351
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Du K, Wei S, Wei Z, Frederick DT, Miao B, Moll T, Tian T, Sugarman E, Gabrilovich DI, Sullivan RJ, Liu L, Flaherty KT, Boland GM, Herlyn M, Zhang G. Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma. Nat Commun 2021; 12:6023. [PMID: 34654806 PMCID: PMC8519947 DOI: 10.1038/s41467-021-26299-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 09/27/2021] [Indexed: 02/05/2023] Open
Abstract
Both genomic and transcriptomic signatures have been developed to predict responses of metastatic melanoma to immune checkpoint blockade (ICB) therapies; however, most of these signatures are derived from pre-treatment biopsy samples. Here, we build pathway-based super signatures in pre-treatment (PASS-PRE) and on-treatment (PASS-ON) tumor specimens based on transcriptomic data and clinical information from a large dataset of metastatic melanoma treated with anti-PD1-based therapies as the training set. Both PASS-PRE and PASS-ON signatures are validated in three independent datasets of metastatic melanoma as the validation set, achieving area under the curve (AUC) values of 0.45-0.69 and 0.85-0.89, respectively. We also combine all test samples and obtain AUCs of 0.65 and 0.88 for PASS-PRE and PASS-ON signatures, respectively. When compared with existing signatures, the PASS-ON signature demonstrates more robust and superior predictive performance across all four datasets. Overall, we provide a framework for building pathway-based signatures that is highly and accurately predictive of response to anti-PD1 therapies based on on-treatment tumor specimens. This work would provide a rationale for applying pathway-based signatures derived from on-treatment tumor samples to predict patients' therapeutic response to ICB therapies.
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Affiliation(s)
- Kuang Du
- Department of Computer Science, Ying Wu College of Computing, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Shiyou Wei
- Department of Thoracic Surgery, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, 27710, USA
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA
| | - Zhi Wei
- Department of Computer Science, Ying Wu College of Computing, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
| | | | - Benchun Miao
- Massachusetts General Hospital Cancer Center, Boston, MA, 02114, USA
| | - Tabea Moll
- Department of Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Tian Tian
- Department of Computer Science, Ying Wu College of Computing, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Eric Sugarman
- Philadelphia College of Osteopathic Medicine, Philadelphia, PA, 19131, USA
| | | | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center, Boston, MA, 02114, USA
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Keith T Flaherty
- Massachusetts General Hospital Cancer Center, Boston, MA, 02114, USA
| | - Genevieve M Boland
- Department of Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA.
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, 19104, USA.
| | - Gao Zhang
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, 27710, USA.
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
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352
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Lau PKH, Feran B, Smith L, Lasocki A, Molania R, Smith K, Weppler A, Angel C, Kee D, Bhave P, Lee B, Young RJ, Iravani A, Yeang HA, Vergara IA, Kok D, Drummond K, Neeson PJ, Sheppard KE, Papenfuss T, Solomon BJ, Sandhu S, McArthur GA. Melanoma brain metastases that progress on BRAF-MEK inhibitors demonstrate resistance to ipilimumab-nivolumab that is associated with the Innate PD-1 Resistance Signature (IPRES). J Immunother Cancer 2021; 9:jitc-2021-002995. [PMID: 34625515 PMCID: PMC8504361 DOI: 10.1136/jitc-2021-002995] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Background Melanoma brain metastases (MBMs) are a challenging clinical problem with high morbidity and mortality. Although first-line dabrafenib–trametinib and ipilimumab–nivolumab have similar intracranial response rates (50%–55%), central nervous system (CNS) resistance to BRAF-MEK inhibitors (BRAF-MEKi) usually occurs around 6 months, and durable responses are only seen with combination immunotherapy. We sought to investigate the utility of ipilimumab–nivolumab after MBM progression on BRAF-MEKi and identify mechanisms of resistance. Methods Patients who received first-line ipilimumab–nivolumab for MBMs or second/third line ipilimumab–nivolumab for intracranial metastases with BRAFV600 mutations with prior progression on BRAF-MEKi and MRI brain staging from March 1, 2015 to June 30, 2018 were included. Modified intracranial RECIST was used to assess response. Formalin-fixed paraffin-embedded samples of BRAFV600 mutant MBMs that were naïve to systemic treatment (n=18) or excised after progression on BRAF-MEKi (n=14) underwent whole transcriptome sequencing. Comparative analyses of MBMs naïve to systemic treatment versus BRAF-MEKi progression were performed. Results Twenty-five and 30 patients who received first and second/third line ipilimumab–nivolumab, were included respectively. Median sum of MBM diameters was 13 and 20.5 mm for the first and second/third line ipilimumab–nivolumab groups, respectively. Intracranial response rate was 75.0% (12/16), and median progression-free survival (PFS) was 41.6 months for first-line ipilimumab–nivolumab. Efficacy of second/third line ipilimumab-nivolumab after BRAF-MEKi progression was poor with an intracranial response rate of 4.8% (1/21) and median PFS of 1.3 months. Given the poor activity of ipilimumab–nivolumab after BRAF-MEKi MBM progression, we performed whole transcriptome sequencing to identify mechanisms of drug resistance. We identified a set of 178 differentially expressed genes (DEGs) between naïve and MBMs with progression on BRAF-MEKi treatment (p value <0.05, false discovery rate (FDR) <0.1). No distinct pathways were identified from gene set enrichment analyses using Kyoto Encyclopedia of Genes and Genomes, Gene Ontogeny or Hallmark libraries; however, enrichment of DEG from the Innate Anti-PD1 Resistance Signature (IPRES) was identified (p value=0.007, FDR=0.03). Conclusions Second-line ipilimumab–nivolumab for MBMs after BRAF-MEKi progression has poor activity. MBMs that are resistant to BRAF-MEKi that also conferred resistance to second-line ipilimumab–nivolumab showed enrichment of the IPRES gene signature.
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Affiliation(s)
- Peter Kar Han Lau
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Molecular Oncology Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Breon Feran
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Lorey Smith
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Arian Lasocki
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ramyar Molania
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Kortnye Smith
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alison Weppler
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Christopher Angel
- Department of Histopathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Damien Kee
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Prachi Bhave
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Belinda Lee
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Richard J Young
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Amir Iravani
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Hanxian Aw Yeang
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ismael A Vergara
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Melanoma Institute Australia, North Sydney, New South Wales, Australia
| | - David Kok
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kate Drummond
- Department of Neurosurgery, The Royal Melbourne Hospital, Melbourne, Victoria, Australia.,Department of Surgery, The University of Melbourne, Melbourne, Victoria, Australia
| | - Paul Joseph Neeson
- Cancer Immunology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Karen E Sheppard
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tony Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Benjamin J Solomon
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shahneen Sandhu
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Grant A McArthur
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
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353
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Yang Z, Deng Y, Cheng J, Wei S, Luo H, Liu L. Tumor-Infiltrating PD-1 hiCD8 +-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers. Front Oncol 2021; 11:695006. [PMID: 34604032 PMCID: PMC8479164 DOI: 10.3389/fonc.2021.695006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/25/2021] [Indexed: 02/05/2023] Open
Abstract
Background Stratification of patients who could benefit from immune checkpoint inhibitor (ICI) therapy is of much importance. PD-1hiCD8+ T cells represent a newly identified and effective biomarker for ICI therapy response biomarker in lung cancer. Accurately quantifying these T cells using commonly available RNA sequencing (RNA-seq) data may extend their applications to more cancer types. Method We built a transcriptome signature of PD-1hiCD8+ T cells from bulk RNA-seq and single-cell RNA-seq (scRNA-seq) data of tumor-infiltrating immune cells. The signature was validated by flow cytometry and in independent datasets. The clinical applications of the signature were explored in non-small-cell lung cancer, melanoma, gastric cancer, urothelial cancer, and a mouse model of breast cancer samples treated with ICI, and systematically evaluated across 21 cancer types in The Cancer Genome Atlas (TCGA). Its associations with other biomarkers were also determined. Results Signature scores could be used to identify the PD-1hiCD8+ T subset and were correlated with the fraction of PD-1hiCD8+ T cells in tumor tissue (Pearson correlation, R=0.76, p=0.0004). Furthermore, in the scRNA-seq dataset, we confirmed the capability of PD-1hiCD8+ T cells to secrete CXCL13, as well as their interactions with other immune cells. In 581 clinical samples and 204 mouse models treated with ICIs, high signature scores were associated with increased survival, and the signature achieved area under the receiver operating characteristic curve scores of 0.755 (ranging from 0.61 to 0.91) in predicting therapy response. In TCGA pan-cancer datasets, our signature scores were consistently correlated with therapy response (R=0.78, p<0.0001) and partially explained the diverse response rates among different cancer types. Finally, our signature generally outperformed other mRNA-based predictors and showed improved predictive performance when used in combination with tumor mutational burden (TMB). The signature score is available in the R package “PD1highCD8Tscore” (https://github.com/Liulab/PD1highCD8Tscore). Conclusion Through estimating the fraction of the PD-1hiCD8+ T cell, our signature could predict response to ICI therapy across multiple cancers and could serve as a complementary biomarker to TMB.
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Affiliation(s)
- Zhenyu Yang
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Yulan Deng
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Jiahan Cheng
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Shiyou Wei
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Hao Luo
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Lunxu Liu
- Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China.,Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
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354
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Hodi FS, Wolchok JD, Schadendorf D, Larkin J, Long GV, Qian X, Saci A, Young TC, Srinivasan S, Chang H, Tang H, Wind-Rotolo M, Rizzo JI, Jackson DG, Ascierto PA. TMB and Inflammatory Gene Expression Associated with Clinical Outcomes following Immunotherapy in Advanced Melanoma. Cancer Immunol Res 2021; 9:1202-1213. [PMID: 34389558 PMCID: PMC9414280 DOI: 10.1158/2326-6066.cir-20-0983] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/29/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023]
Abstract
Outcomes for patients with melanoma have improved over the past decade as a result of the development and FDA approval of immunotherapies targeting cytotoxic T lymphocyte antigen-4 (CTLA-4), programmed death-1 (PD-1), and programmed death ligand 1 (PD-L1). However, these therapies do not benefit all patients, and an area of intensive research investigation is identifying biomarkers that can predict which patients are most likely to benefit from them. Here, we report exploratory analyses of the associations of tumor mutational burden (TMB), a 4-gene inflammatory gene expression signature, and BRAF mutation status with tumor response, progression-free survival, and overall survival in patients with advanced melanoma treated as part of the CheckMate 066 and 067 phase III clinical trials evaluating immuno-oncology therapies. In patients enrolled in CheckMate 067 receiving the anti-PD-1 inhibitor nivolumab (NIVO) alone or in combination with the anti-CTLA-4 inhibitor ipilimumab (IPI) or IPI alone, longer survival appeared to associate with high (>median) versus low (≤median) TMB and with high versus low inflammatory signature scores. For NIVO-treated patients, the results regarding TMB association were confirmed in CheckMate 066. In addition, improved survival was observed with high TMB and absence of BRAF mutation. Weak correlations were observed between PD-L1, TMB, and the inflammatory signature. Combined assessment of TMB, inflammatory gene expression signature, and BRAF mutation status may be predictive for response to immune checkpoint blockade in advanced melanoma.
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Affiliation(s)
- F. Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Corresponding Author: F. Stephen Hodi, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215. Phone: 617-632-5055; Fax: 617-632-6727; E-mail:
| | - Jedd D. Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medicine, New York, New York.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site Essen, Essen, Germany
| | - James Larkin
- Department of Medical Oncology, The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia.,Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, Australia
| | - Xiaozhong Qian
- Department of Translational Medicine, Bristol Myers Squibb, Princeton, New Jersey
| | - Abdel Saci
- Department of Translational Medicine, Bristol Myers Squibb, Princeton, New Jersey
| | - Tina C. Young
- Global Biometrics and Data Sciences, Bristol Myers Squibb, Princeton, New Jersey
| | - Sujaya Srinivasan
- Department of Translational Medicine, Bristol Myers Squibb, Princeton, New Jersey
| | - Han Chang
- Department of Informatics and Predictive Sciences, Bristol Myers Squibb, Princeton, New Jersey
| | - Hao Tang
- Department of Informatics and Predictive Sciences, Bristol Myers Squibb, Princeton, New Jersey
| | - Megan Wind-Rotolo
- Department of Translational Medicine, Bristol Myers Squibb, Princeton, New Jersey
| | - Jasmine I. Rizzo
- Oncology Clinical Development, Bristol Myers Squibb, Princeton, New Jersey
| | - Donald G. Jackson
- Department of Translational Medicine, Bristol Myers Squibb, Princeton, New Jersey
| | - Paolo A. Ascierto
- Unit of Melanoma, Cancer Immunotherapy and Development Therapeutics, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
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355
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Barili V, Vecchi A, Rossi M, Montali I, Tiezzi C, Penna A, Laccabue D, Missale G, Fisicaro P, Boni C. Unraveling the Multifaceted Nature of CD8 T Cell Exhaustion Provides the Molecular Basis for Therapeutic T Cell Reconstitution in Chronic Hepatitis B and C. Cells 2021; 10:2563. [PMID: 34685543 PMCID: PMC8533840 DOI: 10.3390/cells10102563] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022] Open
Abstract
In chronic hepatitis B and C virus infections persistently elevated antigen levels drive CD8+ T cells toward a peculiar differentiation state known as T cell exhaustion, which poses crucial constraints to antiviral immunity. Available evidence indicates that T cell exhaustion is associated with a series of metabolic and signaling deregulations and with a very peculiar epigenetic status which all together lead to reduced effector functions. A clear mechanistic network explaining how intracellular metabolic derangements, transcriptional and signaling alterations so far described are interconnected in a comprehensive and unified view of the T cell exhaustion differentiation profile is still lacking. Addressing this issue is of key importance for the development of innovative strategies to boost host immunity in order to achieve viral clearance. This review will discuss the current knowledge in HBV and HCV infections, addressing how innate immunity, metabolic derangements, extensive stress responses and altered epigenetic programs may be targeted to restore functionality and responsiveness of virus-specific CD8 T cells in the context of chronic virus infections.
