sci Transl Med 2021; 12:12/527/eaax3772. [PMID: 31969487 DOI: 10.1126/scitranslmed.aax3772] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/14/2019] [Accepted: 10/24/2019] [Indexed: 12/25/2022]
Abstract
Heightened secretion of protumorigenic effector proteins is a feature of malignant cells. Yet, the molecular underpinnings and therapeutic implications of this feature remain unclear. Here, we identify a chromosome 1q region that is frequently amplified in diverse cancer types and encodes multiple regulators of secretory vesicle biogenesis and trafficking, including the Golgi-dedicated enzyme phosphatidylinositol (PI)-4-kinase IIIβ (PI4KIIIβ). Molecular, biochemical, and cell biological studies show that PI4KIIIβ-derived PI-4-phosphate (PI4P) synthesis enhances secretion and accelerates lung adenocarcinoma progression by activating Golgi phosphoprotein 3 (GOLPH3)-dependent vesicular release from the Golgi. PI4KIIIβ-dependent secreted factors maintain 1q-amplified cancer cell survival and influence prometastatic processes in the tumor microenvironment. Disruption of this functional circuitry in 1q-amplified cancer cells with selective PI4KIIIβ antagonists induces apoptosis and suppresses tumor growth and metastasis. These results support a model in which chromosome 1q amplifications create a dependency on PI4KIIIβ-dependent secretion for cancer cell survival and tumor progression.
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Affiliation(s)
- Xiaochao Tan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Priyam Banerjee
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edward A Pham
- Departments of Medicine and Microbiology & Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Florentine U N Rutaganira
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kaustabh Basu
- Departments of Medicine and Microbiology & Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neus Bota-Rabassedas
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hou-Fu Guo
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xin Liu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiang Yu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Shi
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David H Peng
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - B Leticia Rodriguez
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiaqi Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Veronica Zheng
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luisa M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.,Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark Smith
- Departments of Medicine and Microbiology & Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Stanford ChEM-H Medicinal Chemistry Knowledge Center, Stanford University, CA 94305, USA
| | - Khanh Nguyen
- Departments of Medicine and Microbiology & Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Grace Lam
- Departments of Medicine and Microbiology & Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ingrid Choong
- Departments of Medicine and Microbiology & Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Abhijit Mazumdar
- Department of Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jamal L Hill
- Department of Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Powel H Brown
- Department of Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Kevan Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Chad J Creighton
- Department of Medicine, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey S Glenn
- Departments of Medicine and Microbiology & Immunology, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Veterans Administration Medical Center, Palo Alto, CA 94304, USA
| | - Jonathan M Kurie
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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38
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Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JPJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun 2021; 12:687. [PMID: 33514726 PMCID: PMC7846738 DOI: 10.1038/s41467-021-20907-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied. We perform reduced representation bisulfite sequencing of invasive lung adenocarcinoma and its precursors, atypical adenomatous hyperplasia, adenocarcinoma in situ and minimally invasive adenocarcinoma. We observe gradual increase of methylation aberrations and significantly higher level of methylation ITH in later-stage lesions. The phylogenetic patterns inferred from methylation aberrations resemble those based on somatic mutations suggesting parallel methylation and genetic evolution. De-convolution reveal higher ratio of T regulatory cells (Tregs) versus CD8 + T cells in later-stage diseases, implying progressive immunosuppression with neoplastic progression. Furthermore, increased global hypomethylation is associated with higher mutation burden, copy number variation burden and AI burden as well as higher Treg/CD8 ratio, highlighting the potential impact of methylation on chromosomal instability, mutagenesis and tumor immune microenvironment during early carcinogenesis of lung adenocarcinomas.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Runzhe Chen
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jian Carrot-Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Nicholas McGranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, SW73RP, UK
| | - Lisha Ying
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, 310022, Hangzhou, China
- Zhejiang Cancer Research Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Chi-Wan Chow
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Myrna C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Brett W Carter
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carmen Behrens
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mara B Antonoff
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Boris Sepesi
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Humam Kadara
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ara A Vaporciyan
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Dan Su
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China.
| | | | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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39
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Treekitkarnmongkol W, Hassane M, Sinjab A, Chang K, Hara K, Rahal Z, Zhang J, Lu W, Sivakumar S, McDowell TL, Kantrowitz J, Zhou J, Lang W, Xu L, Ochieng JK, Nunomura-Nakamura S, Deng S, Behrens C, Raso MG, Fukuoka J, Reuben A, Ostrin EJ, Parra E, Solis LM, Spira AE, McAllister F, Cascone T, Wistuba II, Moghaddam SJ, Scheet PA, Fujimoto J, Kadara H. Augmented Lipocalin-2 Is Associated with Chronic Obstructive Pulmonary Disease and Counteracts Lung Adenocarcinoma Development. Am J Respir Crit Care Med 2021; 203:90-101. [PMID: 32730093 DOI: 10.1164/rccm.202004-1079oc] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 12/30/2022] Open
Abstract
Rationale: Early pathogenesis of lung adenocarcinoma (LUAD) remains largely unknown. We found that, relative to wild-type littermates, the innate immunomodulator Lcn2 (lipocalin-2) was increased in normal airways from mice with knockout of the airway lineage gene Gprc5a (Gprc5a-/-) and that are prone to developing inflammation and LUAD. Yet, the role of LCN2 in lung inflammation and LUAD is poorly understood.Objectives: Delineate the role of Lcn2 induction in LUAD pathogenesis.Methods: Normal airway brushings, uninvolved lung tissues, and tumors from Gprc5a-/- mice before and after tobacco carcinogen exposure were analyzed by RNA sequencing. LCN2 mRNA was analyzed in public and in-house data sets of LUAD, lung squamous cancer (LUSC), chronic obstructive pulmonary disease (COPD), and LUAD/LUSC with COPD. LCN2 protein was immunohistochemically analyzed in a tissue microarray of 510 tumors. Temporal lung tumor development, gene expression programs, and host immune responses were compared between Gprc5a-/- and Gprc5a-/-/Lcn2-/- littermates.Measurements and Main Results: Lcn2 was progressively elevated during LUAD development and positively correlated with proinflammatory cytokines and inflammation gene sets. LCN2 was distinctively elevated in human LUADs, but not in LUSCs, relative to normal lungs and was associated with COPD among smokers and patients with LUAD. Relative to Gprc5a-/- mice, Gprc5a-/-/Lcn2-/- littermates exhibited significantly increased lung tumor development concomitant with reduced T-cell abundance (CD4+) and richness, attenuated antitumor immune gene programs, and increased immune cell expression of protumor inflammatory cytokines.Conclusions: Augmented LCN2 expression is a molecular feature of COPD-associated LUAD and counteracts LUAD development in vivo by maintaining antitumor immunity.
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Affiliation(s)
| | - Maya Hassane
- Department of Biochemistry and Molecular Genetics and
| | | | | | - Kieko Hara
- Department of Translational Molecular Pathology
| | - Zahraa Rahal
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Jiexin Zhang
- Department of Bioinformatics and Computer Biology
| | - Wei Lu
- Department of Translational Molecular Pathology
| | | | - Tina L McDowell
- Department of Translational Molecular Pathology.,Department of Epidemiology
| | - Jacob Kantrowitz
- Section of Computational Biomedicine, School of Medicine, Boston University, Boston, Massachusetts; and
| | | | - Wenhua Lang
- Department of Translational Molecular Pathology
| | - Li Xu
- Department of Translational Molecular Pathology
| | | | | | | | | | | | - Junya Fukuoka
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | | | | | - Edwin Parra
- Department of Translational Molecular Pathology
| | | | - Avrum E Spira
- Section of Computational Biomedicine, School of Medicine, Boston University, Boston, Massachusetts; and
| | - Florencia McAllister
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tina Cascone
- Department of Thoracic Head and Neck Medical Oncology
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40
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Deng S, Ramos-Castaneda M, Velasco WV, Clowers MJ, Gutierrez BA, Noble O, Dong Y, Zarghooni M, Alvarado L, Caetano MS, Yang S, Ostrin EJ, Behrens C, Wistuba II, Stabile LP, Kadara H, Watowich SS, Moghaddam SJ. Interplay between estrogen and Stat3/NF-κB-driven immunomodulation in lung cancer. Carcinogenesis 2020; 41:1529-1542. [PMID: 32603404 PMCID: PMC7896112 DOI: 10.1093/carcin/bgaa064] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/30/2020] [Accepted: 06/19/2020] [Indexed: 12/17/2022] Open
Abstract
K-ras mutant lung adenocarcinoma (LUAD) is the most common type of lung cancer, displays abysmal prognosis and is tightly linked to tumor-promoting inflammation, which is increasingly recognized as a target for therapeutic intervention. We have recently shown a gender-specific role for epithelial Stat3 signaling in the pathogenesis of K-ras mutant LUAD. The absence of epithelial Stat3 in male K-ras mutant mice (LR/Stat3Δ/Δ mice) promoted tumorigenesis and induced a nuclear factor-kappaB (NF-κB)-driven pro-tumor immune response while reducing tumorigenesis and enhancing anti-tumor immunity in female counterparts. In the present study, we manipulated estrogen and NF-κB signaling to study the mechanisms underlying this intriguing gender-disparity. In LR/Stat3Δ/Δ females, estrogen deprivation by bilateral oophorectomy resulted in higher tumor burden, an induction of NF-κB-driven immunosuppressive response, and reduced anti-tumor cytotoxicity, whereas estrogen replacement reversed these changes. On the other hand, exogenous estrogen in males successfully inhibited tumorigenesis, attenuated NF-κB-driven immunosuppression and boosted anti-tumor immunity. Mechanistically, genetic targeting of epithelial NF-κB activity resulted in reduced tumorigenesis and enhanced the anti-tumor immune response in LR/Stat3Δ/Δ males, but not females. Our data suggest that estrogen exerts a context-specific anti-tumor effect through inhibiting NF-κB-driven tumor-promoting inflammation and provide insights into developing novel personalized therapeutic strategies for K-ras mutant LUAD.
