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Gupta V, Vashisht V, Vashisht A, Mondal AK, Alptekin A, Singh H, Kolhe R. Comprehensive Analysis of Clinically Relevant Copy Number Alterations (CNAs) Using a 523-Gene Next-Generation Sequencing Panel and NxClinical Software in Solid Tumors. Genes (Basel) 2024; 15:396. [PMID: 38674331 PMCID: PMC11049607 DOI: 10.3390/genes15040396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Copy number alterations (CNAs) are significant in tumor initiation and progression. Identifying these aberrations is crucial for targeted therapies and personalized cancer diagnostics. Next-generation sequencing (NGS) methods present advantages in scalability and cost-effectiveness, surpassing limitations associated with reference assemblies and probe capacities in traditional laboratory approaches. This retrospective study evaluated CNAs in 50 FFPE tumor samples (breast cancer, ovarian carcinoma, pancreatic cancer, melanoma, and prostate carcinoma) using Illumina's TruSight Oncology 500 (TSO500) and the Affymetrix Oncoscan Molecular Inversion Probe (OS-MIP) (ThermoFisher Scientific, Waltham, MA, USA). NGS analysis with the NxClinical 6.2 software demonstrated a high sensitivity and specificity (100%) for CNA detection, with a complete concordance rate as compared to the OS-MIP. All 54 known CNAs were identified by NGS, with gains being the most prevalent (63%). Notable CNAs were observed in MYC (18%), TP53 (12%), BRAF (8%), PIK3CA, EGFR, and FGFR1 (6%) genes. The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis.
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Affiliation(s)
- Vivek Gupta
- Department of Pathology, Government Institute of Medical Sciences, Greater Noida 201310, India;
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Vishakha Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ahmet Alptekin
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (V.V.); (A.V.); (A.K.M.); (A.A.); (H.S.)
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Hu J, Ascierto P, Cesano A, Herrmann V, Marincola FM. Shifting the paradigm: engaging multicellular networks for cancer therapy. J Transl Med 2024; 22:270. [PMID: 38475820 PMCID: PMC10936124 DOI: 10.1186/s12967-024-05043-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/01/2023] [Indexed: 03/14/2024] Open
Abstract
Most anti-cancer modalities are designed to directly kill cancer cells deploying mechanisms of action (MOAs) centered on the presence of a precise target on cancer cells. The efficacy of these approaches is limited because the rapidly evolving genetics of neoplasia swiftly circumvents the MOA generating therapy-resistant cancer cell clones. Other modalities engage endogenous anti-cancer mechanisms by activating the multi-cellular network (MCN) surrounding neoplastic cells in the tumor microenvironment (TME). These modalities hold a better chance of success because they activate numerous types of immune effector cells that deploy distinct cytotoxic MOAs. This in turn decreases the chance of developing treatment-resistance. Engagement of the MCN can be attained through activation of immune effector cells that in turn kill cancer cells or when direct cancer killing is complemented by the production of proinflammatory factors that secondarily recruit and activate immune effector cells. For instance, adoptive cell therapy (ACT) supplements cancer cell killing with the release of homeostatic and pro-inflammatory cytokines by the immune cells and damage associated molecular patterns (DAMPs) by dying cancer cells. The latter phenomenon, referred to as immunogenic cell death (ICD), results in an exponential escalation of anti-cancer MOAs at the tumor site. Other approaches can also induce exponential cancer killing by engaging the MCN of the TME through the release of DAMPs and additional pro-inflammatory factors by dying cancer cells. In this commentary, we will review the basic principles that support emerging paradigms likely to significantly improve the efficacy of anti-cancer therapy.
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Affiliation(s)
- Joyce Hu
- Sonata Therapeutics, Watertown, MA, 02472, USA.
| | - Paolo Ascierto
- Cancer Immunotherapy and Innovative Therapy, National Tumor Institute, Fondazione G. Pascale, 80131, Naples, Italy
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3
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de Mello RA, Perez KR, Vazquez TP. Current and future trends in neoadjuvant immunotherapy for the treatment of triple-negative breast cancer. Immunotherapy 2024; 16:257-266. [PMID: 38197149 DOI: 10.2217/imt-2022-0277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024] Open
Abstract
Triple-negative breast cancer (TNBC) comprises 15-20% of all breast cancers (BC). Lacking targeted therapy options, TNBC becomes the focal point of clinical investigations aiming not only to identify drugs with enhanced response potential but also to uncover new immunological and/or metabolic pathways conducive to more effective treatments. Currently, neoadjuvant treatment for TNBC relies on standard chemotherapy in conjunction with immunotherapy, given the improved response observed with this drug combination. This review delves into the latest therapeutic updates in TNBC treatment and explores potential advancements shaping the future landscape of this disease in the neoadjuvant setting.