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Affiliation(s)
- Valeria Barili
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Andrea Vecchi
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
| | - Marzia Rossi
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Ilaria Montali
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Camilla Tiezzi
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
| | - Amalia Penna
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
| | - Diletta Laccabue
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Gabriele Missale
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Paola Fisicaro
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Carolina Boni
- Laboratory of Viral Immunopathology, Unit of Infectious Diseases and Hepatology, Azienda Ospedaliero-Universitaria di Parma, 43126 Parma, Italy; (V.B.); (A.V.); (M.R.); (I.M.); (C.T.); (A.P.); (D.L.); (G.M.)
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356
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Liquid Biopsy Biomarkers for Immunotherapy in Non-Small Cell Lung Carcinoma: Lessons Learned and the Road Ahead. J Pers Med 2021; 11:jpm11100971. [PMID: 34683113 PMCID: PMC8540302 DOI: 10.3390/jpm11100971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open
Abstract
Over the recent years, advances in the development of anti-cancer treatments, particularly the implementation of ICIs (immune checkpoint inhibitors), have resulted in increased survival rates in NSCLC (non-small cell lung cancer) patients. However, a significant proportion of patients does not seem respond to immunotherapy, and some individuals even develop secondary resistance to treatment. Therefore, it is imperative to correctly identify the patients that will benefit from ICI therapy in order to tailor therapeutic options in an individualised setting, ultimately benefitting both the patient and the health system. Many different biomarkers have been explored to correctly stratify patients and predict response to immunotherapy, but liquid biopsy approaches have recently arisen as an interesting opportunity to predict and monitor treatment response due to their logistic accessibility. This review summarises the current data and efforts in the field of ICI response biomarkers in NSCLC patients and highlights advantages and limitations as we discuss the road to clinical implementation.
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357
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Wei C, Chen M, Deng W, Bie L, Ma Y, Zhang C, Liu K, Shen W, Wang S, Yang C, Luo S, Li N. Characterization of gastric cancer stem-like molecular features, immune and pharmacogenomic landscapes. Brief Bioinform 2021; 23:6375060. [PMID: 34571533 DOI: 10.1093/bib/bbab386] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/12/2021] [Accepted: 08/27/2021] [Indexed: 12/23/2022] Open
Abstract
Cancer stem cells (CSCs) actively reprogram their tumor microenvironment (TME) to sustain a supportive niche, which may have a dramatic impact on prognosis and immunotherapy. However, our knowledge of the landscape of the gastric cancer stem-like cell (GCSC) microenvironment needs to be further improved. A multi-step process of machine learning approaches was performed to develop and validate the prognostic and predictive potential of the GCSC-related score (GCScore). The high GCScore subgroup was not only associated with stem cell characteristics, but also with a potential immune escape mechanism. Furthermore, we experimentally demonstrated the upregulated infiltration of CD206+ tumor-associated macrophages (TAMs) in the invasive margin region, which in turn maintained the stem cell properties of tumor cells. Finally, we proposed that the GCScore showed a robust capacity for prediction for immunotherapy, and investigated potential therapeutic targets and compounds for patients with a high GCScore. The results indicate that the proposed GCScore can be a promising predictor of prognosis and responses to immunotherapy, which provides new strategies for the precision treatment of GCSCs.
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Affiliation(s)
- Chen Wei
- Department of Internal Medicine, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, 450001, China
| | - Mingkai Chen
- Department of Digestion Internal Medicine, Zhengzhou Yihe Hospital Affiliated to Henan University, Zhengzhou, Henan, 450001, China
| | - Wenying Deng
- Department of Internal Medicine, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, 450001, China
| | - Liangyu Bie
- Department of Internal Medicine, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, 450001, China
| | - Yijie Ma
- Department of Internal Medicine, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, 450001, China
| | - Chi Zhang
- Department of Internal Medicine, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, 450001, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Science, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.,China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
| | - Wei Shen
- Department of Internal Medicine, The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, 453000, China
| | - Shuyi Wang
- Department of Gastrointestinal Surgery & Department of Gastric and Colorectal Surgical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China
| | - Chaogang Yang
- Department of Gastrointestinal Surgery & Department of Gastric and Colorectal Surgical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China
| | - Suxia Luo
- Department of Internal Medicine, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, 450001, China
| | - Ning Li
- Department of Internal Medicine, Affiliated Tumor Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, 450001, China
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358
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Han G, Yang G, Hao D, Lu Y, Thein K, Simpson BS, Chen J, Sun R, Alhalabi O, Wang R, Dang M, Dai E, Zhang S, Nie F, Zhao S, Guo C, Hamza A, Czerniak B, Cheng C, Siefker-Radtke A, Bhat K, Futreal A, Peng G, Wargo J, Peng W, Kadara H, Ajani J, Swanton C, Litchfield K, Ahnert JR, Gao J, Wang L. 9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy. Nat Commun 2021; 12:5606. [PMID: 34556668 PMCID: PMC8460828 DOI: 10.1038/s41467-021-25894-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
Immune checkpoint therapy (ICT) provides substantial clinical benefits to cancer patients, but a large proportion of cancers do not respond to ICT. To date, the genomic underpinnings of primary resistance to ICT remain elusive. Here, we performed immunogenomic analysis of data from TCGA and clinical trials of anti-PD-1/PD-L1 therapy, with a particular focus on homozygous deletion of 9p21.3 (9p21 loss), one of the most frequent genomic defects occurring in ~13% of all cancers. We demonstrate that 9p21 loss confers "cold" tumor-immune phenotypes, characterized by reduced abundance of tumor-infiltrating leukocytes (TILs), particularly, T/B/NK cells, altered spatial TILs patterns, diminished immune cell trafficking/activation, decreased rate of PD-L1 positivity, along with activation of immunosuppressive signaling. Notably, patients with 9p21 loss exhibited significantly lower response rates to ICT and worse outcomes, which were corroborated in eight ICT trials of >1,000 patients. Further, 9p21 loss synergizes with PD-L1/TMB for patient stratification. A "response score" was derived by incorporating 9p21 loss, PD-L1 expression and TMB levels in pre-treatment tumors, which outperforms PD-L1, TMB, and their combination in identifying patients with high likelihood of achieving sustained response from otherwise non-responders. Moreover, we describe potential druggable targets in 9p21-loss tumors, which could be exploited to design rational therapeutic interventions.
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Affiliation(s)
- Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guoliang Yang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- 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
| | - Kyaw Thein
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Benjamin S Simpson
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Jianfeng Chen
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Omar Alhalabi
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fengqi Nie
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shuangtao Zhao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ameer Hamza
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chao Cheng
- Department of Medicine, Epidemiology and Population Science, Baylor College of Medicine, Houston, TX, USA
| | - Arlene Siefker-Radtke
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Weiyi Peng
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Jordi Rodon Ahnert
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (GSBS), Houston, TX, USA.
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359
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Carlino MS, Larkin J, Long GV. Immune checkpoint inhibitors in melanoma. Lancet 2021; 398:1002-1014. [PMID: 34509219 DOI: 10.1016/s0140-6736(21)01206-x] [Citation(s) in RCA: 465] [Impact Index Per Article: 155.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/30/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022]
Abstract
Immune checkpoint inhibitors target the dysfunctional immune system, to induce cancer-cell killing by CD8-positive T cells. Immune checkpoint inhibitors, specifically anti-CTLA4 and anti-PD-1 antibodies, have revolutionised the management of many cancers, particularly advanced melanoma, for which tumour regression and long-term durable cancer control is possible in nearly 50% of patients, compared with less than 10% historically. Despite the absence of adequately powered trial data, combined anti-CTLA4 and anti-PD-1 checkpoint inhibition has the highest 5-year overall survival rate of all therapies in advanced melanoma, and has high activity in melanoma brain metastases. A phase 3 study has shown the addition of an anti-LAG3 antibody to nivolumab improves progression-free survival, but its effect on overall survival and how this combination compares to combined anti-CTLA4 and anti-PD-1 checkpoint inhibition is unknown. At present, there are no highly sensitive and specific biomarkers of response to immune checkpoint inhibitors, and clinical factors, such as volume and sites of disease, serum lactate dehydrogenase, and BRAF mutation status, are used to select initial therapy for patients with advanced melanoma. Immune checkpoint inhibitors can induce autoimmune toxicities by virtue of their mechanism of action. These toxicities, termed immune-related adverse events, occur most frequently with combined anti-CTLA4 and anti-PD-1 checkpoint inhibition; can have a variety of presentations; can affect any organ system (most often the skin, colon, endocrine system, and liver); and appear to mimic classic autoimmune diseases. Immune-related adverse events require prompt recognition and management, which may be different from the autoimmune disease it mimics. Immune checkpoint inhibitors appear to be safe for use in patients with HIV, viral hepatitis, and patients with mild-to-moderate pre-existing autoimmune diseases. Patients with organ transplants can respond to immune checkpoint inhibitors but have a high chance of transplant loss. PD-1 inhibitors are now an established standard of care as adjuvant therapy in high-risk resected stage III or IV melanoma. Neoadjuvant checkpoint inhibition for resectable stage III melanoma, which is currently limited to clinical trials, is emerging as a highly effective therapy.
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Affiliation(s)
- Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Department of Medical Oncology Blacktown and Westmead Hospitals, Sydney, NSW, Australia
| | - James Larkin
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Royal North Shore and Mater Hospitals, North Sydney, Sydney, NSW, Australia.
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360
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Huppert LA, Daud AI. Pembrolizumab and Ipilimumab as Second-Line Therapy for Advanced Melanoma. J Clin Oncol 2021; 39:2637-2639. [PMID: 34138634 DOI: 10.1200/jco.21.00943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Laura A Huppert
- Division of Hematology Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA
| | - Adil I Daud
- Division of Hematology Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA
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361
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Lapuente-Santana Ó, van Genderen M, Hilbers PA, Finotello F, Eduati F. Interpretable systems biomarkers predict response to immune-checkpoint inhibitors. PATTERNS (NEW YORK, N.Y.) 2021; 2:100293. [PMID: 34430923 PMCID: PMC8369166 DOI: 10.1016/j.patter.2021.100293] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Cancer cells can leverage several cell-intrinsic and -extrinsic mechanisms to escape immune system recognition. The inherent complexity of the tumor microenvironment, with its multicellular and dynamic nature, poses great challenges for the extraction of biomarkers of immune response and immunotherapy efficacy. Here, we use RNA-sequencing (RNA-seq) data combined with different sources of prior knowledge to derive system-based signatures of the tumor microenvironment, quantifying immune-cell composition and intra- and intercellular communications. We applied multi-task learning to these signatures to predict different hallmarks of immune responses and derive cancer-type-specific models based on interpretable systems biomarkers. By applying our models to independent RNA-seq data from cancer patients treated with PD-1/PD-L1 inhibitors, we demonstrated that our method to Estimate Systems Immune Response (EaSIeR) accurately predicts therapeutic outcome. We anticipate that EaSIeR will be a valuable tool to provide a holistic description of immune responses in complex and dynamic systems such as tumors using available RNA-seq data.
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Affiliation(s)
- Óscar Lapuente-Santana
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Maisa van Genderen
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Peter A.J. Hilbers
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
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362
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Gu W, Kim M, Wang L, Yang Z, Nakajima T, Tsushima Y. Multi-omics Analysis of Ferroptosis Regulation Patterns and Characterization of Tumor Microenvironment in Patients with Oral Squamous Cell Carcinoma. Int J Biol Sci 2021; 17:3476-3492. [PMID: 34512160 PMCID: PMC8416738 DOI: 10.7150/ijbs.61441] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
Ferroptosis is a newly recognized mechanism of regulated cell death. It was reported to be highly associated with immune therapy and chemotherapy. However, its mechanism of regulation in the tumor microenvironment (TME) and influence on oral squamous cell carcinoma (OSCC) therapy are unknown. We identified a ferroptosis-specific gene-expression signature, an FPscore, developed by a principal component analysis (PCA) algorithm to evaluate the ferroptosis regulation patterns of individual tumor. Multi-omics analysis of ferroptosis regulation patterns was conducted. Three distinct ferroptosis regulation subtypes, which linked to outcomes and the clinical relevance of each patient, were established. A high FPscore of patients with OSCC was associated with a favorable prognosis, a ferroptosis-related immune-activation phenotype, potential sensitivities to the chemotherapy and immunotherapy. Importantly, a high FPscore correlated with a low gene copy number burden and high immune checkpoint expressions. We validated the prognostic value of the FPscore using independent immunotherapy and pan-cancer cohorts. Comprehensive evaluation of individual tumors with distinct ferroptosis regulation patterns provides new mechanistic insights, which may be clinically relevant for the application of combination therapies in OSCC.
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Affiliation(s)
- Wenchao Gu
- Department of Diagnostic Radiology and Nuclear Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Mai Kim
- Department of Oral and Maxillofacial Surgery, and Plastic Surgery, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Lei Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zongcheng Yang
- Department of Implantology, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Jinan, Shandong, People's Republic of China
| | - Takahito Nakajima
- Department of Diagnostic and Interventional Radiology, University of Tsukuba, Ibaraki, Japan
| | - Yoshito Tsushima
- Department of Diagnostic Radiology and Nuclear Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
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363
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Kim N, Eum HH, Lee HO. Clinical Perspectives of Single-Cell RNA Sequencing. Biomolecules 2021; 11:biom11081161. [PMID: 34439827 PMCID: PMC8394304 DOI: 10.3390/biom11081161] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/16/2022] Open
Abstract
The ability of single-cell genomics to resolve cellular heterogeneity is highly appreciated in cancer and is being exploited for precision medicine. In the recent decade, we have witnessed the incorporation of cancer genomics into the clinical decision-making process for molecular-targeted therapies. Compared with conventional genomics, which primarily focuses on the specific and sensitive detection of the molecular targets, single-cell genomics addresses intratumoral heterogeneity and the microenvironmental components impacting the treatment response and resistance. As an exploratory tool, single-cell genomics provides an unprecedented opportunity to improve the diagnosis, monitoring, and treatment of cancer. The results obtained upon employing bulk cancer genomics indicate that single-cell genomics is at an early stage with respect to exploration of clinical relevance and requires further innovations to become a widely utilized technology in the clinic.