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Affiliation(s)
- Shanshan Deng
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marco Ramos-Castaneda
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Walter V Velasco
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael J Clowers
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Berenice A Gutierrez
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Oscar Noble
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yiping Dong
- Department of Oncology Radiotherapy, First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Melody Zarghooni
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucero Alvarado
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mauricio S Caetano
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shuanying Yang
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Edwin J Ostrin
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laura P Stabile
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Humam Kadara
- The University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie S Watowich
- The University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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41
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Lee WC, Reuben A, Hu X, McGranahan N, Chen R, Jalali A, Negrao MV, Hubert SM, Tang C, Wu CC, Lucas AS, Roh W, Suda K, Kim J, Tan AC, Peng DH, Lu W, Tang X, Chow CW, Fujimoto J, Behrens C, Kalhor N, Fukumura K, Coyle M, Thornton R, Gumbs C, Li J, Wu CJ, Little L, Roarty E, Song X, Lee JJ, Sulman EP, Rao G, Swisher S, Diao L, Wang J, Heymach JV, Huse JT, Scheet P, Wistuba II, Gibbons DL, Futreal PA, Zhang J, Gomez D, Zhang J. Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity. Genome Biol 2020; 21:271. [PMID: 33148332 PMCID: PMC7640699 DOI: 10.1186/s13059-020-02175-0] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary. RESULTS We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases. Furthermore, we analyze published WES data from 35 primary NSCLC and metastasis pairs, and transcriptomic data from 4 autopsy cases with metastatic NSCLC and one metastatic lung cancer mouse model. The majority of somatic mutations are shared between primary tumors and paired distant metastases although mutational signatures suggest different mutagenesis processes in play before and after metastatic spread. Subclonal analysis reveals evidence of monoclonal seeding in 41 of 42 patients. Pathway analysis of transcriptomic data reveals that downregulated pathways in metastases are mainly immune-related. Further deconvolution analysis reveals significantly lower infiltration of various immune cell types in metastases with the exception of CD4+ T cells and M2 macrophages. These results are in line with lower densities of immune cells and higher CD4/CD8 ratios in metastases shown by IHC. Analysis of transcriptomic data from autopsy cases and animal models confirms that immunosuppression is also present in extracranial metastases. Significantly higher somatic copy number aberration and allelic imbalance burdens are identified in metastases. CONCLUSIONS Metastasis is a molecularly late event, and immunosuppression driven by different molecular events, including somatic copy number aberration, may be a common characteristic of tumors with metastatic plasticity.
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Affiliation(s)
- Won-Chul Lee
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Runzhe Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shawna M Hubert
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad Tang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Whijae Roh
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kenichi Suda
- Department of Thoracic Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Jihye Kim
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Aik-Choon Tan
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kazutaka Fukumura
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcus Coyle
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rebecca Thornton
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik P Sulman
- New York University Langone School of Medicine, New York, NY, USA
| | - Ganesh Rao
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen Swisher
- Department of Thoracic Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason T Huse
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel Gomez
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Current Address: Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Gaudreau PO, Negrao MV, Mitchell KG, Reuben A, Corsini EM, Li J, Karpinets TV, Wang Q, Diao L, Wang J, Federico L, Parra-Cuentas ER, Khairullah R, Behrens C, Correa AM, Gomez D, Little L, Gumbs C, Kadara HN, Fujimoto J, McGrail DJ, Vaporciyan AA, Swisher SG, Walsh G, Antonoff MB, Weissferdt A, Tran H, Roarty E, Haymaker C, Bernatchez C, Zhang J, Futreal PA, Wistuba II, Cascone T, Heymach JV, Sepesi B, Zhang J, Gibbons DL. Neoadjuvant Chemotherapy Increases Cytotoxic T Cell, Tissue Resident Memory T Cell, and B Cell Infiltration in Resectable NSCLC. J Thorac Oncol 2020; 16:127-139. [PMID: 33096269 DOI: 10.1016/j.jtho.2020.09.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [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: 03/26/2020] [Revised: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The combination of programmed cell death protein-1 or programmed death-ligand 1 immune checkpoint blockade and chemotherapy has revolutionized the treatment of advanced NSCLC, but the mechanisms underlying this synergy remain incompletely understood. In this study, we explored the relationships between neoadjuvant chemotherapy and the immune microenvironment (IME) of resectable NSCLC to identify novel mechanisms by which chemotherapy may enhance the effect of immune checkpoint blockade. METHODS Genomic, transcriptomic, and immune profiling data of 511 patients treated with neoadjuvant chemotherapy followed by surgery (NCT) versus upfront surgery (US) were compared with determined differential characteristics of the IMEs derived from whole-exome sequencing (NCT = 18; US = 73), RNA microarray (NCT = 45; US = 202), flow cytometry (NCT = 17; US = 39), multiplex immunofluorescence (NCT = 10; US = 72), T-cell receptor sequencing (NCT = 16 and US = 63), and circulating cytokines (NCT = 18; US = 73). RESULTS NCT was associated with increased infiltration of cytotoxic CD8+ T cells and CD20+ B cells. Moreover, NCT was associated with increases in CD8+CD103+ and CD4+CD103+PD-1+TIM3- tissue resident memory T cells. Gene expression profiling supported memory function of CD8+ and CD4+ T cells. However, NCT did not affect T-cell receptor clonality, richness, or tumor mutational burden. Finally, NCT was associated with decreased plasma BDNF (TrkB) at baseline and week 4 after surgery. CONCLUSIONS Our study supports that, in the context of resectable NSCLC, neoadjuvant chemotherapy promotes antitumor immunity through T and B cell recruitment in the IME and through a phenotypic change toward cytotoxic and memory CD8+ and CD4+ memory helper T cells.
