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Anang DC, Walter HAW, Lim J, Niewold ITG, van der Weele L, Aronica E, Eftimov F, Raaphorst J, van Schaik BDC, van Kampen AHC, van der Kooi AJ, de Vries N. TCRβ clones in muscle tissue share structural features in patients with idiopathic inflammatory myopathy and are associated with disease activity. Front Immunol 2024; 14:1279055. [PMID: 38268914 PMCID: PMC10806010 DOI: 10.3389/fimmu.2023.1279055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/13/2023] [Indexed: 01/26/2024] Open
Abstract
Objectives To characterize the T cell receptor (TCRβ) repertoire in peripheral blood and muscle tissues of treatment naïve patients with newly diagnosed idiopathic inflammatory myopathies (IIMs). Methods High throughput RNA sequencing of the TCRβ chain was performed in peripheral blood and muscle tissue in twenty newly-diagnosed treatment-naïve IIM patients (9 DM, 5 NM/OM, 5 IMNM and 1 ASyS) and healthy controls. Results thereof were correlated with markers of disease activity. Results Muscle tissue of IIM patients shows more expansion of TCRβ clones and decreased diversity when compared to peripheral blood of IIM as well as healthy controls (both p=0.0001). Several expanded TCRβ clones in muscle are tissue restricted and cannot be retrieved in peripheral blood. These clones have significantly longer CDR3 regions when compared to clones (also) found in circulation (p=0.0002), while their CDR3 region is more hydrophobic (p<0.01). Network analysis shows that clonal TCRβ signatures are shared between patients. Increased clonal expansion in muscle tissue is significantly correlated with increased CK levels (p=0.03), while it tends to correlate with decreased muscle strength (p=0.08). Conclusion Network analysis of clones in muscle of IIM patients shows shared clusters of sequences across patients. Muscle-restricted CDR3 TCRβ clones show specific structural features in their T cell receptor. Our results indicate that clonal TCRβ expansion in muscle tissue might be associated with disease activity. Collectively, these findings support a role for specific clonal T cell responses in muscle tissue in the pathogenesis of the IIM subtypes studied.
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Affiliation(s)
- Dornatien C. Anang
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Genome Analysis, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hannah A. W. Walter
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Johan Lim
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Ilse T. G. Niewold
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Genome Analysis, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Linda van der Weele
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Filip Eftimov
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Joost Raaphorst
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Barbera D. C. van Schaik
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Institute, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Antoine H. C. van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam Public Health Institute, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Anneke J. van der Kooi
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, Netherlands
| | - Niek de Vries
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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2
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Wu X, Zhou Z, Cao Q, Chen Y, Gong J, Zhang Q, Qiang Y, Lu Y, Cao G. Reprogramming of Treg cells in the inflammatory microenvironment during immunotherapy: a literature review. Front Immunol 2023; 14:1268188. [PMID: 37753092 PMCID: PMC10518452 DOI: 10.3389/fimmu.2023.1268188] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
Regulatory T cells (Treg), as members of CD4+ T cells, have garnered extensive attention in the research of tumor progression. Treg cells have the function of inhibiting the immune effector cells, preventing tissue damage, and suppressing inflammation. Under the stimulation of the tumor inflammatory microenvironment (IM), the reprogramming of Treg cells enhances their suppression of immune responses, ultimately promoting tumor immune escape or tumor progression. Reducing the number of Treg cells in the IM or lowering the activity of Treg cells while preventing their reprogramming, can help promote the body's anti-tumor immune responses. This review introduces a reprogramming mechanism of Treg cells in the IM; and discusses the regulation of Treg cells on tumor progression. The control of Treg cells and the response to Treg inflammatory reprogramming in tumor immunotherapy are analyzed and countermeasures are proposed. This work will provide a foundation for downregulating the immunosuppressive role of Treg in the inflammatory environment in future tumor immunotherapy.
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Affiliation(s)
- Xinyan Wu
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zhigang Zhou
- Department of Oncology, Changde Hospital, Xiangya School of Medicine, Central South University, Changde, China
| | - Qiang Cao
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
- School of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Yuquan Chen
- Institute of Medical Information/Library, Chinese Academy of Medical Sciences, Beijing, China
| | - Junling Gong
- School of Public Health, Nanchang University, Qianhu, Nanchang, China
| | - Qi Zhang
- Undergraduate Department, Taishan University, Taian, China
| | - Yi Qiang
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
| | - Yanfeng Lu
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
| | - Guangzhu Cao
- Department of Earth Sciences, Kunming University of Science and Technology, Kunming, China
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3
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Dietz MV, Quintelier KLA, van Kooten JP, de Boer NL, Vink M, Brandt-Kerkhof ARM, Verhoef C, Saeys Y, Aerts JGJV, Willemsen M, Van Gassen S, Madsen EVE. Adjuvant dendritic cell-based immunotherapy after cytoreductive surgery and hyperthermic intraperitoneal chemotherapy in patients with malignant peritoneal mesothelioma: a phase II clinical trial. J Immunother Cancer 2023; 11:e007070. [PMID: 37536940 PMCID: PMC10401259 DOI: 10.1136/jitc-2023-007070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Malignant peritoneal mesothelioma (MPM) is an aggressive malignancy with a poor prognosis. Cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) improves survival outcomes, but recurrence rates remain high. Dendritic cell-based immunotherapy (DCBI) showed promising results in patients with pleural mesothelioma. The primary aim of this trial was to determine feasibility of adjuvant DCBI after CRS-HIPEC. METHODS This open-label, single-center, phase II clinical trial, performed in the Erasmus MC Cancer Institute Rotterdam, the Netherlands, included patients with epithelioid MPM. 4-6 weeks before CRS-HIPEC leukapheresis was performed. 8-10 weeks after surgery, DCBI was administered three times biweekly. Feasibility was defined as administration of at least three adjuvant vaccinations in 75% of patients. Comprehensive immune cell profiling was performed on peripheral blood samples prior to and during treatment. RESULTS All patients who received CRS-HIPEC (n=16) were successfully treated with adjuvant DCBI. No severe toxicity related to DCBI was observed. Median progression-free survival (PFS) was 12 months (IQR 5-23) and median overall survival was not reached. DCBI was associated with increased proliferation of circulating natural killer cells and CD4+ T-helper (Th) cells. Co-stimulatory molecules, including ICOS, HLA-DR, and CD28 were upregulated predominantly on memory or proliferating Th-cells and minimally on CD8+ cytotoxic T-lymphocytes (CTLs) after treatment. However, an increase in CD8+ terminally differentiated effector memory (Temra) cells positively correlated with PFS, whereas co-expression of ICOS and Ki67 on CTLs trended towards a positive correlation. CONCLUSIONS Adjuvant DCBI after CRS-HIPEC in patients with MPM was feasible and safe, and showed promising survival outcomes. DCBI had an immune modulatory effect on lymphoid cells and induced memory T-cell activation. Moreover, an increase of CD8+ Temra cells was more pronounced in patients with longer PFS. These data provide rationale for future combination treatment strategies. TRIAL REGISTRATION NUMBER NTR7060; Dutch Trial Register (NTR).