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Affiliation(s)
- Ramon Andrade de Mello
- Department of Oncology, Oxford Cancer Center, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, OX3 7LE, Oxford, UK
- Department of Oncology, University of Oxford, OX3 7ER, Oxford, UK
- Post Graduation Program in Medicine, Faculty of Medicine, Nine of July University, 015250-000, São Paulo, Brazil
| | - Kátia Roque Perez
- Post Graduation Program in Medicine, Faculty of Medicine, Nine of July University, 015250-000, São Paulo, Brazil
- Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru
| | - Thais Pérez Vazquez
- São Paulo Cancer Institute, University of São Paulo, São Paulo, 01246-000, Brazil
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4
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Fang Q, Shen G, Xie Q, Guan Y, Liu X, Ren D, Zhao F, Liu Z, Ma F, Zhao J. Development of Tumor Markers for Breast Cancer Immunotherapy. Curr Mol Med 2024; 24:547-564. [PMID: 37157196 DOI: 10.2174/1566524023666230508152817] [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] [Received: 01/02/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 05/10/2023]
Abstract
Although breast cancer treatment has been developed remarkably in recent years, it remains the primary cause of death among women. Immune checkpoint blockade therapy has significantly altered the way breast cancer is treated, although not all patients benefit from the changes. At present, the most effective mechanism of immune checkpoint blockade application in malignant tumors is not clear and efficacy may be influenced by many factors, including host, tumor, and tumor microenvironment dynamics. Therefore, there is a pressing need for tumor immunomarkers that can be used to screen patients and help determine which of them would benefit from breast cancer immunotherapy. At present, no single tumor marker can predict treatment efficacy with sufficient accuracy. Multiple markers may be combined to more accurately pinpoint patients who will respond favorably to immune checkpoint blockade medication. In this review, we have examined the breast cancer treatments, developments in research on the role of tumor markers in maximizing the clinical efficacy of immune checkpoint inhibitors, prospects for the identification of novel therapeutic targets, and the creation of individualized treatment plans. We also discuss how tumor markers can provide guidance for clinical practice.
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Affiliation(s)
- Qianqian Fang
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Guoshuang Shen
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Qiqi Xie
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Yumei Guan
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Xinlan Liu
- Department of Oncology, General Hospital of Ningxia Medical University, No. 804 Shengli Road, Xingqing District, Yinchuan, 750004, China
| | - Dengfeng Ren
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Fuxing Zhao
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Zhilin Liu
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Jiuda Zhao
- Breast Disease Diagnosis and Treatment Center of Affiliated Hospital of Qinghai University & Affiliated Cancer Hospital of Qinghai University, Xining, 810000, China
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Mall R, Kanneganti TD. Comparative analysis identifies genetic and molecular factors associated with prognostic clusters of PANoptosis in glioma, kidney and melanoma cancer. Sci Rep 2023; 13:20962. [PMID: 38017056 PMCID: PMC10684528 DOI: 10.1038/s41598-023-48098-1] [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] [Received: 05/27/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023] Open
Abstract
The importance of inflammatory cell death, PANoptosis, in cancer is increasingly being recognized. PANoptosis can promote or inhibit tumorigenesis in context-dependent manners, and a computational approach leveraging transcriptomic profiling of genes involved in PANoptosis has shown that patients can be stratified into PANoptosis High and PANoptosis Low clusters that have significant differences in overall survival for low grade glioma (LGG), kidney renal cell carcinoma (KIRC) and skin cutaneous melanoma (SKCM). However, the molecular mechanisms that contribute to differential prognosis between PANoptosis clusters require further elucidation. Therefore, we performed a comprehensive comparison of genetic, genomic, tumor microenvironment, and pathway characteristics between the PANoptosis High and PANoptosis Low clusters to determine the relevance of each component in driving the differential associations with prognosis for LGG, KIRC and SKCM. Across these cancer types, we found that activation of the proliferation pathway was significantly different between PANoptosis High and Low clusters. In LGG and SKCM, we also found that aneuploidy and immune cell densities and activations contributed to differences in PANoptosis clusters. In individual cancers, we identified important roles for barrier gene pathway activation (in SKCM) and the somatic mutation profiles of driver oncogenes as well as hedgehog signaling pathway activation (in LGG). By identifying these genetic and molecular factors, we can possibly improve the prognosis for at risk-stratified patient populations based on the PANoptosis phenotype in LGG, KIRC and SKCM. This not only advances our mechanistic understanding of cancer but will allow for the selection of optimal treatment strategies.