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Affiliation(s)
- Pierre-Olivier Gaudreau
- Department of Oncology, Queens' University and the Canadian Cancer Trials Group, Kingston, Ontario, Canada
| | - Marcelo V Negrao
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle G Mitchell
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Erin M Corsini
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin R Parra-Cuentas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roohussaba Khairullah
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arlene M Correa
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel Gomez
- Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Humam N Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Garrett Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Annikka Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hai Tran
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily Roarty
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Biologics Development Department, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - P Andrew Futreal
- Department of Genomic Medicine, 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
| | - Tina Cascone
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic and Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Don L Gibbons
- Department of Oncology, Queens' University and the Canadian Cancer Trials Group, Kingston, Ontario, Canada; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Dziarzhytski S, Biednov M, Dicke B, Wang A, Miedema PS, Engel RY, Schunck JO, Redlin H, Weigelt H, Siewert F, Behrens C, Sinha M, Schulte A, Grimm-Lebsanft B, Chiuzbăian SG, Wurth W, Beye M, Rübhausen M, Brenner G. The TRIXS end-station for femtosecond time-resolved resonant inelastic x-ray scattering experiments at the soft x-ray free-electron laser FLASH. Struct Dyn 2020; 7:054301. [PMID: 32953941 PMCID: PMC7498279 DOI: 10.1063/4.0000029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
We present the experimental end-station TRIXS dedicated to time-resolved soft x-ray resonant inelastic x-ray scattering (RIXS) experiments on solid samples at the free-electron laser FLASH. Using monochromatized ultrashort femtosecond XUV/soft x-ray photon pulses in combination with a synchronized optical laser in a pump-probe scheme, the TRIXS setup allows measuring sub-picosecond time-resolved high-resolution RIXS spectra in the energy range from 35 eV to 210 eV, thus spanning the M-edge (M1 and M2,3) absorption resonances of 3d transition metals and N4,5-edges of rare earth elements. A Kirkpatrick-Baez refocusing mirror system at the first branch of the plane grating monochromator beamline (PG1) provides a focus of (6 × 6) μm2 (FWHM) at the sample. The RIXS spectrometer reaches an energy resolution of 35-160 meV over the entire spectral range. The optical laser system based on a chirped pulse optical parametric amplifier provides approximately 100 fs (FWHM) long photon pulses at the fundamental wavelength of 800 nm and a fluence of 120 mJ/cm2 at a sample for optical pump-XUV probe measurements. Furthermore, optical frequency conversion enables experiments at 400 nm or 267 nm with a fluence of 80 and 30 mJ/cm2, respectively. Some of the first (pump-probe) RIXS spectra measured with this setup are shown. The measured time resolution for time-resolved RIXS measurements has been characterized as 287 fs (FWHM) for the used energy resolution.
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Affiliation(s)
| | - M. Biednov
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | - B. Dicke
- Institute of Nanostructure and Solid State Physics, University of Hamburg and Center for Free-Electron Laser Science (CFEL), Notkestr. 85, Hamburg 22607, Germany
| | - A. Wang
- Sorbonne Université, CNRS (UMR 7614), Laboratoire de Chimie Physique-Matière et Rayonnement, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | | | | | | | - H. Redlin
- DESY, Notkestr. 85, Hamburg 22607, Germany
| | - H. Weigelt
- DESY, Notkestr. 85, Hamburg 22607, Germany
| | - F. Siewert
- Helmholtz Zentrum Berlin, Department Optics and Beamlines, Albert-Einstein-Strasse 15, 12489 Berlin, Germany
| | - C. Behrens
- DESY, Notkestr. 85, Hamburg 22607, Germany
| | - M. Sinha
- DESY, Notkestr. 85, Hamburg 22607, Germany
| | - A. Schulte
- DESY, Notkestr. 85, Hamburg 22607, Germany
| | - B. Grimm-Lebsanft
- Institute of Nanostructure and Solid State Physics, University of Hamburg and Center for Free-Electron Laser Science (CFEL), Notkestr. 85, Hamburg 22607, Germany
| | - S. G. Chiuzbăian
- Sorbonne Université, CNRS (UMR 7614), Laboratoire de Chimie Physique-Matière et Rayonnement, 4 Place Jussieu, 75252 Paris Cedex 05, France
| | - W. Wurth
- DESY, Notkestr. 85, Hamburg 22607, Germany
| | - M. Beye
- DESY, Notkestr. 85, Hamburg 22607, Germany
| | - M. Rübhausen
- Institute of Nanostructure and Solid State Physics, University of Hamburg and Center for Free-Electron Laser Science (CFEL), Notkestr. 85, Hamburg 22607, Germany
| | - G. Brenner
- DESY, Notkestr. 85, Hamburg 22607, Germany
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Segura RNL, Catao A, Solis LM, Jiang M, Tamegnon A, Fujimoto J, Rodriguez-Canales J, Chow CWB, Behrens C, Kalhor N, Weissferdt A, Heymach J, Swisher S, Sepesi B, Lee J, Moran C, Futreal A, Zhang J, Parra ER, Wistuba II, Tetzlaff MT, Francisco-Cruz A. Abstract 399: Tertiary lymphoid structures features associate with outcome in non-small cell lung carcinoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Tertiary lymphoid structures (TLS) are ectopic lymphoid structures organized in a nodular pattern secondary to chronic inflammation. The presence of TLS has been associated with efficacious response to immune checkpoint blockade in a wide array of tumor types, including Non-Small Cell Lung Carcinoma (NSCLC). At early stages of NSCLC, TLS are observed in up to 70% of primary tumors where they are also associated with effective anti-tumor immune-responses and response to anti-PD-1 therapy. Despite complete surgical resection, however, up to 50% of patients with early stage NSCLC will eventually relapse. A systematic histomorphologic analysis of TLS and their association with relapse has not been well characterized.