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Affiliation(s)
- Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Hye Hyeon Eum
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: ; Tel.: +82-2-2258-8155
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364
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Chen L, Qu J, Mei Q, Chen X, Fang Y, Chen L, Li Y, Xiang C. Small extracellular vesicles from menstrual blood-derived mesenchymal stem cells (MenSCs) as a novel therapeutic impetus in regenerative medicine. Stem Cell Res Ther 2021; 12:433. [PMID: 34344458 PMCID: PMC8330084 DOI: 10.1186/s13287-021-02511-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023] Open
Abstract
Menstrual blood-derived mesenchymal stem cells (MenSCs) have great potential in regenerative medicine. MenSC has received increasing attention owing to its impressive therapeutic effects in both preclinical and clinical trials. However, the study of MenSC-derived small extracellular vesicles (EVs) is still in its initial stages, in contrast to some common MSC sources (e.g., bone marrow, umbilical cord, and adipose tissue). We describe the basic characteristics and biological functions of MenSC-derived small EVs. We also demonstrate the therapeutic potential of small EVs in fulminant hepatic failure, myocardial infarction, pulmonary fibrosis, prostate cancer, cutaneous wound, type-1 diabetes mellitus, aged fertility, and potential diseases. Subsequently, novel hotspots with respect to MenSC EV-based therapy are proposed to overcome current challenges. While complexities regarding the therapeutic potential of MenSC EVs continue to be unraveled, advances are rapidly emerging in both basic science and clinical medicine. MenSC EV-based treatment has great potential for treating a series of diseases as a novel therapeutic strategy in regenerative medicine.
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Affiliation(s)
- Lijun Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China
| | - Jingjing Qu
- Department of Respiratory Disease, Thoracic Disease Centre, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China
| | - Quanhui Mei
- Department of Intensive Care Unit, The First People's Hospital of Changde City, Changde, Hunan, 415000, People's Republic of China
| | - Xin Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China
| | - Yangxin Fang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China
| | - Lu Chen
- Innovative Precision Medicine (IPM) Group, Hangzhou, Zhejiang, 311215, People's Republic of China
| | - Yifei Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China
| | - Charlie Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, People's Republic of China.
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365
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Fan L, Lei H, Lin Y, Zhou Z, Shu G, Yan Z, Chen H, Zhang T, Yin G. Identification of a Gene Set Correlated With Immune Status in Ovarian Cancer by Transcriptome-Wide Data Mining. Front Mol Biosci 2021; 8:670666. [PMID: 34395521 PMCID: PMC8363306 DOI: 10.3389/fmolb.2021.670666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/16/2021] [Indexed: 12/26/2022] Open
Abstract
Immune checkpoint blocking (ICB) immunotherapy has achieved great success in the treatment of various malignancies. Although not have been approved for the treatment of ovarian cancer (OC), it has been actively tested for the treatment of OC. However, biomarkers that could indicate the immune status of OC and predict the response to ICB are rare. We downloaded RNAseq and clinical data of OC from The Cancer Genome Atlas (TCGA). Data analysis revealed both TMBhigh and immunityhigh were significantly related to better survival of OC. Up-regulated differentially expressed genes (Up-DEGs) were identified by analyzing the gene expression levels. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed in the "GSVA" and "limma" package in R software. The correlation of genes with overall survival was also analyzed by conducted Kaplan-Meier survival analysis. Four genes, CXCL13, FCRLA, MS4A1, and PLA2G2D were found positively correlated with better prognosis of OC and mainly involved in immune response-related pathways. Finally, TIMER and TIDE were used to predict gene immune function and its association with immunotherapy. We found that these four genes were positively correlated with better response to immune checkpoint blockade-based immunotherapy. Altogether, CXCL13, FCRLA, MS4A1, and PLA2G2D may be used as potential therapeutic genes for reflecting OC immune status and predicting response to immunotherapy.
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Affiliation(s)
- Lili Fan
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China.,School of Traditional Chinese Medicine, Jinan University, Guangzhou, China
| | - Han Lei
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Ying Lin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhengwei Zhou
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Guang Shu
- School of Basic Medical Sciences, Central South University, Changsha, China
| | - Zhipeng Yan
- Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Haotian Chen
- School of Basic Medical Sciences, Central South University, Changsha, China
| | - Tianxiang Zhang
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
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366
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Poma AM, Bruno R, Pietrini I, Alì G, Pasquini G, Proietti A, Vasile E, Cappelli S, Chella A, Fontanini G. Biomarkers and Gene Signatures to Predict Durable Response to Pembrolizumab in Non-Small Cell Lung Cancer. Cancers (Basel) 2021; 13:cancers13153828. [PMID: 34359727 PMCID: PMC8345106 DOI: 10.3390/cancers13153828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Not all patients with advanced or metastatic non-small cell lung cancer (NSCLC) respond to pembrolizumab, even if their tumor expresses PD-L1. This is a monocentric study aimed at identifying potential predictive biomarkers for pembrolizumab first-line treatment. Tumor microenvironment was characterized by gene expression analysis in 46 tumor samples from 25 NSCLC patients with and 21 without durable clinical benefit. As expected, patients achieving clinical benefit had a greater infiltration of immune cells. In particular, CD8 T-cell and NK cell scores were strongly associated with durable benefit. Single immune cell markers such as XCL1/2 showed a high performance in predicting durable response to pembrolizumab with an AUC of 0.85. In the same series PD-L1 expression levels had an AUC equal to 0.61. Identified predictive biomarkers can improve patients’ selection, thus optimizing treatment definition. Abstract Pembrolizumab has been approved as first-line treatment for advanced Non-small cell lung cancer (NSCLC) patients with tumors expressing PD-L1 and in the absence of other targetable alterations. However, not all patients that meet these criteria have a durable benefit. In this monocentric study, we aimed at refining the selection of patients based on the expression of immune genes. Forty-six consecutive advanced NSCLC patients treated with pembrolizumab in first-line setting were enrolled. The expression levels of 770 genes involved in the regulation of the immune system was analysed by the nanoString system. PD-L1 expression was evaluated by immunohistochemistry. Patients with durable clinical benefit had a greater infiltration of cytotoxic cells, exhausted CD8, B-cells, CD45, T-cells, CD8 T-cells and NK cells. Immune cell scores such as CD8 T-cell and NK cell were good predictors of durable response with an AUC of 0.82. Among the immune cell markers, XCL1/2 showed the better performance in predicting durable benefit to pembrolizumab, with an AUC of 0.85. Additionally, CD8A, CD8B and EOMES showed a high specificity (>0.86) in identifying patients with a good response to treatment. In the same series, PD-L1 expression levels had an AUC of 0.61. The characterization of tumor microenvironment, even with the use of single markers, can improve patients’ selection for pembrolizumab treatment.
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Affiliation(s)
- Anello Marcello Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, via Savi 10, 56126 Pisa, Italy;
| | - Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, via Roma 67, 56126 Pisa, Italy; (R.B.); (G.A.); (A.P.)
| | - Iacopo Pietrini
- General Pathology, University of Pisa, via Savi 10, 56126 Pisa, Italy;
| | - Greta Alì
- Unit of Pathological Anatomy, University Hospital of Pisa, via Roma 67, 56126 Pisa, Italy; (R.B.); (G.A.); (A.P.)
| | - Giulia Pasquini
- Unit of Medical Oncology, San Jacopo Hospital of Pistoia, 51100 Pistoia, Italy;
| | - Agnese Proietti
- Unit of Pathological Anatomy, University Hospital of Pisa, via Roma 67, 56126 Pisa, Italy; (R.B.); (G.A.); (A.P.)
| | - Enrico Vasile
- Unit of Pneumology, University Hospital of Pisa, via Paradisa 2, 56126 Pisa, Italy; (E.V.); (S.C.); (A.C.)
| | - Sabrina Cappelli
- Unit of Pneumology, University Hospital of Pisa, via Paradisa 2, 56126 Pisa, Italy; (E.V.); (S.C.); (A.C.)
| | - Antonio Chella
- Unit of Pneumology, University Hospital of Pisa, via Paradisa 2, 56126 Pisa, Italy; (E.V.); (S.C.); (A.C.)
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, via Savi 10, 56126 Pisa, Italy;
- Correspondence: ; Tel.: +39-050-992983
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367
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Distinct Immune Signatures Indicative of Treatment Response and Immune-Related Adverse Events in Melanoma Patients under Immune Checkpoint Inhibitor Therapy. Int J Mol Sci 2021; 22:ijms22158017. [PMID: 34360781 PMCID: PMC8348898 DOI: 10.3390/ijms22158017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/14/2022] Open
Abstract
To identify potential early biomarkers of treatment response and immune-related adverse events (irAE), a pilot immune monitoring study was performed in stage IV melanoma patients by flow cytometric analysis of peripheral blood mononuclear cells (PBMC). Overall, 17 patients were treated with either nivolumab or pembrolizumab alone, or with a combination of nivolumab and ipilimumab every three weeks. Of 15 patients for which complete response assessment was available, treatment responders (n = 10) as compared to non-responders (n = 5) were characterized by enhanced PD-1 expression on CD8+ T cells immediately before treatment (median ± median absolute deviation/MAD 26.7 ± 10.4% vs. 17.2 ± 5.3%). Responders showed a higher T cell responsiveness after T cell receptor ex vivo stimulation as determined by measurement of programmed cell death 1 (PD-1) expression on CD3+ T cells before the second cycle of treatment. The percentage of CD8+ effector memory (CD8+CD45RA−CD45RO+CCR7−) T cells was higher in responders compared to non-responders before and immediately after the first cycle of treatment (median ± MAD 39.2 ± 7.3% vs. 30.5 ± 4.1% and 37.7 ± 4.6 vs. 24.0 ± 6.4). Immune-related adverse events (irAE) were accompanied by a higher percentage of activated CD4+ (CD4+CD38+HLADR+) T cells before the second treatment cycle (median ± MAD 14.9 ± 3.9% vs. 5.3 ± 0.4%). In summary, PBMC immune monitoring of immune-checkpoint inhibition (ICI) treatment in melanoma appears to be a promising approach to identify early markers of treatment response and irAEs.
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368
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Tian Q, Gao H, Zhao W, Zhou Y, Yang J. Development and validation of an immune gene set-based prognostic signature in cutaneous melanoma. Future Oncol 2021; 17:4115-4129. [PMID: 34291650 DOI: 10.2217/fon-2021-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We aimed to fully understand the landscape of the skin cutaneous melanoma (SKCM) microenvironment and develop an immune prognostic signature that can predict the prognosis for SKCM patients. RNA sequencing data and clinical information were downloaded from the Cancer Genome Atlas and Gene Expression Omnibus databases. The immune-prognostic signature was constructed by LASSO Cox regression analysis. We calculated the relative abundance of 29 immune-related gene sets based on the mRNA expression profiles of 314 SKCM patients in the Cancer Genome Atlas training set. Hierarchical clustering was performed to classify SKCM patients into three clusters: immunity-high, -medium and -low. The values of our prognostic model in predicting disease progression, metastasis and immunotherapeutic responses were also validated. In conclusion, the prognostic model demonstrated a powerful ability to distinguish and predict SKCM patients' prognosis.
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Affiliation(s)
- Qi Tian
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Huan Gao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Wen Zhao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Yan Zhou
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Jin Yang
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
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369
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Faget J, Peters S, Quantin X, Meylan E, Bonnefoy N. Neutrophils in the era of immune checkpoint blockade. J Immunother Cancer 2021; 9:jitc-2020-002242. [PMID: 34301813 PMCID: PMC8728357 DOI: 10.1136/jitc-2020-002242] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 01/07/2023] Open
Abstract
The immune checkpoint blockade-based immunotherapies are revolutionizing cancer management. Tumor-associated neutrophils (TANs) were recently highlighted to have a pivotal role in modulating the tumor microenvironment and the antitumor immune response. However, these cells were largely ignored during the development of therapies based on programmed cell death receptor or ligand-1 and cytotoxic T lymphocyte antigen-4 immune checkpoint inhibitors (ICIs). Latest evidences of neutrophil functional diversity in tumor raised many questions and suggest that targeting these cells can offer new treatment opportunities in the context of ICI development. Here, we summarized key information on TAN origin, function, and plasticity that should be considered when developing ICIs and provide a detailed review of the ongoing clinical trials that combine ICIs and a second compound that might affect or be affected by TANs. This review article synthetizes important notions from the literature demonstrating that: (1) Cancer development associates with a profound alteration of neutrophil biogenesis and function that can predict and interfere with the response to ICIs, (2) Neutrophil infiltration in tumor is associated with key features of resistance to ICIs, and (3) TANs play an important role in resistance to antiangiogenic drugs reducing their clinical benefit when used in combination with ICIs. Finally, exploring the clinical/translational aspects of neutrophil impact on the response to ICIs offers the opportunity to propose new translational research avenues to better understand TAN biology and treat patients.