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Affiliation(s)
- Michelle V Dietz
- Department of Surgical oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Katrien L A Quintelier
- Data Mining and Modeling for Biomedicine Group, VIB-UGent Center for Inflammation Research Elewaut Unit Molecular Immunology and Inflammatory Unit, Gent, Oost-Vlaanderen, Belgium
- Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, The Netherlands
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | - Job P van Kooten
- Department of Surgical oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Nadine L de Boer
- Department of Surgical oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Madelief Vink
- Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, The Netherlands
| | | | - Cornelis Verhoef
- Department of Surgical oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine Group, VIB-UGent Center for Inflammation Research Elewaut Unit Molecular Immunology and Inflammatory Unit, Gent, Oost-Vlaanderen, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | - Joachim G J V Aerts
- Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, The Netherlands
| | - Marcella Willemsen
- Department of Pulmonary Medicine, Erasmus Medical Center, Rotterdam, Zuid-Holland, The Netherlands
| | - Sofie Van Gassen
- Data Mining and Modeling for Biomedicine Group, VIB-UGent Center for Inflammation Research Elewaut Unit Molecular Immunology and Inflammatory Unit, Gent, Oost-Vlaanderen, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | - Eva V E Madsen
- Department of Surgical oncology, Erasmus Medical Center, Rotterdam, The Netherlands
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4
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Deiana C, Fabbri F, Tavolari S, Palloni A, Brandi G. Improvements in Systemic Therapies for Advanced Malignant Mesothelioma. Int J Mol Sci 2023; 24:10415. [PMID: 37445594 DOI: 10.3390/ijms241310415] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
Malignant pleural mesothelioma (MPM) is a rare and aggressive malignancy associated with poor prognosis and a 5-year survival rate of 12%. Many drugs have been tested over the years with conflicting results. The aim of this review is to provide an overview of current therapies in MPM and how to best interpret the data available on these drugs. Furthermore, we focused on promising treatments under investigation, such as immunotherapy with targets different from anti-PD-1/PD-L1 inhibitors, vaccines, target therapies, and metabolism-based strategies.
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Affiliation(s)
- Chiara Deiana
- Medical Oncology, IRCCS Azienda Ospedaliera, Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Francesca Fabbri
- Medical Oncology, IRCCS Azienda Ospedaliera, Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Simona Tavolari
- Medical Oncology, IRCCS Azienda Ospedaliera, Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Andrea Palloni
- Medical Oncology, IRCCS Azienda Ospedaliera, Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Giovanni Brandi
- Medical Oncology, IRCCS Azienda Ospedaliera, Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
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5
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Desai AP, Kosari F, Disselhorst M, Yin J, Agahi A, Peikert T, Udell J, Johnson SH, Smadbeck J, Murphy S, Karagouga G, McCune A, Schaefer-Klein J, Borad MJ, Cheville J, Vasmatzis G, Baas P, Mansfield A. Dynamics and survival associations of T cell receptor clusters in patients with pleural mesothelioma treated with immunotherapy. J Immunother Cancer 2023; 11:e006035. [PMID: 37279993 PMCID: PMC10255162 DOI: 10.1136/jitc-2022-006035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) are now a first-line treatment option for patients with pleural mesothelioma with the recent approval of ipilimumab and nivolumab. Mesothelioma has a low tumor mutation burden and no robust predictors of survival with ICI. Since ICIs enable adaptive antitumor immune responses, we investigated T-cell receptor (TCR) associations with survival in participants from two clinical trials treated with ICI. METHODS We included patients with pleural mesothelioma who were treated with nivolumab (NivoMes, NCT02497508) or nivolumab and ipilimumab (INITIATE, NCT03048474) after first-line therapy. TCR sequencing was performed with the ImmunoSEQ assay in 49 and 39 pretreatment and post-treatment patient peripheral blood mononuclear cell (PBMC) samples. These data were integrated with TCR sequences found in bulk RNAseq data by TRUST4 program in 45 and 35 pretreatment and post-treatment tumor biopsy samples and TCR sequences from over 600 healthy controls. The TCR sequences were clustered into groups of shared antigen specificity using GIANA. Associations of TCR clusters with overall survival were determined by cox proportional hazard analysis. RESULTS We identified 4.2 million and 12 thousand complementarity-determining region 3 (CDR3) sequences from PBMCs and tumors, respectively, in patients treated with ICI. These CDR3 sequences were integrated with 2.1 million publically available CDR3 sequences from healthy controls and clustered. ICI-enhanced T-cell infiltration and expanded T cell diversity in tumors. Cases with TCR clones in the top tertile in the pretreatment tissue or in circulation had significantly better survival than the bottom two tertiles (p<0.04). Furthermore, a high number of shared TCR clones between pretreatment tissue and in circulation was associated with improved survival (p=0.01). To potentially select antitumor clusters, we filtered for clusters that were (1) not found in healthy controls, (2) recurrent in multiple patients with mesothelioma, and (3) more prevalent in post-treatment than pretreatment samples. The detection of two-specific TCR clusters provided significant survival benefit compared with detection of 1 cluster (HR<0.001, p=0.026) or the detection of no TCR clusters (HR=0.10, p=0.002). These two clusters were not found in bulk tissue RNA-seq data and have not been reported in public CDR3 databases. CONCLUSIONS We identified two unique TCR clusters that were associated with survival on treatment with ICI in patients with pleural mesothelioma. These clusters may enable approaches for antigen discovery and inform future targets for design of adoptive T cell therapies.