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Affiliation(s)
- Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, MS #351, 262 Danny Thomas Place, Memphis, TN, 38105-2794, USA
- Biotechnology Research Center, Technology Innovation Institute, P.O. Box 9639, Abu Dhabi, United Arab Emirates
| | - Thirumala-Devi Kanneganti
- Department of Immunology, St. Jude Children's Research Hospital, MS #351, 262 Danny Thomas Place, Memphis, TN, 38105-2794, USA.
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Noviello TMR, Di Giacomo AM, Caruso FP, Covre A, Mortarini R, Scala G, Costa MC, Coral S, Fridman WH, Sautès-Fridman C, Brich S, Pruneri G, Simonetti E, Lofiego MF, Tufano R, Bedognetti D, Anichini A, Maio M, Ceccarelli M. Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial. Nat Commun 2023; 14:5914. [PMID: 37739939 PMCID: PMC10516894 DOI: 10.1038/s41467-023-40994-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 08/18/2023] [Indexed: 09/24/2023] Open
Abstract
Association with hypomethylating agents is a promising strategy to improve the efficacy of immune checkpoint inhibitors-based therapy. The NIBIT-M4 was a phase Ib, dose-escalation trial in patients with advanced melanoma of the hypomethylating agent guadecitabine combined with the anti-CTLA-4 antibody ipilimumab that followed a traditional 3 + 3 design (NCT02608437). Patients received guadecitabine 30, 45 or 60 mg/m2/day subcutaneously on days 1 to 5 every 3 weeks starting on week 0 for a total of four cycles, and ipilimumab 3 mg/kg intravenously starting on day 1 of week 1 every 3 weeks for a total of four cycles. Primary outcomes of safety, tolerability, and maximum tolerated dose of treatment were previously reported. Here we report the 5-year clinical outcome for the secondary endpoints of overall survival, progression free survival, and duration of response, and an exploratory integrated multi-omics analysis on pre- and on-treatment tumor biopsies. With a minimum follow-up of 45 months, the 5-year overall survival rate was 28.9% and the median duration of response was 20.6 months. Re-expression of immuno-modulatory endogenous retroviruses and of other repetitive elements, and a mechanistic signature of guadecitabine are associated with response. Integration of a genetic immunoediting index with an adaptive immunity signature stratifies patients/lesions into four distinct subsets and discriminates 5-year overall survival and progression free survival. These results suggest that coupling genetic immunoediting with activation of adaptive immunity is a relevant requisite for achieving long term clinical benefit by epigenetic immunomodulation in advanced melanoma patients.
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Affiliation(s)
- Teresa Maria Rosaria Noviello
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
| | - Anna Maria Di Giacomo
- University of Siena, Siena, Italy
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
- NIBIT Foundation Onlus, Siena, Italy
| | - Francesca Pia Caruso
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Naples, Italy
| | | | - Roberta Mortarini
- Human Tumors Immunobiology Unit, Dept. of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Maria Claudia Costa
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Naples, Italy
| | | | - Wolf H Fridman
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Team Cancer, Immune Control and Escape, Paris, France
- University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Catherine Sautès-Fridman
- INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Team Cancer, Immune Control and Escape, Paris, France
- University Paris Descartes Paris 5, Sorbonne Paris Cite, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne University, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - Silvia Brich
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Simonetti
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy
| | | | - Rossella Tufano
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Davide Bedognetti
- Cancer Program, Human Immunology Department, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Andrea Anichini
- Human Tumors Immunobiology Unit, Dept. of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Michele Maio
- University of Siena, Siena, Italy.
- Center for Immuno-Oncology, University Hospital of Siena, Siena, Italy.
- NIBIT Foundation Onlus, Siena, Italy.