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Affiliation(s)
- Julien Faget
- IRCM, Inserm, Univ Montpellier, ICM, Montpellier, France, INSERM U1194, Montpellier, France
| | - Solange Peters
- Department of Oncology CHUV-UNIL, University Hospital Lausanne, Lausanne, Switzerland
| | - Xavier Quantin
- Service d'Oncologie Médicale, Institut régional du Cancer de Montpellier, 34298, Montpellier, France
| | - Etienne Meylan
- Swiss Institute for Experimental Cancer Research, EPFL, Lausanne, Switzerland
| | - Nathalie Bonnefoy
- IRCM, Inserm, Univ Montpellier, ICM, Montpellier, France, INSERM U1194, Montpellier, France
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370
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Characterization of neoantigen-specific T cells in cancer resistant to immune checkpoint therapies. Proc Natl Acad Sci U S A 2021; 118:2025570118. [PMID: 34285073 PMCID: PMC8325261 DOI: 10.1073/pnas.2025570118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Strongly implicated in effective antitumor immune responses, tumor mutation–derived antigens, or neoantigens, are one of the main targets for cancer vaccines despite uncertainty of the efficacy of this approach. Using a high-throughput screening method, we identify an endogenously immunogenic neoantigen in a commonly used mouse lung tumor model. We also found that the endogenous CD8 T cells specific for this neoantigen expand greatly upon treatment with immune checkpoint inhibitors or vaccination despite the lack of associated tumor regression in this model. In addition to informing neoantigen vaccination strategies and providing an accessible system for testing alternative therapeutics, our results provide insights into the mechanisms for the lack of response observed for a majority of patients treated with checkpoint blockade immunotherapies. Neoantigen-specific T cells are strongly implicated as being critical for effective immune checkpoint blockade treatment (ICB) (e.g., anti–PD-1 and anti–CTLA-4) and are being targeted for vaccination-based therapies. However, ICB treatments show uneven responses between patients, and neoantigen vaccination efficiency has yet to be established. Here, we characterize neoantigen-specific CD8+ T cells in a tumor that is resistant to ICB and neoantigen vaccination. Leveraging the use of mass cytometry combined with multiplex major histocompatibility complex (MHC) class I tetramer staining, we screened and identified tumor neoantigen–specific CD8+ T cells in the Lewis Lung carcinoma (LLC) tumor model (mRiok1). We observed an expansion of mRiok1-specific CD8+ tumor-infiltrating lymphocytes (TILs) after ICB targeting PD-1 or CTLA-4 with no sign of tumor regression. The expanded neoantigen-specific CD8+ TILs remained phenotypically and functionally exhausted but displayed cytotoxic characteristics. When combining both ICB treatments, mRiok1-specific CD8+ TILs showed a stem-like phenotype and a higher capacity to produce cytokines, but tumors did not show signs of regression. Furthermore, combining both ICB treatments with neoantigen vaccination did not induce tumor regression either despite neoantigen-specific CD8+ TIL expansion. Overall, this work provides a model for studying neoantigens in an immunotherapy nonresponder model. We showed that a robust neoantigen-specific T-cell response in the LLC tumor model could fail in tumor response to ICB, which will have important implications in designing future immunotherapeutic strategies.
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371
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Hou Y, Liang HL, Yu X, Liu Z, Cao X, Rao E, Huang X, Wang L, Li L, Bugno J, Fu Y, Chmura SJ, Wu W, Luo SZ, Zheng W, Arina A, Jutzy J, McCall AR, Vokes EE, Pitroda SP, Fu YX, Weichselbaum RR. Radiotherapy and immunotherapy converge on elimination of tumor-promoting erythroid progenitor cells through adaptive immunity. Sci Transl Med 2021; 13:13/582/eabb0130. [PMID: 33627484 DOI: 10.1126/scitranslmed.abb0130] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/20/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022]
Abstract
Tumor-induced CD45-Ter119+CD71+ erythroid progenitor cells, termed "Ter cells," promote tumor progression by secreting artemin (ARTN), a neurotrophic peptide that activates REarranged during Transfection (RET) signaling. We demonstrate that both local tumor ionizing radiation (IR) and anti-programmed death ligand 1 (PD-L1) treatment decreased tumor-induced Ter cell abundance in the mouse spleen and ARTN secretion outside the irradiation field in an interferon- and CD8+ T cell-dependent manner. Recombinant erythropoietin promoted resistance to radiotherapy or anti-PD-L1 therapies by restoring Ter cell numbers and serum ARTN concentration. Blockade of ARTN or potential ARTN signaling partners, or depletion of Ter cells augmented the antitumor effects of both IR and anti-PD-L1 therapies in mice. Analysis of samples from patients who received radioimmunotherapy demonstrated that IR-mediated reduction of Ter cells, ARTN, and GFRα3, an ARTN signaling partner, were each associated with tumor regression. Patients with melanoma who received immunotherapy exhibited favorable outcomes associated with decreased expression of GFRα3. These findings demonstrate an out-of-field, or "abscopal," effect mediated by adaptive immunity, which is induced during local tumor irradiation. This effect, in turn, governs the therapeutic effects of radiation and immunotherapy. Therefore, our results identify multiple targets to potentially improve outcomes after radiotherapy and immunotherapy.
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Affiliation(s)
- Yuzhu Hou
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, ShaanXi 710061, China. .,Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Hua L Liang
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Xinshuang Yu
- Department of Oncology, First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong 250014, China
| | - Zhida Liu
- Department of Pathology, University of Texas Southwest Medical Center, Dallas, TX 75235, USA
| | - Xuezhi Cao
- Department of Pathology, University of Texas Southwest Medical Center, Dallas, TX 75235, USA
| | - Enyu Rao
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xiaona Huang
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Liangliang Wang
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Lei Li
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Jason Bugno
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, IL 60637, USA
| | - Yanbin Fu
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Steven J Chmura
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Wenjun Wu
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Sean Z Luo
- Whitney Young High School, Chicago, IL 60607, USA
| | - Wenxin Zheng
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Ainhoa Arina
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Jessica Jutzy
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Anne R McCall
- Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Everett E Vokes
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Sean P Pitroda
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA
| | - Yang-Xin Fu
- Department of Pathology, University of Texas Southwest Medical Center, Dallas, TX 75235, USA.
| | - Ralph R Weichselbaum
- Ludwig Center for Metastasis Research, Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL 60637 USA.
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372
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Lv L, Wei Q, Wang Z, Zhao Y, Chen N, Yi Q. Clinical and Molecular Correlates of NLRC5 Expression in Patients With Melanoma. Front Bioeng Biotechnol 2021; 9:690186. [PMID: 34307322 PMCID: PMC8299757 DOI: 10.3389/fbioe.2021.690186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 11/13/2022] Open
Abstract
NLRC5 is an important regulator in antigen presentation and inflammation, and its dysregulation promotes tumor progression. In melanoma, the impact of NLRC5 expression on molecular phenotype, clinical characteristics, and tumor features is largely unknown. In the present study, public datasets from the Cancer Cell Line Encyclopedia (CCLE), Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and cBioPortal were used to address these issues. We identify that NLRC5 is expressed in both immune cells and melanoma cells in melanoma samples and its expression is regulated by SPI1 and DNA methylation. NLRC5 expression is closely associated with Breslow thickness, Clark level, recurrence, pathologic T stage, and ulceration status in melanoma. Truncating/splice mutations rather than missense mutations in NLRC5 could compromise the expression of downstream genes. Low expression of NLRC5 is associated with poor prognosis, low activity of immune-related signatures, low infiltrating level of immune cells, and low cytotoxic score in melanoma. Additionally, NLRC5 expression correlates with immunotherapy efficacy in melanoma. In summary, these findings suggest that NLRC5 acts as a tumor suppressor in melanoma via modulating the tumor immune microenvironment. Targeting the NLRC5 related pathway might improve efficacy of immunotherapy for melanoma patients.
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Affiliation(s)
- Lei Lv
- Anhui Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qinqin Wei
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zhiwen Wang
- Anhui Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yujia Zhao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Ni Chen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Qiyi Yi
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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373
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Breitenecker K, Homolya M, Luca AC, Lang V, Trenk C, Petroczi G, Mohrherr J, Horvath J, Moritsch S, Haas L, Kurnaeva M, Eferl R, Stoiber D, Moriggl R, Bilban M, Obenauf AC, Ferran C, Dome B, Laszlo V, Győrffy B, Dezso K, Moldvay J, Casanova E, Moll HP. Down-regulation of A20 promotes immune escape of lung adenocarcinomas. Sci Transl Med 2021; 13:eabc3911. [PMID: 34233950 PMCID: PMC7611502 DOI: 10.1126/scitranslmed.abc3911] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 02/15/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022]
Abstract
Inflammation is a well-known driver of lung tumorigenesis. One strategy by which tumor cells escape tight homeostatic control is by decreasing the expression of the potent anti-inflammatory protein tumor necrosis factor alpha-induced protein 3 (TNFAIP3), also known as A20. We observed that tumor cell intrinsic loss of A20 markedly enhanced lung tumorigenesis and was associated with reduced CD8+ T cell-mediated immune surveillance in patients with lung cancer and in mouse models. In mice, we observed that this effect was completely dependent on increased cellular sensitivity to interferon-γ (IFN-γ) signaling by aberrant activation of TANK-binding kinase 1 (TBK1) and increased downstream expression and activation of signal transducer and activator of transcription 1 (STAT1). Interrupting this autocrine feed forward loop by knocking out IFN-α/β receptor completely restored infiltration of cytotoxic T cells and rescued loss of A20 depending tumorigenesis. Downstream of STAT1, programmed death ligand 1 (PD-L1) was highly expressed in A20 knockout lung tumors. Accordingly, immune checkpoint blockade (ICB) treatment was highly efficient in mice harboring A20-deficient lung tumors. Furthermore, an A20 loss-of-function gene expression signature positively correlated with survival of melanoma patients treated with anti-programmed cell death protein 1. Together, we have identified A20 as a master immune checkpoint regulating the TBK1-STAT1-PD-L1 axis that may be exploited to improve ICB therapy in patients with lung adenocarcinoma.
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Affiliation(s)
- Kristina Breitenecker
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
- Institute of Cancer Research, Medical University of Vienna, AT-1090 Vienna, Austria
- Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria
| | - Monika Homolya
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Andreea C Luca
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Veronika Lang
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Christoph Trenk
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Georg Petroczi
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Julian Mohrherr
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Jaqueline Horvath
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Stefan Moritsch
- Institute of Cancer Research, Medical University of Vienna, AT-1090 Vienna, Austria
- Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria
| | - Lisa Haas
- Research Institute of Molecular Pathology, Vienna Biocenter, AT-1030 Vienna, Austria
| | - Margarita Kurnaeva
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Robert Eferl
- Institute of Cancer Research, Medical University of Vienna, AT-1090 Vienna, Austria
- Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria
| | - Dagmar Stoiber
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
- Division Pharmacology, Department of Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, AT-3500 Krems, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, AT-1210 Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine, Medical University of Vienna, AT-1090 Vienna, Austria
- Core Facilities, Medical University of Vienna, AT-1090 Vienna, Austria
| | - Anna C Obenauf
- Research Institute of Molecular Pathology, Vienna Biocenter, AT-1030 Vienna, Austria
| | - Christiane Ferran
- Division of Vascular and Endovascular Surgery and the Center for Vascular Biology Research, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Transplant Institute and the Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Balazs Dome
- Division of Thoracic Surgery, Department of Surgery, and Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria
- 1st Department of Tumor Biology, National Korányi Institute of Pulmonology, Semmelweis University, HU-1121 Budapest, Hungary
- Department of Thoracic Surgery, National Institute of Oncology and Semmelweis University, HU-1122 Budapest, Hungary
| | - Viktoria Laszlo
- Division of Thoracic Surgery, Department of Surgery, and Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria
- 1st Department of Tumor Biology, National Korányi Institute of Pulmonology, Semmelweis University, HU-1121 Budapest, Hungary
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, and 2nd Department of Pediatrics, Semmelweis University, HU-1117 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, HU-1094 Budapest, Hungary
- 2nd Department of Pediatrics, Semmelweis University, HU-1094 Budapest, Hungary
| | - Katalin Dezso
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, HU-1085 Budapest, Hungary
| | - Judit Moldvay
- 1st Department of Pulmonology, National Korányi Institute of Pulmonology, HU-1121 Budapest, Hungary
- SE-NAP Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, HU-1122 Budapest, Hungary
| | - Emilio Casanova
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria
- Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria
| | - Herwig P Moll
- Institute of Pharmacology, Center of Physiology and Pharmacology, Medical University of Vienna, AT-1090 Vienna, Austria.
- Comprehensive Cancer Center (CCC), Medical University of Vienna, AT-1090 Vienna, Austria
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374
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Xiao X, Xu C, Yang W, Yu R. Inconsistent prediction capability of ImmuneCells.Sig across different RNA-seq datasets. Nat Commun 2021; 12:4167. [PMID: 34234113 PMCID: PMC8263582 DOI: 10.1038/s41467-021-24303-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/10/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Xu Xiao
- School of Informatics, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | | | | | - Rongshan Yu
- School of Informatics, Xiamen University, Xiamen, China. .,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.
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375
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Xiong D, Wang Y, You M. Reply to: "Inconsistent prediction capability of ImmuneCells.Sig across different RNA-seq datasets". Nat Commun 2021; 12:4168. [PMID: 34234120 PMCID: PMC8263738 DOI: 10.1038/s41467-021-24304-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/10/2021] [Indexed: 12/29/2022] Open
Affiliation(s)
- Donghai Xiong
- Center for Cancer Prevention, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX, United States
| | - Yian Wang
- Center for Cancer Prevention, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX, United States
| | - Ming You
- Center for Cancer Prevention, Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX, United States.