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Affiliation(s)
- Aakash P Desai
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Farhad Kosari
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Disselhorst
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jun Yin
- Quantitative Health Sciences, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Alireza Agahi
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Tobias Peikert
- Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Julia Udell
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Sarah H Johnson
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - James Smadbeck
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Stephen Murphy
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Giannoula Karagouga
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Alexa McCune
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Janet Schaefer-Klein
- Center for Individualized Medicine, Mayo Clinic Rochester, Rochester, Minnesota, USA
| | - Mitesh J Borad
- Hematology/Medical Oncology, Mayo Clinic, Phoenix, Arizona, USA
| | - John Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - George Vasmatzis
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul Baas
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Aaron Mansfield
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
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6
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van Lieverloo GGA, Al-Soudi A, Wieske L, Klarenbeek PL, Anang DC, Adrichem ME, Niewold I, van Schaik BDC, van Kampen AHC, van Schaik IN, de Vries N, Eftimov F. B-cell and T-cell receptor repertoire in chronic inflammatory demyelinating polyneuropathy, a prospective cohort study. J Peripher Nerv Syst 2023; 28:69-78. [PMID: 36723274 DOI: 10.1111/jns.12533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 01/24/2023] [Accepted: 01/28/2023] [Indexed: 02/02/2023]
Abstract
The immunopathophysiological mechanisms underlying chronic inflammatory demyelinating polyneuropathy (CIDP) in an individual patient are largely unknown. Better understanding of these mechanisms may aid development of biomarkers and targeted therapies. Both B- and T-cell dominant mechanisms have been implicated. We therefore investigated whether B-cell and T-cell receptor (BCR/TCR) repertoires might function as immunological biomarkers in CIDP. In this prospective cohort study, we longitudinally sampled peripheral blood of CIDP patients in three different phases of CIDP: starting induction treatment (IT), starting withdrawal from IVIg maintenance treatment (MT), and patients in remission (R). BCR and TCR repertoires were analyzed using RNA based high throughput sequencing. In baseline samples, the number of total clones, the number of dominant BCR and TCR clones and their impact on the repertoire was similar for patients in the IT, MT, and remission groups compared with healthy controls. Baseline samples in the IT or MT did not predict treatment response or potential relapse at follow-up. Treatment responders in the IT group showed a potential IVIg-induced increase in the number of dominant BCR clones and their impact at follow-up (baseline1.0 [IQR 1.0-2.8] vs. 6 m 3.5 [0.3-6.8]; P < .05, Wilcoxon test). Although the BCR repertoire changed over time, the TCR repertoire remained robustly stable. We conclude that TCR and BCR repertoire distributions do not predict disease activity, treatment response or response to treatment withdrawal.
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Affiliation(s)
- G G A van Lieverloo
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - A Al-Soudi
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center (ARC), Amsterdam UMC, Amsterdam, The Netherlands
| | - L Wieske
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - P L Klarenbeek
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center (ARC), Amsterdam UMC, Amsterdam, The Netherlands
| | - D C Anang
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center (ARC), Amsterdam UMC, Amsterdam, The Netherlands
| | - M E Adrichem
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - I Niewold
- Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center (ARC), Amsterdam UMC, Amsterdam, The Netherlands.,Amsterdam UMC, Department of Genome Analysis, Amsterdam, The Netherlands
| | - B D C van Schaik
- Amsterdam UMC, Department of Epidemiology & Data Science (EDS), Bioinformatics Laboratory, Amsterdam, The Netherlands
| | - A H C van Kampen
- Amsterdam UMC, Department of Epidemiology & Data Science (EDS), Bioinformatics Laboratory, Amsterdam, The Netherlands
| | - I N van Schaik
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - N de Vries
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Department of Rheumatology and Clinical Immunology, Amsterdam Rheumatology and Immunology Center (ARC), Amsterdam UMC, Amsterdam, The Netherlands
| | - F Eftimov
- Department of Neurology and Neurophysiology, Amsterdam Neuroscience, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
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7
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Offin M, Rusch VW, Rimner A, Adusumilli PS, Zauderer MG. Evolving Landscape of Initial Treatments for Patients with Malignant Pleural Mesotheliomas: Clinical Trials to Clinical Practice. Oncologist 2022; 27:610-614. [PMID: 35708504 PMCID: PMC9355824 DOI: 10.1093/oncolo/oyac113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/09/2022] [Indexed: 11/12/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is the most common form of mesothelioma and the type most often studied in prospective clinical trials.This review reports the trials that have shaped first-line treatment for patients with advanced/unresectable MPM and the real-world integration of first-line immune checkpoint inhibitors into clinical practice.