Design: Serial sections from Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens from 33 patients with stage I NSCLC were obtained (23 adenocarcinomas and 10 squamous cell carcinomas). Slides were stained with hematoxylin and eosin (H&E), immunohistochemistry for Vimentin, and 2 multiplex immunofluorescence (mIF) panels (Panel 1: cytokeratin (CK), CD3, CD8, CD68, PD-1, PD-L1 and DAPI Panel 2: CK, CD3 CD8, CD45RO, FOXP3, Granzyme B and DAPI). TLS were classified based on the H&E and Vimentin analysis into lymphoid aggregates (LA), immature TLS (iTLS), and mature TLS (mTLS). Morphometric analysis (number, area, and distance to nearest malignant cell) of intratumoral (IT) and peritumoral (PT) TLS was performed. mIF slides were scanned and IT representative areas were selected for cell densities and percentage quantification of immune-phenotypes. Morphometric analysis of TLSs was correlated with clinical outcomes, and tumor infiltrating immune cells.
Results: Patients who recurred had fewer IT mTLS (1.8 vs 6; p=0.02) and smaller area of mTLS (64541.7μm2 vs 149870.5 μm2; p=0.004) compared with patients who did not recurr.The cell density of IT antigen-experienced cytotoxic T-lymphocytes (CTLs), regulatory T-cells, memory CTLs, and memory CTLs expressing FOXP3 were inversely correlated with the mTLS area (r=-0.6, p≤0.02). Antigen-experienced CTLs (r=-0.61; p≤0.05) and non-CTLs (r=-0.63; p≤0.05) were inversely correlated with the number of IT mTLS.
Conclusion: Detailed morphometric analysis of mTLS offers relevant prognostic information for recurrence at stage I of NSCLC. mTLSs are associated with reduced IT infiltration by PD-1+ TILs. Taken together, germinal center development in mTLSs might convey a protective immune response due to immuno-dominant neoantigen presentation. Supported in part by CPRIT RP160668 grant and UT Lung SPORE.
Citation Format: Rossana Natalia Lazcano Segura, Andre Catao, Luisa M. Solis, Mei Jiang, Auriole Tamegnon, Junya Fujimoto, Jaime Rodriguez-Canales, Chi-Wan B. Chow, Carmen Behrens, Neda Kalhor, Annika Weissferdt, John Heymach, Stephen Swisher, Boris Sepesi, Jack Lee, Cesar Moran, Andrew Futreal, Jianjun Zhang, Edwin R. Parra, Ignacio I. Wistuba, Michael T. Tetzlaff, Alejandro Francisco-Cruz. Tertiary lymphoid structures features associate with outcome in non-small cell lung carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 399.
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Affiliation(s)
| | | | | | - Mei Jiang
- MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | | | | | | | - Jack Lee
- MD Anderson Cancer Center, Houston, TX
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Sinjab A, Han G, Treekitkarnmongkol W, Brennan P, Hara K, Chang K, Bogatenkova E, Sanchez-Espiridion B, Behrens C, Zhang J, Sepesi B, Cascone T, Gibbons DL, Chen J, Eapen G, Ostrin EJ, Fujimoto J, Spira AE, Scheet PA, Wistuba II, Wang L, Kadara H. Abstract 1518: A single-cell transcriptomic atlas of lung adenocarcinoma and adjacent normal-appearing tissue. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Lung adenocarcinoma (LUAD) is the most frequently diagnosed histological subtype of lung cancer and accounts for most smoking-related cancer deaths, warranting strategies for early intervention. Earlier work revealed genome-wide aberrations in LUADs and the adjacent premalignant field, known as “field carcinogenesis”, that are pertinent to LUAD pathogenesis. Yet, we still poorly understand the cellular and molecular architecture of LUAD and its nearby “field”. To fill this void, we performed, using the 10X Genomics system and NovaSeq 6000 platform, single-cell RNA sequencing (scRNA-seq) analysis of 4 early-stage resected LUADs as well as 11 matched normal lung tissues with differing spatial proximity from the tumors. We first analyzed 15,739 cells from a LUAD and matched tumor-adjacent and -distant normal tissues from patient 1. The resulting fraction of EPCAM+ cells from this analysis was approximately 4%. For deeper single-cell resolution of LUAD, we thus performed scRNA-seq of separately sorted/enriched epithelial cells (EPCAM+; n = 50,883) and non-epithelial cells (EPCAM-; n= 91,093) from patients 2, 3 and 4, each with an early-stage LUAD and three matched spatially-distributed normal-appearing tissues. Overall, we achieved on average approximately 150,000 reads and 1,956 genes detected per cell. Divergent populations of malignant and non-malignant cells and multiple epithelial and immune subsets clustered in an overall spatially modulated pattern according to proximity to the tumor. Hierarchical clustering revealed multiple distinct populations of airway lineage cells, including alveolar type 1 (AT1), alveolar type 2 (AT2), AT1/AT2 bipotential cells, club, goblet, basal and ciliated cells, with cells from the resected LUAD present in some but not all clusters. By analysis of epithelial-enriched fractions, we were also able to identify and interrogate rare cell subpopulations including CFTR-expressing ionocytes. By inference of copy number variation along with analysis of key oncogene expression patterns, we also identified epithelial cells that represent potential tumor cells-of-origin. Spatial reprogramming of field carcinogenesis encompassed immune cell populations including tumor-exclusive FOXP3+ regulatory T cells with marked over-expression of the major immune checkpoints CTLA4 and TIGIT. In contrast, for at least some of the cases, tumors were nearly devoid of natural killer cells, and abundance of CD8+ T cells dampened with increasing proximity to the tumor. Our single-cell surveys offer insights into novel cues in LUAD pathogenesis. Efforts are underway to interrogate the single-cell epithelial and immune landscape of additional LUADs and matched nearby normal-appearing lung, including those from non-smokers, to better understand the evolution of the disease and, thus, identify a low-hanging fruit of targets for early management of this fatal malignancy.