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
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7
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Mogenet A, Finetti P, Denicolai E, Greillier L, Boudou-Rouquette P, Goldwasser F, Lumet G, Ceccarelli M, Birnbaum D, Bedognetti D, Mamessier E, Barlesi F, Bertucci F, Tomasini P. Immunologic constant of rejection as a predictive biomarker of immune checkpoint inhibitors efficacy in non-small cell lung cancer. J Transl Med 2023; 21:637. [PMID: 37726776 PMCID: PMC10507965 DOI: 10.1186/s12967-023-04463-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 08/22/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Anti-PD1/PDL1 immune checkpoint inhibitors (ICI) transformed the prognosis of patients with advanced non-small cell lung cancer (NSCLC). However, the response rate remains disappointing and toxicity may be life-threatening, making urgent identification of biomarkers predictive for efficacy. Immunologic Constant of Rejection signature (ICR) is a 20-gene expression signature of cytotoxic immune response with prognostic value in some solid cancers. Our objective was to assess its predictive value for benefit from anti-PD1/PDL1 in patients with advanced NSCLC. METHODS We retrospectively profiled 44 primary tumors derived from NSCLC patients treated with ICI as single-agent in at least the second-line metastatic setting. Transcriptomic analysis was performed using the nCounter® analysis system and the PanCancer Immune Profiling Panel. We then pooled our data with clinico-biological data from four public gene expression data sets, leading to a total of 162 NSCLC patients treated with single-agent anti-PD1/PDL1. ICR was applied to all samples and correlation was searched between ICR classes and the Durable Clinical Benefit (DCB), defined as stable disease or objective response according to RECIST 1.1 for a minimum of 6 months after the start of ICI. RESULTS The DCB rate was 29%; 22% of samples were classified as ICR1, 30% ICR2, 22% ICR3, and 26% ICR4. These classes were not associated with the clinico-pathological variables, but showed enrichment from ICR1 to ICR4 in quantitative/qualitative markers of immune response. ICR2-4 class was associated with a 5.65-fold DCB rate when compared with ICR1 class. In multivariate analysis, ICR classification remained associated with DCB, independently from PDL1 expression and other predictive immune signatures. By contrast, it was not associated with disease-free survival in 556 NSCLC TCGA patients untreated with ICI. CONCLUSION The 20-gene ICR signature was independently associated with benefit from anti-PD1/PDL1 ICI in patients with advanced NSCLC. Validation in larger retrospective and prospective series is warranted.
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Affiliation(s)
- Alice Mogenet
- Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille Univ, APHM, INSERM, CNRS, CRCM, Hôpital Nord, Marseille, France
| | - Pascal Finetti
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR1068, CNRS UMR725, Laboratoire d'Oncologie Prédictive, Aix Marseille Univ, Marseille, France
| | - Emilie Denicolai
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR1068, CNRS UMR725, Laboratoire d'Oncologie Prédictive, Aix Marseille Univ, Marseille, France
| | - Laurent Greillier
- Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille Univ, APHM, INSERM, CNRS, CRCM, Hôpital Nord, Marseille, France
| | - Pascaline Boudou-Rouquette
- Department of Medical Oncology, Cochin Hospital, AP-HP, Paris, France-University of Paris Descartes, ARIANE, CARPEM, Paris, France
| | - François Goldwasser
- Department of Medical Oncology, Cochin Hospital, AP-HP, Paris, France-University of Paris Descartes, ARIANE, CARPEM, Paris, France
| | - Gwenael Lumet
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR1068, CNRS UMR725, Laboratoire d'Oncologie Prédictive, Aix Marseille Univ, Marseille, France
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Daniel Birnbaum
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR1068, CNRS UMR725, Laboratoire d'Oncologie Prédictive, Aix Marseille Univ, Marseille, France
| | - Davide Bedognetti
- Division of Translational Medicine, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Emilie Mamessier
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR1068, CNRS UMR725, Laboratoire d'Oncologie Prédictive, Aix Marseille Univ, Marseille, France
| | - Fabrice Barlesi
- Paris-Saclay University and Medical Oncology, Gustave Roussy, Cancer Campus, Villejuif, France
| | - François Bertucci
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR1068, CNRS UMR725, Laboratoire d'Oncologie Prédictive, Aix Marseille Univ, Marseille, France.
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix Marseille Univ, 232, Bd de Sainte-Marguerite, 13009, Marseille, France.
| | - Pascale Tomasini
- Multidisciplinary Oncology and Therapeutic Innovations Department, Aix Marseille Univ, APHM, INSERM, CNRS, CRCM, Hôpital Nord, Marseille, France
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM UMR1068, CNRS UMR725, Laboratoire d'Oncologie Prédictive, Aix Marseille Univ, Marseille, France
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8
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Riley-Gillis B, Tsaih SW, King E, Wollenhaupt S, Reeb J, Peck AR, Wackman K, Lemke A, Rui H, Dezso Z, Flister MJ. Machine learning reveals genetic modifiers of the immune microenvironment of cancer. iScience 2023; 26:107576. [PMID: 37664640 PMCID: PMC10470213 DOI: 10.1016/j.isci.2023.107576] [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: 01/06/2023] [Revised: 05/01/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Heritability in the immune tumor microenvironment (iTME) has been widely observed yet remains largely uncharacterized. Here, we developed a machine learning approach to map iTME modifiers within loci from genome-wide association studies (GWASs) for breast cancer (BrCa) incidence. A random forest model was trained on a positive set of immune-oncology (I-O) targets, and then used to assign I-O target probability scores to 1,362 candidate genes in linkage disequilibrium with 155 BrCa GWAS loci. Cluster analysis of the most probable candidates revealed two subfamilies of genes related to effector functions and adaptive immune responses, suggesting that iTME modifiers impact multiple aspects of anticancer immunity. Two of the top ranking BrCa candidates, LSP1 and TLR1, were orthogonally validated as iTME modifiers using BrCa patient biopsies and comparative mapping studies, respectively. Collectively, these data demonstrate a robust and flexible framework for functionally fine-mapping GWAS risk loci to identify translatable therapeutic targets.