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Affiliation(s)
- Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
| | - Valerie W Rusch
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prasad S Adusumilli
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marjorie G Zauderer
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
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8
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Redwood AJ, Dick IM, Creaney J, Robinson BWS. What’s next in cancer immunotherapy? - The promise and challenges of neoantigen vaccination. Oncoimmunology 2022; 11:2038403. [PMID: 35186441 PMCID: PMC8855878 DOI: 10.1080/2162402x.2022.2038403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The process of tumorigenesis leaves a series of indelible genetic changes in tumor cells, that when expressed, have the potential to be tumor-specific immune targets. Neoantigen vaccines that capitalize on this potential immunogenicity have shown efficacy in preclinical models and have now entered clinical trials. Here we discuss the status of personalized neoantigen vaccines and the current major challenges to this nascent field. In particular, we focus on the types of antigens that can be targeted by vaccination and on the role that preexisting immunosuppression, and in particular T-cell exhaustion, will play in the development of effective cancer vaccines.
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Affiliation(s)
- Alec J. Redwood
- Institute of Respiratory Health, University of Western Australia, Perth,Australia
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
| | - Ian M. Dick
- Institute of Respiratory Health, University of Western Australia, Perth,Australia
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Jenette Creaney
- Institute of Respiratory Health, University of Western Australia, Perth,Australia
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
- School of Biomedical Sciences, University of Western Australia, Perth, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Australia
| | - Bruce W. S. Robinson
- Institute of Respiratory Health, University of Western Australia, Perth,Australia
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Australia
- Medical School, University of Western Australia, Perth, Australia
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9
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Lu C, Yang D, Klement JD, Colson YL, Oberlies NH, Pearce CJ, Colby AH, Grinstaff MW, Ding HF, Shi H, Liu K. G6PD functions as a metabolic checkpoint to regulate granzyme B expression in tumor-specific cytotoxic T lymphocytes. J Immunother Cancer 2022; 10:jitc-2021-003543. [PMID: 35017152 PMCID: PMC8753452 DOI: 10.1136/jitc-2021-003543] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 12/19/2022] Open
Abstract
Background Granzyme B is a key effector of cytotoxic T lymphocytes (CTLs), and its expression level positively correlates with the response of patients with mesothelioma to immune checkpoint inhibitor immunotherapy. Whether metabolic pathways regulate Gzmb expression in CTLs is incompletely understood. Methods A tumor-specific CTL and tumor coculture model and a tumor-bearing mouse model were used to determine the role of glucose-6-phosphate dehydrogenase (G6PD) in CTL function and tumor immune evasion. A link between granzyme B expression and patient survival was analyzed in human patients with epithelioid mesothelioma. Results Mesothelioma cells alone are sufficient to activate tumor-specific CTLs and to enhance aerobic glycolysis to induce a PD-1hi Gzmblo CTL phenotype. However, inhibition of lactate dehydrogenase A, the key enzyme of the aerobic glycolysis pathway, has no significant effect on tumor-induced CTL activation. Tumor cells induce H3K9me3 deposition at the promoter of G6pd, the gene that encodes the rate-limiting enzyme G6PD in the pentose phosphate pathway, to downregulate G6pd expression in tumor-specific CTLs. G6PD activation increases acetyl-coenzyme A (CoA) production to increase H3K9ac deposition at the Gzmb promoter and to increase Gzmb expression in tumor-specific CTLs converting them from a Gzmblo to a Gzmbhi phenotype, thus increasing CTL tumor lytic activity. Activation of G6PD increases Gzmb+ tumor-specific CTLs and suppresses tumor growth in tumor-bearing mice. Consistent with these findings, GZMB expression level was found to correlate with increased survival in patients with epithelioid mesothelioma. Conclusion G6PD is a metabolic checkpoint in tumor-activated CTLs. The H3K9me3/G6PD/acetyl-CoA/H3K9ac/Gzmb pathway is particularly important in CTL activation and immune evasion in epithelioid mesothelioma.