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376
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Haas L, Elewaut A, Gerard CL, Umkehrer C, Leiendecker L, Pedersen M, Krecioch I, Hoffmann D, Novatchkova M, Kuttke M, Neumann T, da Silva IP, Witthock H, Cuendet MA, Carotta S, Harrington KJ, Zuber J, Scolyer RA, Long GV, Wilmott JS, Michielin O, Vanharanta S, Wiesner T, Obenauf AC. Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma. NATURE CANCER 2021; 2:693-708. [PMID: 35121945 PMCID: PMC7613740 DOI: 10.1038/s43018-021-00221-9] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/17/2021] [Indexed: 01/01/2023]
Abstract
How targeted therapies and immunotherapies shape tumors, and thereby influence subsequent therapeutic responses, is poorly understood. In the present study, we show, in melanoma patients and mouse models, that when tumors relapse after targeted therapy with MAPK pathway inhibitors, they are cross-resistant to immunotherapies, despite the different modes of action of these therapies. We find that cross-resistance is mediated by a cancer cell-instructed, immunosuppressive tumor microenvironment that lacks functional CD103+ dendritic cells, precluding an effective T cell response. Restoring the numbers and functionality of CD103+ dendritic cells can re-sensitize cross-resistant tumors to immunotherapy. Cross-resistance does not arise from selective pressure of an immune response during evolution of resistance, but from the MAPK pathway, which not only is reactivated, but also exhibits an increased transcriptional output that drives immune evasion. Our work provides mechanistic evidence for cross-resistance between two unrelated therapies, and a scientific rationale for treating patients with immunotherapy before they acquire resistance to targeted therapy.
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Affiliation(s)
- Lisa Haas
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Anais Elewaut
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Camille L Gerard
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Christian Umkehrer
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Lukas Leiendecker
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | | | - Izabela Krecioch
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - David Hoffmann
- Institute of Molecular Biotechnology, Vienna Biocenter, Vienna, Austria
| | - Maria Novatchkova
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Mario Kuttke
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Institute of Vascular Biology and Thrombosis Research, Medical University of Vienna, Vienna, Austria
| | - Tobias Neumann
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Ines Pires da Silva
- Melanoma Institute Australia, University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | | | - Michel A Cuendet
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Molecular Modeling Group, Swiss Institute of Bioinformatics, UNIL Sorge, Lausanne, Switzerland
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Richard A Scolyer
- Melanoma Institute Australia, University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Royal Prince Alfred Hospital & NSW Health Pathology, Sydney, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Royal North Shore Hospital, Sydney, New South Wales, Australia
- Mater Hospital, North Sydney, New South Wales, Australia
| | - James S Wilmott
- Melanoma Institute Australia, University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Olivier Michielin
- Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Molecular Modeling Group, Swiss Institute of Bioinformatics, UNIL Sorge, Lausanne, Switzerland
| | | | - Thomas Wiesner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anna C Obenauf
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria.
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377
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Ahn SG, Kim SK, Shepherd JH, Cha YJ, Bae SJ, Kim C, Jeong J, Perou CM. Clinical and genomic assessment of PD-L1 SP142 expression in triple-negative breast cancer. Breast Cancer Res Treat 2021; 188:165-178. [PMID: 33770313 PMCID: PMC8233296 DOI: 10.1007/s10549-021-06193-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/10/2021] [Indexed: 01/12/2023]
Abstract
PURPOSE The SP142 PD-L1 assay is a companion diagnostic for atezolizumab in metastatic triple-negative breast cancer (TNBC). We strove to understand the biological, genomic, and clinical characteristics associated with SP142 PD-L1 positivity in TNBC patients. METHODS Using 149 TNBC formalin-fixed paraffin-embedded tumor samples, tissue microarray (TMA) and gene expression microarrays were performed in parallel. The VENTANA SP142 assay was used to identify PD-L1 expression from TMA slides. We next generated a gene signature reflective of SP142 status and evaluated signature distribution according to TNBCtype and PAM50 subtypes. A SP142 gene expression signature was identified and was biologically and clinically evaluated on the TNBCs of TCGA, other cohorts, and on other malignancies treated with immune checkpoint inhibitors (ICI). RESULTS Using SP142, 28.9% of samples were PD-L1 protein positive. The SP142 PD-L1-positive TNBC had higher CD8+ T cell percentage, stromal tumor-infiltrating lymphocyte levels, and higher rate of the immunomodulatory TNBCtype compared to PD-L1-negative samples. The recurrence-free survival was prolonged in PD-L1-positive TNBC. The SP142-guided gene expression signature consisted of 94 immune-related genes. The SP142 signature was associated with a higher pathologic complete response rate and better survival in multiple TNBC cohorts. In the TNBC of TCGA, this signature was correlated with lymphocyte-infiltrating signature scores, but not with tumor mutational burden or total neoantigen count. In other malignancies treated with ICIs, the SP142 genomic signature was associated with improved response and survival. CONCLUSIONS We provide multi-faceted evidence that SP142 PDL1-positive TNBC have immuno-genomic features characterized as highly lymphocyte-infiltrated and a relatively favorable survival.
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Affiliation(s)
- Sung Gwe Ahn
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, 712 Eon-juro, Gangnam-gu, Seoul, Republic of Korea
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Seon-Kyu Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB),, Daejeon, Korea
| | - Jonathan H Shepherd
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Yoon Jin Cha
- Department of Pathology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Soong June Bae
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, 712 Eon-juro, Gangnam-gu, Seoul, Republic of Korea
| | - Chungyeul Kim
- Department of Pathology, Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Joon Jeong
- Department of Surgery, Gangnam Severance Hospital, Yonsei University College of Medicine, 712 Eon-juro, Gangnam-gu, Seoul, Republic of Korea.
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
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378
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Clinical and Molecular Heterogeneity in Patients with Innate Resistance to Anti-PD-1 +/- Anti-CTLA-4 Immunotherapy in Metastatic Melanoma Reveals Distinct Therapeutic Targets. Cancers (Basel) 2021; 13:cancers13133186. [PMID: 34202352 PMCID: PMC8267740 DOI: 10.3390/cancers13133186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Immune checkpoint therapies have significantly improved the survival of patients with metastatic melanoma, however approximately 50% of patients exhibit no response. Understanding the underlying clinical, pathologic and genetic factors associated with failed response to immunotherapies is key to identifying therapeutic strategies to overcome resistance. Here, we investigated the baseline tumour characteristics of patients with innate resistance to anti-PD-1-based immunotherapies. This study is the first on non-responders to integrate detailed clinical and molecular analyses and has identified two distinct clusters of patients with clinically relevant key targetable proteins. Abstract While immune checkpoint inhibitors targeting the CTLA-4 and PD-1 receptors have significantly improved outcomes of many patients with metastatic melanoma, there remains a group of patients who demonstrate no benefit. In this study, we sought to characterise patients who do not respond to anti-PD-1-based therapies based on their clinical, genetic and immune profiles. Forty patients with metastatic melanoma who did not respond to anti-PD-1 +/− anti-CTLA-4 treatment were identified. Targeted RNA sequencing (n = 37) was performed on pretreatment formalin-fixed paraffin-embedded (FFPE) melanoma specimens. Patients clustered into two groups based on the expression profiles of 26 differentially expressed genes: an immune gene rich group (n = 17) expressing genes associated with immune and T cell signalling, and a second group (n = 20) expressing genes associated with metabolism, signal transduction and neuronal signalling. Multiplex immunohistochemistry validated significantly higher densities of tumour-infiltrating lymphocytes (TILs) and macrophages in the immune gene-rich group. This TIL-high subset of patients also demonstrated higher expression of alternative immune-regulatory drug targets compared to the TIL-low group. Patients were also subdivided into rapid progressors and other progressors (cut-off 2 mo progression-free survival), with significantly lower TILs (p = 0.04) and CD68+ macrophages (p = 0.0091) in the rapid progressors. Furthermore, a trend towards a higher tumour burden was observed in rapid progressors (p = 0.06). These data highlight the need for a personalised and multilayer (clinical and molecular) approach for identifying the most appropriate treatments for anti-PD-1 resistant patients and provides insight into how individual treatment strategies can be achieved.
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379
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Chen ZG, Wang Y, Fong WP, Hu MT, Liang JY, Wang L, Li YH. A quantitative score of immune cell infiltration predicts the prognosis in pancreatic ductal adenocarcinoma. Int Immunopharmacol 2021; 98:107890. [PMID: 34174701 DOI: 10.1016/j.intimp.2021.107890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/06/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022]
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by an extensive and dense fibrous stroma, which plays an active role in tumor growth and metastasis. Despite the growing importance of the tumor microenvironment in PDAC prognosis, the immune cell infiltration landscape of PDAC has not been elucidated. In this study, we applied a credible computational algorithm to comprehensively estimate the immune cell infiltration (ICI) patterns of 876 PDAC patients. Two ICI phenotypes were identified, and a ICIscore was constructed using ssGSEA algorithm. The ICIscore could significantly predict the prognosis and chemotherapy benefit of PDAC patients in both the discovery and the five validation cohorts. Multivariate cox analysis also identified the independent predictive role of the ICIscore in PDAC prognosis. A high ICIscore subtype was characterized by immune-active signaling pathways and anti-tumor immunity while a low ICIscore subtype was associated with tumor progressive signaling pathways. Four immunotherapy cohorts further supported the use of the ICIscore as a prognostic biomarker for patients receiving immune checkpoint inhibitors in other cancer types. The ICIscore reveals a close relationship between the ICI environment and prognosis and may provide new treatment strategies for PDAC patients.
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Affiliation(s)
- Zhi-Gang Chen
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yun Wang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - William Pat Fong
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ming-Tao Hu
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jie-Ying Liang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Lingyun Wang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China.
| | - Yu-Hong Li
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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380
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Shklovskaya E, Rizos H. MHC Class I Deficiency in Solid Tumors and Therapeutic Strategies to Overcome It. Int J Mol Sci 2021; 22:ijms22136741. [PMID: 34201655 PMCID: PMC8268865 DOI: 10.3390/ijms22136741] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
It is now well accepted that the immune system can control cancer growth. However, tumors escape immune-mediated control through multiple mechanisms and the downregulation or loss of major histocompatibility class (MHC)-I molecules is a common immune escape mechanism in many cancers. MHC-I molecules present antigenic peptides to cytotoxic T cells, and MHC-I loss can render tumor cells invisible to the immune system. In this review, we examine the dysregulation of MHC-I expression in cancer, explore the nature of MHC-I-bound antigenic peptides recognized by immune cells, and discuss therapeutic strategies that can be used to overcome MHC-I deficiency in solid tumors, with a focus on the role of natural killer (NK) cells and CD4 T cells.
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381
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Pan-cancer characterization of lncRNA modifiers of immune microenvironment reveals clinically distinct de novo tumor subtypes. NPJ Genom Med 2021; 6:52. [PMID: 34140519 PMCID: PMC8211863 DOI: 10.1038/s41525-021-00215-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/25/2021] [Indexed: 01/20/2023] Open
Abstract
The emerging field of long noncoding RNA (lncRNA)-immunity has provided a new perspective on cancer immunity and immunotherapies. The lncRNA modifiers of infiltrating immune cells in the tumor immune microenvironment (TIME) and their impact on tumor behavior and disease prognosis remain largely uncharacterized. In the present study, a systems immunology framework integrating the noncoding transcriptome and immunogenomics profiles of 9549 tumor samples across 30 solid cancer types was used, and 36 lncRNAs were identified as modifier candidates underlying immune cell infiltration in the TIME at the pan-cancer level. These TIME lncRNA modifiers (TIL-lncRNAs) were able to subclassify various tumors into three de novo pan-cancer subtypes characterized by distinct immunological features, biological behaviors, and disease prognoses. Finally, a TIL-lncRNA-derived immune state index (TISI) that was reflective of immunological and oncogenic states but also predictive of patients' prognosis was proposed. Furthermore, the TISI provided additional prognostic value for existing tumor immunological and molecular subtypes. By applying the TISI to tumors from different clinical immunotherapy cohorts, the TISI was found to be significantly negatively correlated with immune-checkpoint genes and to have the ability to predict the effectiveness of immunotherapy. In conclusion, the present study provided comprehensive resources and insights for future functional and mechanistic studies on lncRNA-mediated cancer immunity and highlighted the potential of the clinical application of lncRNA-based immunotherapeutic strategies in precision immunotherapy.
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382
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Liu R, Yang F, Yin JY, Liu YZ, Zhang W, Zhou HH. Influence of Tumor Immune Infiltration on Immune Checkpoint Inhibitor Therapeutic Efficacy: A Computational Retrospective Study. Front Immunol 2021; 12:685370. [PMID: 34220837 PMCID: PMC8248490 DOI: 10.3389/fimmu.2021.685370] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/03/2021] [Indexed: 01/13/2023] Open
Abstract
The tumor immune microenvironment (TIME) is likely an important determinant of sensitivity to immune checkpoint inhibitor (ICI) treatment. However, a comprehensive analysis covering the complexity and diversity of the TIME and its influence on ICI therapeutic efficacy is still lacking. Data from 782 samples from 10 ICI clinical trials were collected. To infer the infiltration of 22 subsets of immune cells, CIBERSORTx was applied to the bulk tumor transcriptomes. The associations between each cell fraction and the response to ICI treatment, progression-free survival (PFS) and overall survival (OS) were evaluated, modeling cellular proportions as quartiles. Activity of the interferon-γ pathway, the cytolytic activity score and the MHC score were associated with good prognosis in melanoma. Of the immune cells investigated, M1 macrophages, activated memory CD4+ T cells, T follicular helper (Tfh) cells and CD8+ T cells correlated with response and prolonged PFS and OS, while resting memory CD4+ T cells was associated with unfavorable prognosis in melanoma and urothelial cancer. Consensus clustering revealed four immune subgroups with distinct responses to ICI therapy and survival patterns. The cluster with high proportions of infiltrated CD8+ T cells, activated memory CD4+ T cells, and Tfh cells and low levels of resting memory CD4+ T cells exhibited a higher tumor mutation burden and neoantigen load in melanoma and conferred a higher probability of response and improved survival. Local systemic immune cellular differences were associated with outcomes after ICI therapy. Further investigations of the tumor-infiltrating cellular immune response will lay the foundation for achieving durable efficacy.