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Affiliation(s)
- Bridget Riley-Gillis
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Shirng-Wern Tsaih
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Emily King
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Amy R. Peck
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Kelsey Wackman
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Angela Lemke
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Zoltan Dezso
- Genomics Research Center, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA 94080, USA
| | - Michael J. Flister
- Genomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA
- Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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9
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Venetis K, Sajjadi E, Ivanova M, Peccatori FA, Fusco N, Guerini-Rocco E. Characterization of the immune environment in pregnancy-associated breast cancer. Future Oncol 2023. [PMID: 37376974 DOI: 10.2217/fon-2022-1321] [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: 06/29/2023] Open
Abstract
Pregnancy-associated breast cancer (PrBC) is a rare and clinically challenging condition. Specific immune mechanisms and pathways are involved in maternal-fetal tolerance and tumor-host immunoediting. The comprehension of the molecular processes underpinning this immune synergy in PrBC is needed to improve patients' clinical management. Only a few studies focused on the immune biology of PrBC and attempted to identify bona fide biomarkers. Therefore, clinically actionable information remains extremely puzzling for these patients. In this review article, we discuss the current knowledge on the immune environment of PrBC, in comparison with pregnancy-unrelated breast cancer and in the context of maternal immune changes during pregnancy. A particular emphasis is given to the actual role of potential immune-related biomarkers for PrBC clinical management.
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Affiliation(s)
- Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
| | - Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Fedro Alessandro Peccatori
- Fertility & Procreation Unit, Division of Gynecologic Oncology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, 20141, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, Milan, 20122, Italy
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10
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Roelands J, Kuppen PJK, Ahmed EI, Mall R, Masoodi T, Singh P, Monaco G, Raynaud C, de Miranda NFCC, Ferraro L, Carneiro-Lobo TC, Syed N, Rawat A, Awad A, Decock J, Mifsud W, Miller LD, Sherif S, Mohamed MG, Rinchai D, Van den Eynde M, Sayaman RW, Ziv E, Bertucci F, Petkar MA, Lorenz S, Mathew LS, Wang K, Murugesan S, Chaussabel D, Vahrmeijer AL, Wang E, Ceccarelli A, Fakhro KA, Zoppoli G, Ballestrero A, Tollenaar RAEM, Marincola FM, Galon J, Khodor SA, Ceccarelli M, Hendrickx W, Bedognetti D. An integrated tumor, immune and microbiome atlas of colon cancer. Nat Med 2023; 29:1273-1286. [PMID: 37202560 PMCID: PMC10202816 DOI: 10.1038/s41591-023-02324-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/28/2023] [Indexed: 05/20/2023]
Abstract
The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches.
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Affiliation(s)
- Jessica Roelands
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Eiman I Ahmed
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi, United Arab Emirates
| | - Tariq Masoodi
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Parul Singh
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Gianni Monaco
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Neuropathology, Medical Center-University of Freiburg, Freiburg, Germany
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
| | - Christophe Raynaud
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | | | - Luigi Ferraro
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples Federico II, Naples, Italy
| | | | - Najeeb Syed
- Integrated Genomics Services, Research Branch, Sidra Medicine, Doha, Qatar
| | - Arun Rawat
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Amany Awad
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - William Mifsud
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Weill-Cornell Medicine Qatar, Doha, Qatar
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Shimaa Sherif
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Mahmoud G Mohamed
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Women's Wellness and Research Center, Hamad Medical Corporation, Doha, Qatar
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
| | - Darawan Rinchai
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Marc Van den Eynde
- Institut Roi Albert II, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | - Rosalyn W Sayaman
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Francois Bertucci
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, Marseille, France
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Mahir Abdulla Petkar
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Stephan Lorenz
- Integrated Genomics Services, Research Branch, Sidra Medicine, Doha, Qatar
| | - Lisa Sara Mathew
- Integrated Genomics Services, Research Branch, Sidra Medicine, Doha, Qatar
| | - Kun Wang
- Integrated Genomics Services, Research Branch, Sidra Medicine, Doha, Qatar
| | | | - Damien Chaussabel
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Computational Sciences Department, The Jackson Laboratory, Farmington, CT, USA
| | | | - Ena Wang
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Nurix Therapeutics, San Francisco, CA, USA
| | - Anna Ceccarelli
- Medical Oncology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Khalid A Fakhro
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Weill-Cornell Medicine Qatar, Doha, Qatar
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Francesco M Marincola
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Sonata Therapeutics, Watertown, MA, USA
| | - Jérôme Galon
- Inserm, Laboratory of Integrative Cancer Immunology, Equipe Labellisée Ligue Contre Le Cancer, Centre de Recherche de Cordeliers, Université de Paris, Sorbonne Université, Paris, France
| | - Souhaila Al Khodor
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Michele Ceccarelli
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples Federico II, Naples, Italy
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Wouter Hendrickx
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
| | - Davide Bedognetti
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy.