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Affiliation(s)
- Chunwan Lu
- School of Life Sciences, Tianjin University, Tianjin, China .,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA
| | - Dafeng Yang
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA.,Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - John D Klement
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA.,Charlie Norwood VA Medical Center, Augusta, GA, USA
| | - Yolonda L Colson
- Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA
| | | | - Aaron H Colby
- Ionic Pharmaceuticals, Brookline, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Mark W Grinstaff
- Ionic Pharmaceuticals, Brookline, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Han-Fei Ding
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA
| | - Huidong Shi
- Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, GA, USA .,Georgia Cancer Center, Medical College of Georgia, Augusta, GA, USA.,Charlie Norwood VA Medical Center, Augusta, GA, USA
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10
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Wang W, Ye LF, Bao H, Hu MT, Han M, Tang HM, Ren C, Wu X, Shao Y, Wang FH, Zhou ZW, Li YH, Xu RH, Wang DS. Heterogeneity and evolution of tumour immune microenvironment in metastatic gastroesophageal adenocarcinoma. Gastric Cancer 2022; 25:1017-1030. [PMID: 35904677 PMCID: PMC9587966 DOI: 10.1007/s10120-022-01324-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 07/16/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Tumour immune microenvironment heterogeneity is prevalent in numerous cancers and can negatively impact immunotherapy response. Immune heterogeneity and evolution in gastroesophageal adenocarcinoma (GEA) have not been studied in the past. METHODS Together with a multi-region sampling of normal, primary and metastatic tissues, we performed whole exome sequencing, TCR sequencing as well as immune cell infiltration estimation through deconvolution of gene expression signals. RESULTS We discovered high TCR repertoire and immune cell infiltration heterogeneity among metastatic sites, while they were homogeneous among primary and normal samples. Metastatic sites shared high levels of abundant TCR clonotypes with blood, indicating immune surveillance via blood. Metastatic sites also had low levels of tumour-eliminating immune cells and were undergoing heavy immunomodulation compared to normal and primary tumour tissues. There was co-evolution of neo-antigen and TCR repertoire, but only in patients with late diverging mutational evolution. Co-evolution of TCR repertoire and immune cell infiltration was seen in all except one patient. CONCLUSIONS Our findings revealed immune heterogeneity and co-evolution in GEA, which may inform immunotherapy decision-making.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Liu-Fang Ye
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060 People’s Republic of China ,Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dong feng, East Road, Guangzhou, 510060 People’s Republic of China
| | - Hua Bao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu China
| | - Ming-Tao Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060 People’s Republic of China ,Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dong feng, East Road, Guangzhou, 510060 People’s Republic of China
| | - Ming Han
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu China
| | - Hai-Meng Tang
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu China
| | - Chao Ren
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060 People’s Republic of China ,Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dong feng, East Road, Guangzhou, 510060 People’s Republic of China
| | - Xue Wu
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu China
| | - Yang Shao
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu China ,School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feng-Hua Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060 People’s Republic of China ,Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dong feng, East Road, Guangzhou, 510060 People’s Republic of China
| | - Zhi-Wei Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Department of Gastric Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, 510060 People’s Republic of China
| | - Yu-Hong Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060 People’s Republic of China ,Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dong feng, East Road, Guangzhou, 510060 People’s Republic of China
| | - Rui-Hua Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060 People’s Republic of China ,Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dong feng, East Road, Guangzhou, 510060 People’s Republic of China
| | - De-Shen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, 510060 People’s Republic of China ,Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060 People’s Republic of China ,Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dong feng, East Road, Guangzhou, 510060 People’s Republic of China
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11
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Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes. Nat Commun 2021; 12:6341. [PMID: 34732713 PMCID: PMC8566602 DOI: 10.1038/s41467-021-26505-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/06/2021] [Indexed: 12/21/2022] Open
Abstract
Young women's breast cancer (YWBC) has poor prognosis and known interactions with parity. Women diagnosed within 5-10 years of childbirth, defined as postpartum breast cancer (PPBC), have poorer prognosis compared to age, stage, and biologic subtype-matched nulliparous patients. Genomic differences that explain this poor prognosis remain unknown. In this study, using RNA expression data from clinically matched estrogen receptor positive (ER+) cases (n = 16), we observe that ER+ YWBC can be differentiated based on a postpartum or nulliparous diagnosis. The gene expression signatures of PPBC are consistent with increased cell cycle, T-cell activation and reduced estrogen receptor and TP53 signaling. When applied to a large YWBC cohort, these signatures for ER+ PPBC associate with significantly reduced 15-year survival rates in high compared to low expressing cases. Cumulatively these results provide evidence that PPBC is a unique entity within YWBC with poor prognostic phenotypes.
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12
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Casarrubios M, Cruz-Bermúdez A, Nadal E, Insa A, García Campelo MDR, Lázaro M, Dómine M, Majem M, Rodríguez-Abreu D, Martínez-Martí A, de Castro-Carpeño J, Cobo M, López-Vivanco G, Del Barco E, Bernabé Caro R, Viñolas N, Barneto Aranda I, Viteri S, Massuti B, Barquín M, Laza-Briviesca R, Sierra-Rodero B, Parra ER, Sanchez-Espiridion B, Rocha P, Kadara H, Wistuba II, Romero A, Calvo V, Provencio M. Pretreatment Tissue TCR Repertoire Evenness Is Associated with Complete Pathologic Response in Patients with NSCLC Receiving Neoadjuvant Chemoimmunotherapy. Clin Cancer Res 2021; 27:5878-5890. [PMID: 34376534 PMCID: PMC9401519 DOI: 10.1158/1078-0432.ccr-21-1200] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/01/2021] [Accepted: 08/03/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Characterization of the T-cell receptor (TCR) repertoire may be a promising source for predictive biomarkers of pathologic response to immunotherapy in locally advanced non-small cell lung cancer (NSCLC). EXPERIMENTAL DESIGN In this study, next-generation TCR sequencing was performed in peripheral blood and tissue samples of 40 patients with NSCLC, before and after neoadjuvant chemoimmunotherapy (NADIM clinical trial, NCT03081689), considering their complete pathologic response (CPR) or non-CPR. Beyond TCR metrics, tissue clones were ranked by their frequency and spatiotemporal evolution of top 1% clones was determined. RESULTS We have found a positive association between an uneven TCR repertoire in tissue samples at diagnosis and CPR at surgery. Moreover, TCR most frequently ranked clones (top 1%) present in diagnostic biopsies occupied greater frequency in the total clonal space of CPR patients, achieving an AUC ROC to identify CPR patients of 0.967 (95% confidence interval, 0.897-1.000; P = 0.001), and improving the results of PD-L1 tumor proportion score (TPS; AUC = 0.767; P = 0.026) or tumor mutational burden (TMB; AUC = 0.550; P = 0.687). Furthermore, tumors with high pretreatment top 1% clonal space showed similar immune cell populations but a higher immune reactive gene expression profile. Finally, the selective expansion of pretreatment tissue top 1% clones in peripheral blood of CPR patients suggests also a peripheral immunosurveillance, which could explain the high survival rate of these patients. CONCLUSIONS We have identified two parameters derived from TCR repertoire analysis that could outperform PD-L1 TPS and TMB as predictive biomarkers of CPR after neoadjuvant chemoimmunotherapy, and unraveled possible mechanisms of CPR involving enhanced tumor immunogenicity and peripheral immunosurveillance.