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Affiliation(s)
- Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Fang Yang
- Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Ying-Zi Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Changsha, China
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383
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Bagaev A, Kotlov N, Nomie K, Svekolkin V, Gafurov A, Isaeva O, Osokin N, Kozlov I, Frenkel F, Gancharova O, Almog N, Tsiper M, Ataullakhanov R, Fowler N. Conserved pan-cancer microenvironment subtypes predict response to immunotherapy. Cancer Cell 2021; 39:845-865.e7. [PMID: 34019806 DOI: 10.1016/j.ccell.2021.04.014] [Citation(s) in RCA: 498] [Impact Index Per Article: 166.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/14/2020] [Accepted: 04/23/2021] [Indexed: 12/18/2022]
Abstract
The clinical use of molecular targeted therapy is rapidly evolving but has primarily focused on genomic alterations. Transcriptomic analysis offers an opportunity to dissect the complexity of tumors, including the tumor microenvironment (TME), a crucial mediator of cancer progression and therapeutic outcome. TME classification by transcriptomic analysis of >10,000 cancer patients identifies four distinct TME subtypes conserved across 20 different cancers. The TME subtypes correlate with patient response to immunotherapy in multiple cancers, with patients possessing immune-favorable TME subtypes benefiting the most from immunotherapy. Thus, the TME subtypes act as a generalized immunotherapy biomarker across many cancer types due to the inclusion of malignant and microenvironment components. A visual tool integrating transcriptomic and genomic data provides a global tumor portrait, describing the tumor framework, mutational load, immune composition, anti-tumor immunity, and immunosuppressive escape mechanisms. Integrative analyses plus visualization may aid in biomarker discovery and the personalization of therapeutic regimens.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Nathan Fowler
- BostonGene, Waltham, MA 02453, USA; Department of Lymphoma and Myeloma, Unit 0429, the University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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384
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Pang B, Hao Y. Integrated Analysis of the Transcriptome Profile Reveals the Potential Roles Played by Long Noncoding RNAs in Immunotherapy for Sarcoma. Front Oncol 2021; 11:690486. [PMID: 34178688 PMCID: PMC8226247 DOI: 10.3389/fonc.2021.690486] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Background Long-term survival is still low for high-risk patients with soft tissue sarcoma treated with standard management options, including surgery, radiation, and chemotherapy. Immunotherapy is a promising new potential treatment paradigm. However, the application of immune checkpoint inhibitors for the treatment of patients with sarcoma did not yield promising results in a clinical trial. Therefore, there is a considerable need to identify factors that may lead to immune checkpoint inhibitor resistance. Methods In this study, we performed a bioinformatic analysis of The Cancer Genome Atlas (TCGA) to detect key long noncoding RNAs (lncRNAs) that were correlated with immune checkpoint inhibitory molecules in sarcoma. The expression levels of these lncRNAs and their correlation with patient prognosis were explored. The upstream long noncoding RNAs were also examined via 450K array data from the TCGA. The potential roles of these lncRNAs were further examined via KEGG and GO analysis using DAVID online software. Finally, the relationship between these lncRNAs and immune cell infiltration in tumors and their effect on immune checkpoint inhibitors were further explored. Results We identified lncRNAs correlated with tumor cell immune evasion in sarcoma. The expression of these lncRNAs was upregulated and correlated with worse prognosis in sarcoma and other human cancer types. Moreover, low DNA methylation occupation of these lncRNA loci was detected. Negative correlations between DNA methylation and lncRNA expression were also found in sarcoma and other human cancer types. KEGG and GO analyses indicated that these lncRNAs correlated with immune evasion and negative regulation of the immune response in sarcoma. Finally, high expression of these lncRNAs correlated with more suppressive immune cell infiltration and reduced sensitivity to immune checkpoint inhibitors in sarcoma and other human cancer types. Conclusion Our results suggest that long noncoding RNAs confer immune checkpoint inhibitor resistance in human cancer. Further characterization of these lncRNAs may help to elucidate the mechanisms underlying immune checkpoint inhibitor resistance and uncover a novel therapeutic intervention point for immunotherapy.
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Affiliation(s)
- Boran Pang
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Clinical and Translational Research Center for 3D Printing Technology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongqiang Hao
- Shanghai Key Laboratory of Orthopaedic Implants, Department of Orthopaedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Clinical and Translational Research Center for 3D Printing Technology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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385
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Hong F, Meng Q, Zhang W, Zheng R, Li X, Cheng T, Hu D, Gao X. Single-Cell Analysis of the Pan-Cancer Immune Microenvironment and scTIME Portal. Cancer Immunol Res 2021; 9:939-951. [PMID: 34117085 DOI: 10.1158/2326-6066.cir-20-1026] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/17/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
Single-cell sequencing opens a new era for the investigation of tumor immune microenvironments (TIME). However, at single-cell resolution, a pan-cancer analysis that addresses the identity and diversity of TIMEs is lacking. Here, we first built a pan-cancer single-cell reference of TIMEs with refined subcell types and recognized new cell type-specific transcription factors. We then presented a pan-cancer view of the common features of the TIME and compared the variation of each immune cell type across patients and tumor types in the aspects of abundance, cell states, and cell communications. We found that the abundance and the cell states of dysfunctional T cells were most variable, whereas those of regulatory T cells were relatively stable. A subset of tumor-associated macrophages (TAM), PLTP + C1QC + TAMs, may regulate the abundance of dysfunctional T cells through cytokine/chemokine signaling. The ligand-receptor communication network of TIMEs was tumor-type specific and dominated by the tumor-enriched immune cells. We additionally developed the single-cell TIME (scTIME) portal (http://scTIME.sklehabc.com) with the scTIME-specific analysis modules and a unified cell annotation. In addition to the immune cell compositions and correlation analysis using refined cell type classifications, the portal also provides cell-cell interaction and cell type-specific gene signature analysis. Our single-cell pan-cancer analysis and scTIME portal will provide more insights into the features of TIMEs, as well as the molecular and cellular mechanisms underlying immunotherapies.
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Affiliation(s)
- Fang Hong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Qianqian Meng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Weiyu Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Ruiqin Zheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Xiaoyun Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Deqing Hu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Cancer Institute and Hospital of Tianjin Medical University, Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Xin Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
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386
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Wang YC, Wang X, Yu J, Ma F, Li Z, Zhou Y, Zeng S, Ma X, Li YR, Neal A, Huang J, To A, Clarke N, Memarzadeh S, Pellegrini M, Yang L. Targeting monoamine oxidase A-regulated tumor-associated macrophage polarization for cancer immunotherapy. Nat Commun 2021; 12:3530. [PMID: 34112755 PMCID: PMC8192781 DOI: 10.1038/s41467-021-23164-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 04/07/2021] [Indexed: 02/05/2023] Open
Abstract
Targeting tumor-associated macrophages (TAMs) is a promising strategy to modify the immunosuppressive tumor microenvironment and improve cancer immunotherapy. Monoamine oxidase A (MAO-A) is an enzyme best known for its function in the brain; small molecule MAO inhibitors (MAOIs) are clinically used for treating neurological disorders. Here we observe MAO-A induction in mouse and human TAMs. MAO-A-deficient mice exhibit decreased TAM immunosuppressive functions corresponding with enhanced antitumor immunity. MAOI treatment induces TAM reprogramming and suppresses tumor growth in preclinical mouse syngeneic and human xenograft tumor models. Combining MAOI and anti-PD-1 treatments results in synergistic tumor suppression. Clinical data correlation studies associate high intratumoral MAOA expression with poor patient survival in a broad range of cancers. We further demonstrate that MAO-A promotes TAM immunosuppressive polarization via upregulating oxidative stress. Together, these data identify MAO-A as a critical regulator of TAMs and support repurposing MAOIs for TAM reprogramming to improve cancer immunotherapy.
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Affiliation(s)
- Yu-Chen Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Xi Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Jiaji Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Zhe Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Yang Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Samuel Zeng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Xiaoya Ma
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Yan-Ruide Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Adam Neal
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jie Huang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Angela To
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Nicole Clarke
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Sanaz Memarzadeh
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- The VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Lili Yang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA.
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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387
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Pezeshki PS, Mahdavi Sharif P, Rezaei N. Resistance mechanisms to programmed cell death protein 1 and programmed death ligand 1 inhibitors. Expert Opin Biol Ther 2021; 21:1575-1590. [PMID: 33984254 DOI: 10.1080/14712598.2021.1929919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: In the past few years, administrating monoclonal humanized antibodies, namely checkpoint inhibitors, against programmed cell death protein 1 (PD-1), and its ligand (PD-L1), has yielded reassuring tumor regression rates. Anti-PD-1/PD-L1 checkpoint inhibitors disrupt the engagement of PD-1 on T-cells and their ligands on tumor or other target cells and reactivate the tumor-specific T infiltrating lymphocytes (TILs), which are mostly in a state of anergy before the PD-1/PD-L1 blockade. However, a limited number of patients initially respond, and the others show a primary (innate) resistance. Moreover, the rate of relapse and tumor progression after a partial, or even complete response (secondary or acquired resistance) is relatively considerable.Areas covered: This paper presents a comprehensive discussion on the mechanisms of primary and secondary resistance to PD-1/PD-L1 blockade. Loss of T-cell infiltration or T-cell exclusion, lack of PD-L1 or PD-1 expression, and also lack of tumor immunogenicity are among the most important mechanisms, and also biomarkers of resistance in patients undergoing PD-1/PD-L1 blockade. Several somatic mutations in tumors are known to be related to at least one of the resistance mechanisms.Expert opinion: Identification of the novel resistance mechanisms suggests further combinatorial therapies to tackle primary and secondary resistance to PD-1/PD-L1 blockade.
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Affiliation(s)
- Parmida Sadat Pezeshki
- Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Pouya Mahdavi Sharif
- Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Cancer Immunology Project (CIP), Universal Scientific Education and Research Network (USERN), Sheffield, UK
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Two Complementarity Immunotherapeutics in Non-Small-Cell Lung Cancer Patients-Mechanism of Action and Future Concepts. Cancers (Basel) 2021; 13:cancers13112836. [PMID: 34200219 PMCID: PMC8201041 DOI: 10.3390/cancers13112836] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/19/2021] [Accepted: 05/31/2021] [Indexed: 12/19/2022] Open
Abstract
Simple Summary Here, we focused on the most important mechanisms of action of combined immunotherapy with modern anticancer approaches in patients with non-small-cell lung cancer. This knowledge is extremely important for lung cancer clinicians. First, it facilitates proper involvement of the patient in the treatment and monitoring its effectiveness. More importantly, the knowledge of the immunotherapy mechanisms will certainly allow quick recognition of the side effects of such a therapy, which are totally different of those observed after chemotherapy. Side effects of combination therapies can occur at any stage of treatment, and even after completion thereof. This review article could particularly explain the mechanism of action of combined immunotherapy, which have different targets in patients. Abstract Due to the limited effectiveness of immunotherapy used as first-line monotherapy in patients with non-small-cell lung cancer (NSCLC), the concepts of combining classical immunotherapy based on immune checkpoint antibodies with other treatment methods have been developed. Pembrolizumab and atezolizumab were registered in combination with chemotherapy for the treatment of metastatic NSCLC, while durvalumab found its application in consolidation therapy after successful chemoradiotherapy in patients with locally advanced NSCLC. Exceptionally attractive, due to their relatively low toxicity and high effectiveness, are treatment approaches in which a combination of two different immunotherapy methods is applied. This method is based on observations from clinical trials in which nivolumab and ipilimumab were used as first-line therapy for advanced NSCLC. It turned out that the dual blockade of immune checkpoints activated T lymphocytes in different compartments of the immune response, at the same time affecting the downregulation of immune suppressor cells (regulatory T cells). These experiments not only resulted in the registration of combination therapy with nivolumab and ipilimumab, but also initiated other clinical trials using immune checkpoint inhibitors (ICIs) in combination with other ICIs or activators of costimulatory molecules found on immune cells. There are also studies in which ICIs are associated with molecules that modify the tumour environment. This paper describes the mechanism of the synergistic effect of a combination of different immunotherapy methods in NSCLC patients.
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389
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Early memory differentiation and cell death resistance in T cells predicts melanoma response to sequential anti-CTLA4 and anti-PD1 immunotherapy. Genes Immun 2021; 22:108-119. [PMID: 34079092 DOI: 10.1038/s41435-021-00138-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 11/09/2022]
Abstract
Immune checkpoint blockers (ICBs)-based immunotherapy has revolutionised oncology. However, the benefits of ICBs are limited to only a subset of patients. Herein, the biomarkers-driven application of ICBs promises to increase their efficacy. Such biomarkers include lymphocytic IFNγ-signalling and/or cytolytic activity (granzymes and perforin-1) footprints, whose levels in pre-treatment tumours can predict favourable patient survival following ICB-treatment. However, it is not clear whether such biomarkers have the same value in predicting survival of patients receiving first-line anti-CTLA4 ICB-therapy, and subsequently anti-PD1 ICB-therapy (i.e., sequential ICB-immunotherapy regimen). To address this, we applied highly integrated systems/computational immunology approaches to existing melanoma bulk-tumour transcriptomic and single-cell (sc)RNAseq data originating from immuno-oncology clinical studies applying ICB-treatment. Interestingly, we observed that CD8+/CD4+T cell-associated IFNγ-signalling or cytolytic activity signatures fail to predict tumour response in patients treated with anti-CTLA4 ICB-therapy as a first-line and anti-PD1 ICB-therapy in the second-line setting. On the contrary, signatures associated with early memory CD8+/CD4+T cells (integrating TCF1-driven stem-like transcriptional programme), capable of resisting cell death/apoptosis, better predicted objective response rates to ICB-immunotherapy, and favourable survival in the setting of sequential ICB-immunotherapy. These observations suggest that sequencing of ICB-therapy might have a specific impact on the T cell-repertoire and may influence the predictive value of tumoural immune biomarkers.