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11
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Yang T, Kang L, Li D, Song Y. Immunotherapy for HER-2 positive breast cancer. Front Oncol 2023; 13:1097983. [PMID: 37007133 PMCID: PMC10061112 DOI: 10.3389/fonc.2023.1097983] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
Immunotherapy is a developing treatment for advanced breast cancer. Immunotherapy has clinical significance for the treatment of triple-negative breast cancers and human epidermal growth factor receptor-2 positive (HER2+) breast cancers. As a proved effective passive immunotherapy, clinical application of the monoclonal antibodies trastuzumab, pertuzumab and T-DM1 (ado-trastuzumab emtansine) has significantly improved the survival of patients with HER2+ breast cancers. Immune checkpoint inhibitors that block programmed death receptor-1 and its ligand (PD-1/PD-L1) have also shown benefits for breast cancer in various clinical trials. Adoptive T-cell immunotherapies and tumor vaccines are emerging as novel approaches to treating breast cancer, but require further study. This article reviews recent advances in immunotherapy for HER2+ breast cancers.
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van Weverwijk A, de Visser KE. Mechanisms driving the immunoregulatory function of cancer cells. Nat Rev Cancer 2023; 23:193-215. [PMID: 36717668 DOI: 10.1038/s41568-022-00544-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/13/2022] [Indexed: 01/31/2023]
Abstract
Tumours display an astonishing variation in the spatial distribution, composition and activation state of immune cells, which impacts their progression and response to immunotherapy. Shedding light on the mechanisms that govern the diversity and function of immune cells in the tumour microenvironment will pave the way for the development of more tailored immunomodulatory strategies for the benefit of patients with cancer. Cancer cells, by virtue of their paracrine and juxtacrine communication mechanisms, are key contributors to intertumour heterogeneity in immune contextures. In this Review, we discuss how cancer cell-intrinsic features, including (epi)genetic aberrations, signalling pathway deregulation and altered metabolism, play a key role in orchestrating the composition and functional state of the immune landscape, and influence the therapeutic benefit of immunomodulatory strategies. Moreover, we highlight how targeting cancer cell-intrinsic parameters or their downstream immunoregulatory pathways is a viable strategy to manipulate the tumour immune milieu in favour of antitumour immunity.
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Affiliation(s)
- Antoinette van Weverwijk
- Division of Tumour Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Karin E de Visser
- Division of Tumour Biology & Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands.
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13
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Jarroudi OA, Bairi KE, Curigliano G, Afqir S. Immune-Checkpoint Inhibitors: A New Line of Attack in Triple-Negative Breast Cancer. Cancer Treat Res 2023; 188:29-62. [PMID: 38175341 DOI: 10.1007/978-3-031-33602-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Poor prognosis is a distinctive feature of triple-negative breast cancer (TNBC). Chemotherapy has long represented the main and unique treatment for patients with TNBC. Recently, immune checkpoint inhibitors (ICIs) were investigated in several clinical trials and were approved for clinical use in TNBC patients that express programmed cell death protein-1 (PD-1) in combination with chemotherapy in the first-line setting. ICIs are also being investigated in the neoadjuvant and adjuvant settings for TNBC. This chapter aims to discuss different ICIs used to treat all TNBC stages to date.
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Affiliation(s)
- Ouissam Al Jarroudi
- Faculty of Medicine and Pharmacy, Mohammed Ist University, Oujda, Morocco.