Citation Format: Ansam Sinjab, Guangchun Han, Warapen Treekitkarnmongkol, Patrick Brennan, Kieko Hara, Kyle Chang, Elena Bogatenkova, Beatriz Sanchez-Espiridion, Carmen Behrens, Jianjun Zhang, Boris Sepesi, Tina Cascone, Don L. Gibbons, Jichao Chen, George Eapen, Edwin J. Ostrin, Junya Fujimoto, Avrum E. Spira, Paul A. Scheet, Ignacio I. Wistuba, Linghua Wang, Humam Kadara. A single-cell transcriptomic atlas of lung adenocarcinoma and adjacent normal-appearing tissue [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1518.
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Affiliation(s)
| | | | | | | | - Kieko Hara
- 1UT MD Anderson Cancer Center, Houston, TX
| | - Kyle Chang
- 1UT MD Anderson Cancer Center, Houston, TX
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46
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Wang S, Rong R, Yang DM, Fujimoto J, Yan S, Cai L, Yang L, Luo D, Behrens C, Parra ER, Yao B, Xu L, Wang T, Zhan X, Wistuba II, Minna J, Xie Y, Xiao G. Computational Staining of Pathology Images to Study the Tumor Microenvironment in Lung Cancer. Cancer Res 2020; 80:2056-2066. [PMID: 31915129 PMCID: PMC7919065 DOI: 10.1158/0008-5472.can-19-1629] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 05/28/2019] [Revised: 11/15/2019] [Accepted: 12/27/2019] [Indexed: 01/15/2023]
Abstract
The spatial organization of different types of cells in tumor tissues reveals important information about the tumor microenvironment (TME). To facilitate the study of cellular spatial organization and interactions, we developed Histology-based Digital-Staining, a deep learning-based computation model, to segment the nuclei of tumor, stroma, lymphocyte, macrophage, karyorrhexis, and red blood cells from standard hematoxylin and eosin-stained pathology images in lung adenocarcinoma. Using this tool, we identified and classified cell nuclei and extracted 48 cell spatial organization-related features that characterize the TME. Using these features, we developed a prognostic model from the National Lung Screening Trial dataset, and independently validated the model in The Cancer Genome Atlas lung adenocarcinoma dataset, in which the predicted high-risk group showed significantly worse survival than the low-risk group (P = 0.001), with a HR of 2.23 (1.37-3.65) after adjusting for clinical variables. Furthermore, the image-derived TME features significantly correlated with the gene expression of biological pathways. For example, transcriptional activation of both the T-cell receptor and programmed cell death protein 1 pathways positively correlated with the density of detected lymphocytes in tumor tissues, while expression of the extracellular matrix organization pathway positively correlated with the density of stromal cells. In summary, we demonstrate that the spatial organization of different cell types is predictive of patient survival and associated with the gene expression of biological pathways. SIGNIFICANCE: These findings present a deep learning-based analysis tool to study the TME in pathology images and demonstrate that the cell spatial organization is predictive of patient survival and is associated with gene expression.See related commentary by Rodriguez-Antolin, p. 1912.
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Affiliation(s)
- Shidan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ruichen Rong
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Donghan M Yang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shirley Yan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ling Cai
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lin Yang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Danni Luo
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carmen Behrens
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bo Yao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Xiaowei Zhan
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, Texas
- Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, Texas.
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas
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Corsini EM, Wang J, Wu CC, Fujimoto J, Negrao MV, Chen R, Quek K, Mitchell KG, Chow CWB, Little L, Gumbs C, Song X, Behrens C, Correa AM, Antonoff MB, Swisher SG, Heymach JV, Zhang J, Wistuba II, Futreal PA, Sepesi B, Zhang J. Genomic assessment distinguishes intrapulmonary metastases from synchronous primary lung cancers. J Thorac Dis 2020; 12:1952-1959. [PMID: 32642098 PMCID: PMC7330333 DOI: 10.21037/jtd-20-1] [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] [Indexed: 12/27/2022]
Abstract
Background Multiple synchronous lung tumors (MSLT), particularly within a single lobe, represent a diagnostic and treatment challenge. While histologic assessment was once the only method to possibly distinguish multiple primary lung cancers, there is a growing interest in identifying unique genomic features or mutations to best characterize these processes. Methods In order to differentiate multiple primary lung malignancies from intrapulmonary metastases in patients with MSLT, we performed whole exome sequencing (WES) on 10 tumor samples from 4 patients with MSLT. Results Shared mutations between tumors from the same patient varied from 0-91%. Patient 3 shared no common mutations; however, in Patients 2 and 4, identical mutations were identified among all tumors from each patient, suggesting that the three tumors identified in Patient 3 represent separate primary lung cancers, while those of Patients 1, 2 and 4 signify hematogenous and lymphatic spread. Conclusions A high proportion of shared mutations between different lung tumors is likely indicative of intrapulmonary metastatic disease, while tumors with distinct genomic profiles likely represent multiple primary malignancies driven by distinct molecular events. Application of genomic profiling in the clinical setting may prove to be important to precise management of patients with MSLT.