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390
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Jiang ZB, Wang WJ, Xu C, Xie YJ, Wang XR, Zhang YZ, Huang JM, Huang M, Xie C, Liu P, Fan XX, Ma YP, Yan PY, Liu L, Yao XJ, Wu QB, Lai-Han Leung E. Luteolin and its derivative apigenin suppress the inducible PD-L1 expression to improve anti-tumor immunity in KRAS-mutant lung cancer. Cancer Lett 2021; 515:36-48. [PMID: 34052328 DOI: 10.1016/j.canlet.2021.05.019] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022]
Abstract
Upregulated expression of immune checkpoint molecules correlates with exhausted phenotype and impaired function of cytotoxic T cells to evade host immunity. By disrupting the interaction of PD-L1 and PD1, immune checkpoint inhibitors can restore immune system function against cancer cells. Growing evidence have demonstrated apigenin and luteolin, which are flavonoids abundant in common fruits and vegetables, can suppress growth and induce apoptosis of multiple types of cancer cells with their potent anti-inflammatory, antioxidant and anticancer properties. In this study, the effects and underlying mechanisms of luteolin, apigenin, and anti-PD-1 antibody combined with luteolin or apigenin on the PD-L1 expression and anti-tumorigenesis in KRAS-mutant lung cancer were investigated. Luteolin and apigenin significantly inhibited lung cancer cell growth, induced cell apoptosis, and down-regulated the IFN-γ-induced PD-L1 expression by suppressing the phosphorylation of STAT3. Both luteolin and apigenin showed potent anti-cancer activities in the H358 xenograft and Lewis lung carcinoma model in vivo, and the treatment with monoclonal PD1 antibody enhanced the infiltration of T cells into tumor tissues. Apigenin exhibited anti-tumor activity in Genetically engineered KRASLA2 mice. In conclusion, both apigenin and luteolin significantly suppressed lung cancer with KRAS mutant proliferation, and down-regulated the IFN-γ induced PD-L1 expression. Treatment with the combination of PD-1 blockade and apigenin/luteolin has a synergistic effect and might be a prospective therapeutic strategy for NSCLC with KRAS-mutant.
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Affiliation(s)
- Ze-Bo Jiang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Wen-Jun Wang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Cong Xu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Ya-Jia Xie
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Xuan-Run Wang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Yi-Zhong Zhang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Ju-Min Huang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Min Huang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Chun Xie
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Pei Liu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Xing-Xing Fan
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Yu-Po Ma
- Department of Internal Medicine, Stony Brook Medicine, Stony Brook University Medical Center, Stony Brook, NY, 11794, USA; Research & Development Division, iCell Gene Therapeutics LLC, Stony Brook, NY, USA
| | - Pei-Yu Yan
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China
| | - Liang Liu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China
| | - Xiao-Jun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China.
| | - Qi-Biao Wu
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China.
| | - Elaine Lai-Han Leung
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Macao, Taipa, Macau (SAR), China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, China; Zhuhai Hospital of Traditional Chinese and Western Medicine, Zhuhai City, Guangdong, China.
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391
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Meireson A, Tavernier SJ, Van Gassen S, Sundahl N, Demeyer A, Spaas M, Kruse V, Ferdinande L, Van Dorpe J, Hennart B, Allorge D, Haerynck F, Decaestecker K, Rottey S, Saeys Y, Ost P, Brochez L. Immune Monitoring in Melanoma and Urothelial Cancer Patients Treated with Anti-PD-1 Immunotherapy and SBRT Discloses Tumor Specific Immune Signatures. Cancers (Basel) 2021; 13:cancers13112630. [PMID: 34071888 PMCID: PMC8198315 DOI: 10.3390/cancers13112630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Currently available biomarkers for response to checkpoint inhibitors are incomplete and predominantly focus on tumor tissue analysis e.g., tumor mutational burden, programmed cell death-ligand 1 (PD-L1) expression. Biomarkers in peripheral blood would allow a more dynamic monitoring and could offer a way for sequential adaptation of treatment strategy. We conducted an in-depth analysis of baseline and on-treatment systemic immune features in a cohort of stage III/IV melanoma and stage IV urothelial cancer (UC) patients treated with anti-programmed cell death-1 (anti-PD-1) therapy combined with stereotactic body radiotherapy (SBRT) in a similar regimen/schedule. Baseline immunity was clearly different between these two cohorts, indicating a less active immune landscape in UC patients. This study also detected signatures of proliferation in the CD8+ T-cell compartment pre-treatment and early after anti-PD-1 initiation that were positively correlated with clinical outcome in both tumor types. In addition our data support the biological relevance of PD-1/PD-L1 expression on circulating immune cell subsets, especially in melanoma. Abstract (1) Background: Blockade of the PD-1/PD-L1 pathway has revolutionized the oncology field in the last decade. However, the proportion of patients experiencing a durable response is still limited. In the current study, we performed an extensive immune monitoring in patients with stage III/IV melanoma and stage IV UC who received anti-PD-1 immunotherapy with SBRT. (2) Methods: In total 145 blood samples from 38 patients, collected at fixed time points before and during treatment, were phenotyped via high-parameter flow cytometry, luminex assay and UPLC-MS/MS. (3) Results: Baseline systemic immunity in melanoma and UC patients was different with a more prominent myeloid compartment and a higher neutrophil to lymphocyte ratio in UC. Proliferation (Ki67+) of CD8+ T-cells and of the PD-1+/PD-L1+ CD8+ subset at baseline correlated with progression free survival in melanoma. In contrast a higher frequency of PD-1/PD-L1 expressing non-proliferating (Ki67−) CD8+ and CD4+ T-cells before treatment was associated with worse outcome in melanoma. In UC, the expansion of Ki67+ CD8+ T-cells and of the PD-L1+ subset relative to tumor burden correlated with clinical outcome. (4) Conclusion: This study reveals a clearly different immune landscape in melanoma and UC at baseline, which may impact immunotherapy response. Signatures of proliferation in the CD8+ T-cell compartment prior to and early after anti-PD-1 initiation were positively correlated with clinical outcome in both cohorts. PD-1/PD-L1 expression on circulating immune cell subsets seems of clinical relevance in the melanoma cohort.
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Affiliation(s)
- Annabel Meireson
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Dermatology Research Unit, Ghent University Hospital, 9000 Ghent, Belgium
| | - Simon J. Tavernier
- Centre for Primary Immunodeficiency Ghent, Primary Immune Deficiency Research Lab, Department of Internal Medicine and Pediatrics, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, 9000 Ghent, Belgium; (S.J.T.); (F.H.)
- VIB Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, 9000 Ghent, Belgium
| | - Sofie Van Gassen
- VIB Center for Inflammation Research, Unit of Data Mining and Modeling for Biomedicine, 9000 Ghent, Belgium;
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Nora Sundahl
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, 9000 Ghent, Belgium
| | - Annelies Demeyer
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Dermatology Research Unit, Ghent University Hospital, 9000 Ghent, Belgium
| | - Mathieu Spaas
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, 9000 Ghent, Belgium
| | - Vibeke Kruse
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Department of Medical Oncology, Ghent University Hospital, 9000 Ghent, Belgium
| | | | - Jo Van Dorpe
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Department of Pathology, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Benjamin Hennart
- Unité Fonctionnelle de Toxicologie, CHU Lille, F-59000 Lille, France; (B.H.); (D.A.)
- ULR 4483-IMPact de l’Environnement Chimique sur la Santé Humaine (IMPECS), Université de Lille, F-59000 Lille, France
| | - Delphine Allorge
- Unité Fonctionnelle de Toxicologie, CHU Lille, F-59000 Lille, France; (B.H.); (D.A.)
- ULR 4483-IMPact de l’Environnement Chimique sur la Santé Humaine (IMPECS), Université de Lille, F-59000 Lille, France
| | - Filomeen Haerynck
- Centre for Primary Immunodeficiency Ghent, Primary Immune Deficiency Research Lab, Department of Internal Medicine and Pediatrics, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, 9000 Ghent, Belgium; (S.J.T.); (F.H.)
| | - Karel Decaestecker
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Department of Urology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Sylvie Rottey
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Department of Medical Oncology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Yvan Saeys
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- VIB Center for Inflammation Research, Unit of Data Mining and Modeling for Biomedicine, 9000 Ghent, Belgium;
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Piet Ost
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, 9000 Ghent, Belgium
| | - Lieve Brochez
- Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; (A.M.); (N.S.); (A.D.); (M.S.); (V.K.); (J.V.D.); (K.D.); (S.R.); (Y.S.); (P.O.)
- Dermatology Research Unit, Ghent University Hospital, 9000 Ghent, Belgium
- Correspondence:
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392
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Yang J, Zhao S, Wang J, Sheng Q, Liu Q, Shyr Y. Immu-Mela: An open resource for exploring immunotherapy-related multidimensional genomic profiles in melanoma. J Genet Genomics 2021; 48:361-368. [PMID: 34127402 PMCID: PMC8349898 DOI: 10.1016/j.jgg.2021.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
There are increasing studies aimed to reveal genomic hallmarks predictive of immune checkpoint blockade (ICB) treatment response, which generated a large number of data and provided an unprecedented opportunity to identify response-related features and evaluate their robustness across cohorts. However, those valuable data sets are not easily accessible to the research community. To take full advantage of existing large-scale immuno-genomic profiles, we developed Immu-Mela (http://bioinfo.vanderbilt.edu/database/Immu-Mela/), a multidimensional immuno-genomic portal that provides interactive exploration of associations between ICB responsiveness and multi-omics features in melanoma, including genetic, transcriptomics, immune cells, and single-cell populations. Immu-Mela also enables integrative analysis of any two genomic features. We demonstrated the value of Immu-Mela by identifying known and novel genomic features associated with ICB response. In addition, Immu-Mela allows users to upload their data sets (unrestricted to any cancer types) and co-analyze with existing data to identify and validate signatures of interest. Immu-Mela reduces barriers between researchers and complex genomic data, facilitating discoveries in cancer immunotherapy.
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Affiliation(s)
- Jing Yang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville TN 37203, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN 37203, USA
| | - Shilin Zhao
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville TN 37203, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN 37203, USA
| | - Jing Wang
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville TN 37203, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN 37203, USA
| | - Quanhu Sheng
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville TN 37203, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN 37203, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville TN 37203, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN 37203, USA.
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville TN 37203, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville TN 37203, USA.
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Chen XJ, Liu S, Han DM, Han DZ, Sun WJ, Zhao XC, Liang JQ, Yu L. FUT8-AS1 Inhibits the Malignancy of Melanoma Through Promoting miR-145-5p Biogenesis and Suppressing NRAS/MAPK Signaling. Front Oncol 2021; 10:586085. [PMID: 34094894 PMCID: PMC8170315 DOI: 10.3389/fonc.2020.586085] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/20/2020] [Indexed: 12/24/2022] Open
Abstract
Melanoma is the major lethal skin malignancy. However, the critical molecular drivers governing melanoma progression and prognosis are still not clear. By analyzing The Cancer Genome Atlas (TCGA) data, we identified FUT8-AS1 as a prognosis-related long non-coding RNA (lncRNA) in melanoma. We further confirmed that FUT8-AS1 is downregulated in melanoma. Reduced expression of FUT8-AS1 is correlated with aggressive clinical factors and inferior overall survival. Using in vitro functional assays, our findings demonstrated that ectopic expression of FUT8-AS1 represses melanoma cell proliferation, migration, and invasion. FUT8-AS1 silencing promotes melanoma cell proliferation, migration, and invasion. Furthermore, in vivo functional assays demonstrated that FUT8-AS1 represses melanoma growth and metastasis. Mechanistically, FUT8-AS1 was found to bind NF90, repress the interaction between NF90 and primary miR-145 (pri-miR-145), relieve the repressive roles of NF90 on mature miR-145-5p biogenesis, and thus promote miR-145-5p biogenesis and upregulate mature miR-145-5p level. The expression of FUT8-AS1 is positively correlated with miR-145-5p in melanoma tissues. Via upregulating miR-145-5p, FUT8-AS1 reduces the expression of NRAS, a target of miR-145-5. FUT8-AS1 further represses MAPK signaling via downregulating NRAS. Functional rescue assays demonstrated that inhibition of miR-145-5p reverses the tumor suppressive roles of FUT8-AS1 in melanoma. The oncogenic roles of FUT8-AS1 silencing are also blocked by MAPK signaling inhibitor MEK162. In conclusion, these findings demonstrate that FUT8-AS1 exerts tumor suppressive roles in melanoma via regulating NF90/miR-145-5p/NRAS/MAPK signaling axis. Targeting FUT8-AS1 and its downstream molecular signaling axis represent promising therapeutic strategies for melanoma.
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Affiliation(s)
- Xiang-Jun Chen
- Department of Burns and Plastic Surgery, The 969th Hospital of PLA, Hohhot, China
| | - Sha Liu
- Department of Burns and Plastic Surgery, The 969th Hospital of PLA, Hohhot, China
| | - Dong-Mei Han
- Department of Burns and Plastic Surgery, The 969th Hospital of PLA, Hohhot, China
| | - De-Zhi Han
- Department of Burns and Plastic Surgery, The 969th Hospital of PLA, Hohhot, China
| | - Wei-Jing Sun
- Department of Burns and Plastic Surgery, The 969th Hospital of PLA, Hohhot, China
| | - Xiao-Chun Zhao
- Department of Burns and Plastic Surgery, The 969th Hospital of PLA, Hohhot, China
| | - Jun-Qing Liang
- The Affiliated People's Hospital of Inner Mongolia Medical University, Inner Mongolia Autonomous Region Cancer Hospital, Hohhot, China
| | - Li Yu
- Department of Intensive Care Unit, The 969th Hospital of PLA, Hohhot, China
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Oba J, Woodman SE. The genetic and epigenetic basis of distinct melanoma types. J Dermatol 2021; 48:925-939. [PMID: 34008215 DOI: 10.1111/1346-8138.15957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
Melanoma represents the deadliest skin cancer. Recent therapeutic developments, including targeted and immune therapies have revolutionized clinical management and improved patient outcome. This progress was achieved by rigorous molecular and functional studies followed by robust clinical trials. The identification of key genomic alterations and gene expression profiles have propelled the understanding of distinct characteristics within melanoma subtypes. The aim of this review is to summarize and highlight the main genetic and epigenetic findings of melanomas and highlight their pathological and therapeutic importance.