- Department of Medical Oncology, Mohammed VI University Hospital, Oujda, Morocco.
| | - Khalid El Bairi
- Faculty of Medicine and Pharmacy, Mohammed Ist University, Oujda, Morocco
- Department of Medical Oncology, Mohammed VI University Hospital, Oujda, Morocco
| | - Giuseppe Curigliano
- European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hematology, University of Milan, Milan, Italy
| | - Said Afqir
- Faculty of Medicine and Pharmacy, Mohammed Ist University, Oujda, Morocco
- Department of Medical Oncology, Mohammed VI University Hospital, Oujda, Morocco
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14
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Tiwari A, Oravecz T, Dillon LA, Italiano A, Audoly L, Fridman WH, Clifton GT. Towards a consensus definition of immune exclusion in cancer. Front Immunol 2023; 14:1084887. [PMID: 37033994 PMCID: PMC10073666 DOI: 10.3389/fimmu.2023.1084887] [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: 10/31/2022] [Accepted: 02/14/2023] [Indexed: 04/11/2023] Open
Abstract
Background The immune cell topography of solid tumors has been increasingly recognized as an important predictive factor for progression of disease and response to immunotherapy. The distribution pattern of immune cells in solid tumors is commonly classified into three categories - namely, "Immune inflamed", "Immune desert" and "Immune excluded" - which, to some degree, connect immune cell presence and positioning within the tumor microenvironment to anti-tumor activity. Materials and methods In this review, we look at the ways immune exclusion has been defined in published literature and identify opportunities to develop consistent, quantifiable definitions, which in turn, will allow better determination of the underlying mechanisms that span cancer types and, ultimately, aid in the development of treatments to target these mechanisms. Results The definitions of tumor immune phenotypes, especially immune exclusion, have largely been conceptual. The existing literature lacks in consistency when it comes to practically defining immune exclusion, and there is no consensus on a definition. Majority of the definitions use somewhat arbitrary cut-offs in an attempt to place each tumor into a distinct phenotypic category. Tumor heterogeneity is often not accounted for, which limits the practical application of a definition. Conclusions We have identified two key issues in existing definitions of immune exclusion, establishing clinically relevant cut-offs within the spectrum of immune cell infiltration as well as tumor heterogeneity. We propose an approach to overcome these limitations, by reporting the degree of immune cell infiltration, tying cut-offs to clinically meaningful outcome measures, maximizing the number of regions of a tumor that are analyzed and reporting the degree of heterogeneity. This will allow for a consensus practical definition for operationalizing this categorization into clinical trial and signal-seeking endpoints.
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Affiliation(s)
- Ankur Tiwari
- Department of Surgery, University of Texas Health Science Center San Antonio, San Antonio, TX, United States
| | | | | | | | | | - Wolf Hervé Fridman
- Centre de Recherche des Cordeliers, National Institute for Health and Medical Research (INSERM), Sorbonne Université, Université Sorbonne Paris-Cité (USPC), Université de Paris, Equipe Inflammation, Paris, France
| | - Guy Travis Clifton
- Parthenon Therapeutics, Boston, MA, United States
- *Correspondence: Guy Travis Clifton,
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15
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Chen H, Pu S, Mei N, Liu X, He J, Zhang H. Identification of prognostic biomarkers among ICAMs in the breast cancer microenvironment. Cancer Biomark 2022; 35:379-393. [PMID: 36373309 DOI: 10.3233/cbm-220073] [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: 11/13/2022]
Abstract
BACKGROUND Intercellular adhesion molecules (ICAMs) in the tumor microenvironment are closely related to immunity and affect the prognosis of cancer patients. OBJECTIVE The aim of our study is to explore the correlation between ICAM expression, mutation, methylation and immunity and their prognostic value in breast cancer (BC) is not clear. METHODS Online databases and tools such as UALCAN, COSMIC, cBioPortal, MethSurv, PrognoScan, Kaplan-Meier Plotter, GSCA and TIMER were utilized in this study. RESULTS We found that the mRNA and protein expression levels of ICAM1 were upregulated in triple-negative breast cancer (TNBC) compared with normal tissues, and TNBC patients with high expression of ICAM1 had better overall survival (OS) and recurrence-free survival (RFS). The main types of ICAM1 gene variants were missense mutation and amplification, and ICAM1 showed a lower level of methylation in TNBC cancer tissues than in normal tissues, which was contrary to the high expression levels of ICAM1 mRNA and protein. Next, the function of ICAM1 was mainly related to the activation of apoptosis, epithelial-mesenchymal transition (EMT) and inhibition of the androgen receptor (AR) and estrogen receptor (ER) pathways. Meanwhile, functional pathway enrichment results showed that ICAM1 was also involved in the immune regulation process of BC. Furthermore, the expression of ICAM1 was positively associated with 6 types of tumor-infiltrating immune cells (CD8+ T cells, CD4+ T cells, B cells, neutrophils, macrophages and dendritic cells) and was also positively related to the expression of programmed cell death-1 (PD-1), programmed cell death-ligand 1 (PD-L1) and cytotoxic T lymphocyte-associated antigen-4 (CTLA4). CONCLUSIONS Our research indicated that ICAM1 was likely to be a potential therapeutic target in TNBC.