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Affiliation(s)
- Erin M Corsini
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jinliang Wang
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Medical Oncology, Chinese PLA General Hospital, Beijing 100853, China
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcelo V Negrao
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Runzhe Chen
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelly Quek
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyle G Mitchell
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi-Wan B Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arlene M Correa
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Zhang
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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48
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Suresh S, Chen B, Zhu J, Golden RJ, Lu C, Evers BM, Novaresi N, Smith B, Zhan X, Schmid V, Jun S, Karacz CM, Peyton M, Zhong L, Wen Z, Sathe AA, Xing C, Behrens C, Wistuba II, Xiao G, Xie Y, Fu YX, Minna JD, Mendell JT, O'Donnell KA. eIF5B drives integrated stress response-dependent translation of PD-L1 in lung cancer. Nat Cancer 2020; 1:533-545. [PMID: 32984844 PMCID: PMC7511089 DOI: 10.1038/s43018-020-0056-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 03/17/2020] [Indexed: 12/24/2022]
Abstract
Cancer cells express high levels of PD-L1, a ligand of the PD-1 receptor on T cells, allowing tumors to suppress T cell activity. Clinical trials utilizing antibodies that disrupt the PD-1/PD-L1 checkpoint have yielded remarkable results, with anti-PD-1 immunotherapy approved as first-line therapy for lung cancer patients. We used CRISPR-based screening to identify regulators of PD-L1 in human lung cancer cells, revealing potent induction of PD-L1 upon disruption of heme biosynthesis. Impairment of heme production activates the integrated stress response (ISR), allowing bypass of inhibitory upstream open reading frames in the PD-L1 5' UTR, resulting in enhanced PD-L1 translation and suppression of anti-tumor immunity. We demonstrated that ISR-dependent PD-L1 translation requires the translation initiation factor eIF5B. eIF5B overexpression, which is frequent in lung adenocarcinomas and associated with poor prognosis, is sufficient to induce PD-L1. These findings illuminate mechanisms of immune checkpoint activation and identify targets for therapeutic intervention.
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Affiliation(s)
- Shruthy Suresh
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - BeiBei Chen
- Quantitative Biomedical Research Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jingfei Zhu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ryan J Golden
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Changzheng Lu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Bret M Evers
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Nicole Novaresi
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Bethany Smith
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xiaowei Zhan
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Vanessa Schmid
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sojeong Jun
- Children's Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chelsea M Karacz
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Michael Peyton
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lin Zhong
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Zhuoyu Wen
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Adwait Amod Sathe
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
- Eugene McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Carmen Behrens
- Department of Thoracic Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Thoracic Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Guanghua Xiao
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yang Xie
- Quantitative Biomedical Research Center, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yang-Xin Fu
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, United States
| | - John D Minna
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
- Hamon Center for Regenerative Medicine, UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Kathryn A O'Donnell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
- Hamon Center for Regenerative Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
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49
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Della Corte CM, Sen T, Gay CM, Ramkumar K, Diao L, Cardnell RJ, Rodriguez BL, Stewart CA, Papadimitrakopoulou VA, Gibson L, Fradette JJ, Wang Q, Fan Y, Peng DH, Negrao MV, Wistuba II, Fujimoto J, Solis Soto LM, Behrens C, Skoulidis F, Heymach JV, Wang J, Gibbons DL, Byers LA. STING Pathway Expression Identifies NSCLC With an Immune-Responsive Phenotype. J Thorac Oncol 2020; 15:777-791. [PMID: 32068166 PMCID: PMC7202130 DOI: 10.1016/j.jtho.2020.01.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [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: 05/31/2019] [Revised: 12/17/2019] [Accepted: 01/15/2020] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Although the combination of anti-programmed cell death-1 or anti-programmed cell death ligand-1 (PD-L1) with platinum chemotherapy is a standard of care for NSCLC, clinical responses vary. Even though predictive biomarkers (which include PD-L1 expression, tumor mutational burden, and inflamed immune microenvironment) are validated for immunotherapy, their relevance to chemoimmunotherapy combinations is less clear. We have recently reported that activation of the stimulator of interferon genes (STING) innate immune pathway enhances immunotherapy response in SCLC. Here, we hypothesize that STING pathway activation may predict and underlie predictive correlates of antitumor immunity in NSCLC. METHODS We analyzed transcriptomic and proteomic profiles in two NSCLC cohorts from our institution (treatment-naive patients in the Profiling of Resistance Patterns and Oncogenic Signaling Pathways in Evaluation of Cancers of the Thorax study and relapsed patients in the Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination study) and The Cancer Genome Atlas (N = 1320). Tumors were stratified by STING activation on the basis of protein or mRNA expression of cyclic GMP-AMP synthase, phospho-STING, and STING-mediated chemokines (chemokine ligand 5 [CCL5] and C-X-C motif chemokine 10 [CXCL10]). STING activation in patient tumors and in platinum-treated preclinical NSCLC models was correlated with biomarkers of immunotherapy response. RESULTS STING activation is associated with higher levels of intrinsic DNA damage, targetable immune checkpoints, and chemokines in treatment-naive and relapsed lung adenocarcinoma. We observed that tumors with lower STING and immune gene expression show higher frequency of serine-threonine kinase 11 (STK11) mutations; however, we identified a subset of these tumors that are TP53 comutated and display high immune- and STING-related gene expression. Treatment with cisplatin increases STING pathway activation and PD-L1 expression in multiple NSCLC preclinical models, including adeno- and squamous cell carcinoma. CONCLUSIONS STING pathway activation in NSCLC predicts features of immunotherapy response and is enhanced by cisplatin treatment. This suggests a possible predictive biomarker and mechanism for improved response to chemoimmunotherapy combinations.