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Affiliation(s)
- Marta Casarrubios
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Alberto Cruz-Bermúdez
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain.,Corresponding Authors: Alberto Cruz-Bermúdez, Servicio de Oncología Médica, Instituto de Investigación, Sanitaria Puerta de Hierro, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid 28222, Spain. E-mail: ; and Mariano Provencio,
| | - Ernest Nadal
- Institut Català d'Oncologia, L'Hospitalet de Llobregat, L'Hospitalet De Llobregat, Barcelona, Spain
| | - Amelia Insa
- Fundación INCLIVA, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | | | | | - Manuel Dómine
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | | | | | - Alex Martínez-Martí
- Hospital Universitario e Instituto de Oncología Vall d'Hebron (VHIO), Barcelona, Spain
| | | | - Manuel Cobo
- Hospital Universitario Regional de Málaga, Málaga, Spain
| | | | | | | | | | | | - Santiago Viteri
- Instituto Oncológico Dr. Rosell. Hospital Universitario Quiron Dexeus, Grupo QuironSalud, Barcelona, Spain
| | | | - Miguel Barquín
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Raquel Laza-Briviesca
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Belén Sierra-Rodero
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Edwin R. Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pedro Rocha
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I. Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Atocha Romero
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Virginia Calvo
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Mariano Provencio
- Servicio de Oncología Médica, Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana (IDIPHISA), Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain.,Corresponding Authors: Alberto Cruz-Bermúdez, Servicio de Oncología Médica, Instituto de Investigación, Sanitaria Puerta de Hierro, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid 28222, Spain. E-mail: ; and Mariano Provencio,
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13
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Zhang S, Gong C, Ruiz-Martinez A, Wang H, Davis-Marcisak E, Deshpande A, Popel AS, Fertig EJ. Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response. ACTA ACUST UNITED AC 2021; 1-2. [PMID: 34708216 PMCID: PMC8547770 DOI: 10.1016/j.immuno.2021.100002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Response to cancer immunotherapies depends on the complex and dynamic interactions between T cell recognition and killing of cancer cells that are counteracted through immunosuppressive pathways in the tumor microenvironment. Therefore, while measurements such as tumor mutational burden provide biomarkers to select patients for immunotherapy, they neither universally predict patient response nor implicate the mechanisms that underlie immunotherapy resistance. Recent advances in single-cell RNA sequencing technology measure cellular heterogeneity within cells of an individual tumor but have yet to realize the promise of predictive oncology. In addition to data, mechanistic multiscale computational models are developed to predict treatment response. Incorporating single-cell data from tumors to parameterize these computational models provides deeper insights into prediction of clinical outcome in individual patients. Here, we integrate whole-exome sequencing and scRNA-seq data from Triple-Negative Breast Cancer patients to model neoantigen burden in tumor cells as input to a spatial Quantitative System Pharmacology model. The model comprises a four-compartmental Quantitative System Pharmacology sub-model to represent a whole patient and a spatial agent-based sub-model to represent tumor volumes at the cellular scale. We use the high-throughput single-cell data to model the role of antigen burden and heterogeneity relative to the tumor microenvironment composition on predicted immunotherapy response. We demonstrate how this integrated modeling and single-cell analysis framework can be used to relate neoantigen heterogeneity to immunotherapy treatment outcomes. Our results demonstrate feasibility of merging single-cell data to initialize cell states in multiscale computational models such as the spQSP for personalized prediction of clinical outcomes to immunotherapy.
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Affiliation(s)
- Shuming Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Chang Gong
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alvaro Ruiz-Martinez
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Emily Davis-Marcisak
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Atul Deshpande
- Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Elana J Fertig
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Oncology and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, United States
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14
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Shevyrev D, Tereshchenko V, Kozlov V. Immune Equilibrium Depends on the Interaction Between Recognition and Presentation Landscapes. Front Immunol 2021; 12:706136. [PMID: 34394106 PMCID: PMC8362327 DOI: 10.3389/fimmu.2021.706136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
In this review, we described the structure and organization of antigen-recognizing repertoires of B and T cells from the standpoint of modern immunology. We summarized the latest advances in bioinformatics analysis of sequencing data from T and B cell repertoires and also presented contemporary ideas about the mechanisms of clonal diversity formation at different stages of organism development. At the same time, we focused on the importance of the allelic variants of the HLA genes and spectra of presented antigens for the formation of T-cell receptors (TCR) landscapes. The main idea of this review is that immune equilibrium and proper functioning of immunity are highly dependent on the interaction between the recognition and the presentation landscapes of antigens. Certain changes in these landscapes can occur during life, which can affect the protective function of adaptive immunity. We described some mechanisms associated with these changes, for example, the conversion of effector cells into regulatory cells and vice versa due to the trans-differentiation or bystander effect, changes in the clonal organization of the general TCR repertoire due to homeostatic proliferation or aging, and the background for the altered presentation of some antigens due to SNP mutations of MHC, or the alteration of the presenting antigens due to post-translational modifications. The authors suggest that such alterations can lead to an increase in the risk of the development of oncological and autoimmune diseases and influence the sensitivity of the organism to different infectious agents.