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Affiliation(s)
- Junna Oba
- Genomics Unit, Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Scott E Woodman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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395
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Wang X, Li B, Kim YJ, Wang YC, Li Z, Yu J, Zeng S, Ma X, Choi IY, Di Biase S, Smith DJ, Zhou Y, Li YR, Ma F, Huang J, Clarke N, To A, Gong L, Pham AT, Moon H, Pellegrini M, Yang L. Targeting monoamine oxidase A for T cell-based cancer immunotherapy. Sci Immunol 2021; 6:eabh2383. [PMID: 33990379 DOI: 10.1126/sciimmunol.abh2383] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022]
Abstract
Monoamine oxidase A (MAO-A) is an enzyme best known for its function in the brain, where it breaks down neurotransmitters and thereby influences mood and behavior. Small-molecule MAO inhibitors (MAOIs) have been developed and are clinically used for treating depression and other neurological disorders. However, the involvement of MAO-A in antitumor immunity has not been reported. Here, we observed induction of the Maoa gene in tumor-infiltrating immune cells. Maoa knockout mice exhibited enhanced antitumor T cell immunity and suppressed tumor growth. MAOI treatment significantly suppressed tumor growth in preclinical mouse syngeneic and human xenograft tumor models in a T cell-dependent manner. Combining MAOI and anti-PD-1 treatments generated synergistic tumor suppression effects. Clinical data correlation studies associated intratumoral MAOA expression with T cell dysfunction and decreased patient survival in a broad range of cancers. We further demonstrated that MAO-A restrains antitumor T cell immunity through controlling intratumoral T cell autocrine serotonin signaling. Together, these data identify MAO-A as an immune checkpoint and support repurposing MAOI antidepressants for cancer immunotherapy.
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Affiliation(s)
- Xi Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Bo Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Yu Jeong Kim
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Yu-Chen Wang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Zhe Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Jiaji Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Samuel Zeng
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Xiaoya Ma
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - In Young Choi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Stefano Di Biase
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Drake J Smith
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Yang Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Yan-Ruide Li
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Feiyang Ma
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Jie Huang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Nicole Clarke
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Angela To
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Laura Gong
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Alexander T Pham
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Heesung Moon
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Lili Yang
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, the David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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396
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Lelliott EJ, Kong IY, Zethoven M, Ramsbottom KM, Martelotto LG, Meyran D, Jiang Zhu J, Costacurta M, Kirby L, Sandow JJ, Lim L, Dominguez PM, Todorovski I, Haynes NM, Beavis PA, Neeson PJ, Hawkins ED, McArthur GA, Parish IA, Johnstone RW, Oliaro J, Sheppard KE, Kearney CJ, Vervoort SJ. CDK4/6 inhibition promotes anti-tumor immunity through the induction of T cell memory. Cancer Discov 2021; 11:2582-2601. [PMID: 33990344 DOI: 10.1158/2159-8290.cd-20-1554] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/05/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022]
Abstract
Pharmacological inhibitors of cyclin dependent kinases 4 and 6 (CDK4/6) are an approved treatment for hormone receptor-positive breast cancer and are currently under evaluation across hundreds of clinical trials for other cancer types. The clinical success of these inhibitors is largely attributed to well-defined tumor-intrinsic cytostatic mechanisms, while their emerging role as immunomodulatory agents is less understood. Using integrated epigenomic, transcriptomic and proteomic analyses, we demonstrated a novel action of CDK4/6 inhibitors in promoting the phenotypic and functional acquisition of immunological T cell memory. Short-term priming with a CDK4/6 inhibitor promoted long-term endogenous anti-tumor T cell immunity in mice, enhanced the persistence and therapeutic efficacy of chimeric antigen receptor (CAR)-T cells, and induced an RB-dependent T cell phenotype supportive of favorable responses to immune checkpoint blockade in melanoma patients. Together, these mechanistic insights significantly broaden the prospective utility of CDK4/6 inhibitors as clinical tools to boost anti-tumor T cell immunity.
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Affiliation(s)
| | - Isabella Y Kong
- Inflammation, Walter and Eliza Hall Institute of Medical Research
| | | | | | | | | | | | | | - Laura Kirby
- Cancer Research, Peter MacCallum Cancer Centre
| | - Jarrod J Sandow
- Advanced Biology and Technology, The Walter and Eliza Hall Institute
| | - Lydia Lim
- Division of Research, Peter MacCallum Cancer Centre
| | | | | | - Nicole M Haynes
- Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Research Centre
| | - Paul J Neeson
- Cancer Immunology Research, Peter MacCallum Cancer Centre
| | - Edwin D Hawkins
- Immunology Division, Walter and Eliza Hall Institute of Medical Research
| | | | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Research Centre
| | | | | | | | | | - Stephin J Vervoort
- Gene Regulation Laboratory, Cancer Therapeutics Program, Peter MacCallum Cancer Centre
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397
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Stenzel U, Horn S. bathometer: lightning fast depth-of-reads query. Bioinformatics 2021; 37:4233-4234. [PMID: 33983362 PMCID: PMC9502157 DOI: 10.1093/bioinformatics/btab372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022] Open
Abstract
Motivation The query for the number of reads overlapping a given region is a common step in the analysis of Illumina sequencing data. Sometimes, these queries are not conveniently precomputable. It seems beneficial to make this kind of arbitrary query as fast and convenient as possible. Results We present Bathometer, a tool that indexes BAM files in a space efficient way, which allows ad hoc queries for the number of reads overlapping any given genomic region to be answered much more quickly than by counting with common tools such as Samtools, while incurring much less disk I/O. Availabilityand implementation Bathometer is implemented in C, licensed under the GNU General Public License version 3+ and freely downloadable from Bitbucket (https://bitbucket.org/ustenzel/bathometer) Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- U Stenzel
- Rudolf Schönheimer Institute of Biochemistry, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - S Horn
- Rudolf Schönheimer Institute of Biochemistry, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany.,Department of Dermatology, University Hospital Essen, Hufelandstr. 55, 45122 Essen, Germany.,German Cancer Consortium (DKTK), University Hospital Essen, Hufelandstr. 55, 45122 Essen, Germany
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398
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Nacer DF, Liljedahl H, Karlsson A, Lindgren D, Staaf J. Pan-cancer application of a lung-adenocarcinoma-derived gene-expression-based prognostic predictor. Brief Bioinform 2021; 22:6272790. [PMID: 33971670 PMCID: PMC8574611 DOI: 10.1093/bib/bbab154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/17/2021] [Accepted: 04/02/2021] [Indexed: 12/24/2022] Open
Abstract
Gene-expression profiling can be used to classify human tumors into molecular subtypes or risk groups, representing potential future clinical tools for treatment prediction and prognostication. However, it is less well-known how prognostic gene signatures derived in one malignancy perform in a pan-cancer context. In this study, a gene-rule-based single sample predictor (SSP) called classifier for lung adenocarcinoma molecular subtypes (CLAMS) associated with proliferation was tested in almost 15 000 samples from 32 cancer types to classify samples into better or worse prognosis. Of the 14 malignancies that presented both CLAMS classes in sufficient numbers, survival outcomes were significantly different for breast, brain, kidney and liver cancer. Patients with samples classified as better prognosis by CLAMS were generally of lower tumor grade and disease stage, and had improved prognosis according to other type-specific classifications (e.g. PAM50 for breast cancer). In all, 99.1% of non-lung cancer cases classified as better outcome by CLAMS were comprised within the range of proliferation scores of lung adenocarcinoma cases with a predicted better prognosis by CLAMS. This finding demonstrates the potential of tuning SSPs to identify specific levels of for instance tumor proliferation or other transcriptional programs through predictor training. Together, pan-cancer studies such as this may take us one step closer to understanding how gene-expression-based SSPs act, which gene-expression programs might be important in different malignancies, and how to derive tools useful for prognostication that are efficient across organs.
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399
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Zhu G, Su H, Johnson CH, Khan SA, Kluger H, Lu L. Intratumour microbiome associated with the infiltration of cytotoxic CD8+ T cells and patient survival in cutaneous melanoma. Eur J Cancer 2021; 151:25-34. [PMID: 33962358 DOI: 10.1016/j.ejca.2021.03.053] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/11/2021] [Accepted: 03/31/2021] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The gut microbiome plays an important role in systemic inflammation and immune response. Microbes can translocate and reside in tumour niches. However, it is unclear how the intratumour microbiome affects immunity in human cancer. The purpose of this study was to investigate the association between intratumour bacteria, infiltrating CD8+ T cells and patient survival in cutaneous melanoma. METHODS Using The Cancer Genome Altas's cutaneous melanoma RNA sequencing data, levels of intratumour bacteria and infiltrating CD8+ T cells were determined. Correlation between intratumour bacteria and infiltrating CD8+ T cells or chemokine gene expression and survival analysis of infiltrating CD8+ T cells and Lachnoclostridium in cutaneous melanoma were performed. RESULTS Patients with low levels of CD8+ T cells have significantly shorter survival than those with high levels. The adjusted hazard ratio was 1.57 (low vs high) (95% confidence interval: 1.17-2.10, p = 0.002). Intratumour bacteria of the Lachnoclostridium genus ranked top in a positive association with infiltrating CD8+ T cells (correlation coefficient = 0.38, p = 9.4 × 10-14), followed by Gelidibacter (0.31, p = 1.13 × 10-9), Flammeovirga (0.29, p = 1.96 × 10-8) and Acinetobacter (0.28, p = 8.94 × 10-8). These intratumour genera positively correlated with chemokine CXCL9, CXCL10 and CCL5 expression. The high Lachnoclostridium load significantly reduced the mortality risk (p = 0.0003). However, no statistically significant correlation was observed between intratumour Lachnoclostridium abundance and the levels of either NK, B or CD4+ T cells. CONCLUSION Intratumour-residing gut microbiota could modulate chemokine levels and affect CD8+ T-cell infiltration, consequently influencing patient survival in cutaneous melanoma. Manipulating the intratumour gut microbiome may benefit patient outcomes for those undergoing immunotherapy.
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Affiliation(s)
- Gongjian Zhu
- Gansu Provincial Academy of Medical Science, Gansu Provincial Cancer Hospital, Lanzhou, 730050, China; Department of Chronic Disease Epidemiology, Yale School of Public Health, School of Medicine, Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Haixiang Su
- Gansu Provincial Academy of Medical Science, Gansu Provincial Cancer Hospital, Lanzhou, 730050, China
| | - Caroline H Johnson
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Sajid A Khan
- Department of Surgery, Division of Surgical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Harriet Kluger
- Department of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, School of Medicine, Yale Cancer Center, Yale University, New Haven, CT, USA.
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400
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Kelly GM, Al-Ejeh F, McCuaig R, Casciello F, Ahmad Kamal N, Ferguson B, Pritchard AL, Ali S, Silva IP, Wilmott JS, Long GV, Scolyer RA, Rao S, Hayward NK, Gannon F, Lee JS. G9a Inhibition Enhances Checkpoint Inhibitor Blockade Response in Melanoma. Clin Cancer Res 2021; 27:2624-2635. [PMID: 33589432 DOI: 10.1158/1078-0432.ccr-20-3463] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/24/2020] [Accepted: 02/05/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE G9a histone methyltransferase exerts oncogenic effects in several tumor types and its inhibition promotes anticancer effects. However, the impact on checkpoint inhibitor blockade response and the utility of G9a or its target genes as a biomarker is poorly studied. We aimed to examine whether G9a inhibition can augment the efficacy of checkpoint inhibitor blockade and whether LC3B, a G9a target gene, can predict treatment response. EXPERIMENTAL DESIGN Clinical potential of LC3B as a biomarker of checkpoint inhibitor blockade was assessed using patient samples including tumor biopsies and circulating tumor cells from liquid biopsies. Efficacy of G9a inhibition to enhance checkpoint inhibitor blockade was examined using a mouse model. RESULTS Patients with melanoma who responded to checkpoint inhibitor blockade were associated with not only a higher level of tumor LC3B but also a higher proportion of cells expressing LC3B. A higher expression of MAP1LC3B or LC3B protein was associated with longer survival and lower incidence of acquired resistance to checkpoint inhibitor blockade, suggesting LC3B as a potential predictive biomarker. We demonstrate that G9a histone methyltransferase inhibition is able to not only robustly induce LC3B level to augment the efficacy of checkpoint inhibitor blockade, but also induces melanoma cell death. CONCLUSIONS Checkpoint inhibitor blockade response is limited to a subset of the patient population. These results have implications for the development of LC3B as a predictive biomarker of checkpoint inhibitor blockade to guide patient selection, as well as G9a inhibition as a strategy to extend the proportion of patients responding to immunotherapy.
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Affiliation(s)
- Gregory M Kelly
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Fares Al-Ejeh
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Robert McCuaig
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Francesco Casciello
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | | | - Blake Ferguson
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | - Sayed Ali
- Faculty of Education, Science, Technology & Mathematics, University of Canberra, Canberra, Australia
- St John of God Midland Public and Private Hospitals, Midland, Western Australia, Australia
| | - Ines P Silva
- Melanoma Institute Australia, University of Sydney, Wollstonecraft, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
| | - James S Wilmott
- Melanoma Institute Australia, University of Sydney, Wollstonecraft, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, University of Sydney, Wollstonecraft, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Mater Hospital, North Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, University of Sydney, Wollstonecraft, New South Wales, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Sudha Rao
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Frank Gannon
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Jason S Lee
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
- School of Medicine, University of Queensland, Herston, Queensland, Australia
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
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