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Affiliation(s)
- Carminia M Della Corte
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Triparna Sen
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carl M Gay
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kavya Ramkumar
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert J Cardnell
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bertha Leticia Rodriguez
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - C Allison Stewart
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Laura Gibson
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jared J Fradette
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qi Wang
- Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Youhong Fan
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David H Peng
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Division of Hematology and Medical Oncology, Department of Medicine, NYU Langone Health, New York, New York
| | - Marcelo V Negrao
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fujimoto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M Solis Soto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ferdinandos Skoulidis
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lauren A Byers
- Departments of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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50
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Cascone T, Sepesi B, Lin HY, Kalhor N, Parra ER, Jiang M, Godoy MCB, Zhang J, Fossella FV, Tsao AS, Lam VK, Lu C, Mott FE, Simon GR, Antonoff MB, Mehran RJ, Rice DC, Behrens C, Weissferdt A, Moran C, Vaporciyan AA, Lee JJ, Swisher SG, Gibbons DL, Wistuba II, William WN, Heymach JV. A Phase I/II Study of Neoadjuvant Cisplatin, Docetaxel, and Nintedanib for Resectable Non-Small Cell Lung Cancer. Clin Cancer Res 2020; 26:3525-3536. [PMID: 32193228 DOI: 10.1158/1078-0432.ccr-19-4180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/16/2020] [Accepted: 03/16/2020] [Indexed: 12/31/2022]
Abstract
PURPOSE Nintedanib enhances the activity of chemotherapy in metastatic non-small cell lung cancer (NSCLC). In this phase I/II study, we assessed safety and efficacy of nintedanib plus neoadjuvant chemotherapy, using major pathologic response (MPR) as primary endpoint. PATIENTS AND METHODS Eligible patients had stage IB (≥4 cm)-IIIA resectable NSCLC. A safety run-in phase was followed by an expansion phase with nintedanib 200 mg orally twice a day (28 days), followed by three cycles of cisplatin (75 mg/m2), docetaxel (75 mg/m2) every 21 days plus nintedanib, followed by surgery. With 33 planned patients, the study had 90% power to detect an MPR increase from 15% to 35%. RESULTS Twenty-one patients (stages I/II/III, N = 1/8/12) were treated. One of 15 patients treated with nintedanib 200 mg achieved MPR [7%, 95% confidence interval (CI), 0.2%-32%]. Best ORR in 20 evaluable patients was 30% (6/20, 95% CI, 12%-54%). Twelve-month recurrence-free survival and overall survival were 66% (95% CI, 47%-93%) and 91% (95% CI, 79%-100%), respectively. Most frequent treatment-related grade 3-4 toxicities were transaminitis and electrolyte abnormalities. On the basis of an interim analysis the study was discontinued for futility. Higher levels of CD3+ and cytotoxic CD3+CD8+ T cells were found in treated tumors of patients who were alive than in those who died (652.8 vs. 213.4 cells/mm2, P = 0.048; 142.3 vs. 35.6 cells/mm2, P = 0.018). CONCLUSIONS Although tolerated, neoadjuvant nintedanib plus chemotherapy did not increase MPR rate compared with chemotherapy historical controls. Additional studies of the combination in this setting are not recommended. Posttreatment levels of tumor-infiltrating T cells were associated with patient survival. Use of MPR facilitates the rapid evaluation of neoadjuvant therapies.See related commentary by Blakely and McCoach, p. 3499.
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Affiliation(s)
- Tina Cascone
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Thoracic & Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Heather Y Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mei Jiang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Myrna C B Godoy
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frank V Fossella
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anne S Tsao
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vincent K Lam
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Charles Lu
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frank E Mott
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - George R Simon
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mara B Antonoff
- Department of Thoracic & Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Reza J Mehran
- Department of Thoracic & Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David C Rice
- Department of Thoracic & Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Annikka Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cesar Moran
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ara A Vaporciyan
- Department of Thoracic & Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen G Swisher
- Department of Thoracic & Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - William N William
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Oncology Center, Hospital BP, a Beneficência Portuguesa de São Paulo, São Paulo, Brazil
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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