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Affiliation(s)
- Daniil Shevyrev
- Laboratory of Clinical Immunopathology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Valeriy Tereshchenko
- Laboratory of Molecular Immunology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Vladimir Kozlov
- Laboratory of Clinical Immunopathology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
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15
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Yan D, Yang J, Ji Z, Wang J, Lu X, Huang Y, Zhong C, Li L. Profiling T cell receptor β-chain in responders after immunization with recombinant hepatitis B vaccine. J Gene Med 2021; 23:e3367. [PMID: 34048625 DOI: 10.1002/jgm.3367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/22/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND T cells with edited T cell receptor β-chain variable (TRBV) are involved in the immune response to recombinant hepatitis B surface antigen (rHBsAg) vaccine and the production of hepatitis B surface antibody (HBsAb). The immune repertoire (IR) profile and mechanism of vaccination positive responders (VPR) with rHBsAg are not fully understood. METHODS The IR of six VPRs (HBsAb+, HbsAg-) with rHBsAg vaccination was established by the high throughput sequencing technique and bioinformatics analysis and compared with those in five vaccination negative responders (VNRs) (HbsAb-, HbsAg-) who were also inoculated with rHBsAg. The repertoire features of the BV, BJ and V (CDR3) J genes and immune diversity in peripheral blood mononuclear cells, respectively, were analyzed for each subject. RESULTS There was no significant difference in sequencing amplification indices of each sample. However, TRBV15/BJ2-3 demonstrated significantly high expression levels in VPR compared to those in the VNR group (both p < 0.05). Further results showed that the BV15/BJ2-5 level was significantly increased for VPR compared to that of VNR group. Interestingly, the motif of CDR3 in TRBV15/BJ2-5 was mostly expressed as "GGETQ" or "GETQ". Additionally, there was no remarkable difference between the two groups of distribution with respect to the different clone expression levels of V (CDR3) J. CONCLUSIONS The features of IR in the VPR and VNR will contribute to the exploration of the mechanism of the positive response to rHBsAg, and also contribute to development of optimized hepatitis B vaccine, in addition to providing a partial interpretation of the VNR who has a relatively low infection with HBV.
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Affiliation(s)
- Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongkang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ju Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yandi Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengli Zhong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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16
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Dumoulin DW, Cornelissen R, Bezemer K, Baart SJ, Aerts JGJV. Long-Term Follow-Up of Mesothelioma Patients Treated with Dendritic Cell Therapy in Three Phase I/II Trials. Vaccines (Basel) 2021; 9:vaccines9050525. [PMID: 34069348 PMCID: PMC8158710 DOI: 10.3390/vaccines9050525] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/29/2022] Open
Abstract
Background: Malignant pleural mesothelioma (MPM) is a fatal neoplasm with, if untreated, poor survival of approximately nine months from diagnosis. Until recently, phase II–III immunotherapy trials did not show any significant benefit. The lack of immunotherapy efficacy can be explained by the fact that mesothelioma is a tumor with an “immune desert” phenotype, meaning a non-inflamed tumor characterized by low T-cell infiltration. By administration of DCs, which were ex-vivo cultured, exposed to (tumor-associated) antigens, and subsequently activated, this “immune desert” phenotype might be turned into an “inflamed” phenotype. Three phase I/II studies have been performed and published using activated DCs, which support this concept. We here report on the long-term survival of patients treated with DCs in three phase I/II studies. Methods: Survival data of the phase I/II trials using DC therapy in MPM patients were obtained and subsequently analyzed. In the first two trials, DCs were loaded with autologous tumor lysate. In the third trial, DCs were loaded with allogeneic mesothelioma tumor cell line lysate. Results: In the three studies combined, 29 patients with MPM were treated with DC vaccination between 2006 and 2015. At data cut-off, the median OS was 27 months (95% CI: 21–47 months). OS at 2 years was 55.2% (95% CI: 39.7–76.6%), and OS at 5 years was 20.7% (95% CI: 10.1–42.2%). Conclusions: The long-term survival of DC therapy in MPM in these three trials is promising, which is the basis for the randomized phase II/III DENIM study. This DENIM study is currently enrolling, and the results of which have to be awaited for definite conclusions.
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Affiliation(s)
- Daphne W. Dumoulin
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (R.C.); (K.B.); (J.G.J.V.A.)
- Correspondence:
| | - Robin Cornelissen
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (R.C.); (K.B.); (J.G.J.V.A.)
| | - Koen Bezemer
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (R.C.); (K.B.); (J.G.J.V.A.)
| | - Sara J. Baart
- Department of Biostatistics, Erasmus MC, 3015 GD Rotterdam, The Netherlands;
| | - Joachim G. J. V. Aerts
- Department of Pulmonary Medicine, Erasmus MC Cancer Institute, 3015 GD Rotterdam, The Netherlands; (R.C.); (K.B.); (J.G.J.V.A.)
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17
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Gray SG. Emerging avenues in immunotherapy for the management of malignant pleural mesothelioma. BMC Pulm Med 2021; 21:148. [PMID: 33952230 PMCID: PMC8097826 DOI: 10.1186/s12890-021-01513-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The role of immunotherapy in cancer is now well-established, and therapeutic options such as checkpoint inhibitors are increasingly being approved in many cancers such as non-small cell lung cancer (NSCLC). Malignant pleural mesothelioma (MPM) is a rare orphan disease associated with prior exposure to asbestos, with a dismal prognosis. Evidence from clinical trials of checkpoint inhibitors in this rare disease, suggest that such therapies may play a role as a treatment option for a proportion of patients with this cancer. MAIN TEXT While the majority of studies currently focus on the established checkpoint inhibitors (CTLA4 and PD1/PDL1), there are many other potential checkpoints that could also be targeted. In this review I provide a synopsis of current clinical trials of immunotherapies in MPM, explore potential candidate new avenues that may become future targets for immunotherapy and discuss aspects of immunotherapy that may affect the clinical outcomes of such therapies in this cancer. CONCLUSIONS The current situation regarding checkpoint inhibitors in the management of MPM whilst encouraging, despite impressive durable responses, immune checkpoint inhibitors do not provide a long-term benefit to the majority of patients with cancer. Additional studies are therefore required to further delineate and improve our understanding of both checkpoint inhibitors and the immune system in MPM. Moreover, many new potential checkpoints have yet to be studied for their therapeutic potential in MPM. All these plus the existing checkpoint inhibitors will require the development of new biomarkers for patient stratification, response and also for predicting or monitoring the emergence of resistance to these agents in MPM patients. Other potential therapeutic avenues such CAR-T therapy or treatments like oncolytic viruses or agents that target the interferon pathway designed to recruit more immune cells to the tumor also hold great promise in this hard to treat cancer.
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Affiliation(s)
- Steven G Gray
- Thoracic Oncology Research Group, Central Pathology Laboratory, CPL 30, TCDSJ Cancer Institute, St James's Hospital, Dublin, D08 RX0X, Ireland.
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland.
- School of Biology, Technical University of Dublin, Dublin, Ireland.
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Cancer neoantigens as potential targets for immunotherapy. Clin Exp Metastasis 2021; 39:51-60. [PMID: 33950415 PMCID: PMC8097110 DOI: 10.1007/s10585-021-10091-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022]
Abstract
Immune checkpoint inhibitors (ICIs) targeting the cytotoxic T-lymphocyte-associated protein-4 (CTLA-4) and programed cell death protein 1 (PD-1) or its ligand PD-L1 have increased the survival and cure rates for patients with many cancer types in various disease settings. However, only 10–40% of cancer patients benefited from these ICIs, of whom ~ 20% have treatment interruption or discontinuation due to immune-related adverse events that can be severe and even fatal. Current efforts in precision immunotherapy are focused on improving biomarker-based patient selection for currently available ICIs and exploring rationale combination and novel strategies to expand the benefit of immunotherapy to more cancer patients. Neoantigens arise from ~ 10% of the non-synonymous somatic mutations in cancer cells, are important targets of T cell-mediated anti-tumor immunity for individual patients. Advances in next generation sequencing technology and computational bioinformatics have enable the identification of genomic alterations, putative neoantigens, and gene expression profiling in individual tumors for personal oncology in a rapid and cost-effective way. Among the genomic biomarkers, defective mismatch DNA repair (dMMR), microsatellite instability high (MSI-H) and high tumor mutational burden (H-TMB) have received FDA approvals for selecting patients for ICI treatment. All these biomarkers measure high neoantigen load and tumor antigenicity, supporting the current development of neoantigen-based personalized cancer vaccines for patients with high TMB tumor. Several studies have shown neoantigen vaccines are feasible, safe and have promising clinical activity in patients with high TMB tumors in both metastatic and adjuvant settings. This review summarizes the emerging data and technologies for neoantigen-based personalized immunotherapy.
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Bracci L, Fragale A, Gabriele L, Moschella F. Towards a Systems Immunology Approach to Unravel Responses to Cancer Immunotherapy. Front Immunol 2020; 11:582744. [PMID: 33193392 PMCID: PMC7649803 DOI: 10.3389/fimmu.2020.582744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
Immunotherapy, particularly immune checkpoint blockade and chimeric antigen receptor (CAR)-T cells, holds a great promise against cancer. These treatments have markedly improved survival in solid as well as in hematologic tumors previously considered incurable. However, durable responses occur in a fraction of patients, and existing biomarkers (e.g. PD-L1) have shown limited prediction power. This scenario highlights the need to dissect the complex interplay between immune and tumor cells to identify reliable biomarkers of response to be used for patients’ selection. In this context, systems immunology represents indeed the new frontier to address important clinical challenges in biomarker discovery. Through the integration of multiple layers of data obtained with several high-throughput approaches, systems immunology may give insights on the vast range of inter-individual differences and on the influences of genes and factors that cooperatively shape the individual immune response to a given treatment. In this Mini Review, we give an overview of the current high-throughput methodologies, including genomics, epigenomics, transcriptomics, metabolomics, proteomics, and multi-parametric phenotyping suitable for systems immunology as well as on the key steps of data integration and biological interpretation. Additionally, we review recent studies in which multi-omics technologies have been used to characterize mechanisms of response and to identify powerful biomarkers of response to checkpoint inhibitors, CAR-T cell therapy, dendritic cell-based and peptide-based cancer vaccines. We also highlight the need of favoring the collaboration of researchers with complementary expertise and of integrating multi-omics data into biological networks with the final goal of developing accurate markers of therapeutic response.
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Affiliation(s)
- Laura Bracci
- Tumor Immunology Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Fragale
- Tumor Immunology Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Gabriele
- Tumor Immunology Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Federica Moschella
- Tumor Immunology Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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