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Affiliation(s)
- Heyan Chen
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shengyu Pu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Nan Mei
- Department of Hematology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaoxu Liu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Huimin Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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16
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Sherif S, Roelands J, Mifsud W, Ahmed EI, Raynaud CM, Rinchai D, Sathappan A, Maaz A, Saleh A, Ozer E, Fakhro KA, Mifsud B, Thorsson V, Bedognetti D, Hendrickx WRL. The immune landscape of solid pediatric tumors. J Exp Clin Cancer Res 2022; 41:199. [PMID: 35690832 PMCID: PMC9188257 DOI: 10.1186/s13046-022-02397-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Large immunogenomic analyses have demonstrated the prognostic role of the functional orientation of the tumor microenvironment in adult solid tumors, this variable has been poorly explored in the pediatric counterpart.
Methods
We performed a systematic analysis of public RNAseq data (TARGET) for five pediatric tumor types (408 patients): Wilms tumor (WLM), neuroblastoma (NBL), osteosarcoma (OS), clear cell sarcoma of the kidney (CCSK) and rhabdoid tumor of the kidney (RT). We assessed the performance of the Immunologic Constant of Rejection (ICR), which captures an active Th1/cytotoxic response. We also performed gene set enrichment analysis (ssGSEA) and clustered more than 100 well characterized immune traits to define immune subtypes and compared their outcome.
Results
A higher ICR score was associated with better survival in OS and high risk NBL without MYCN amplification but with poorer survival in WLM. Clustering of immune traits revealed the same five principal modules previously described in adult tumors (TCGA). These modules divided pediatric patients into six immune subtypes (S1-S6) with distinct survival outcomes. The S2 cluster showed the best overall survival, characterized by low enrichment of the wound healing signature, high Th1, and low Th2 infiltration, while the reverse was observed in S4. Upregulation of the WNT/Beta-catenin pathway was associated with unfavorable outcomes and decreased T-cell infiltration in OS.
Conclusions
We demonstrated that extracranial pediatric tumors could be classified according to their immune disposition, unveiling similarities with adults’ tumors. Immunological parameters might be explored to refine diagnostic and prognostic biomarkers and to identify potential immune-responsive tumors.
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Bian Z, Chen J, Liu C, Ge Q, Zhang M, Meng J, Liang C. Landscape of the intratumroal microenvironment in bladder cancer: Implications for prognosis and immunotherapy. Comput Struct Biotechnol J 2022; 21:74-85. [PMID: 36514337 PMCID: PMC9730156 DOI: 10.1016/j.csbj.2022.11.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction This study aims to present the landscape of the intratumoral microenvironment and by which establish a classification system that can be used to predict the prognosis of bladder cancer patients and their response to anti-PD-L1 immunotherapy. Methods The expression profiles of 1554 bladder cancer cases were downloaded from seven public datasets. Single-sample gene set enrichment analysis (ssGSEA), univariate Cox regression analysis, and meta-analysis were employed to establish the bladder cancer immune prognostic index (BCIPI). Extensive analyses were executed to investigate the association between BCIPI and overall survival, tumor-infiltrated immunocytes, immunotherapeutic response, mutation load, etc. Results The results obtained from seven independent cohorts and meta-analyses suggested that the BCIPI is an effective classification system for estimating bladder cancer patients' overall survival. Patients in the BCIPI-High subgroup revealed different immunophenotypic outcomes from those in the BCIPI-Low subgroup regarding tumor-infiltrated immunocytes and mutated genes. Subsequent analysis suggested that patients in the BCIPI-High subgroup were more sensitive to anti-PD-L1 immunotherapy than those in the BCIPI-Low subgroup. Conclusions The newly established BCIPI is a valuable tool for predicting overall survival outcomes and immunotherapeutic responses in patients with bladder cancer.
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Key Words
- AJCC, American Joint Committee on Cancer
- Anti-PD-L1, Antitumor response to atezolizumab
- BCG, Bacillus Calmette-Guerin
- BCIPI, Bladder cancer immune prognostic index
- Bladder cancer
- CNVs, Copy number variations
- FDA, Food and Drug Administration
- FPKM, Fragments per kilobase per million
- Genomic
- ICI, Immune checkpoint inhibitor
- IHC, Immunohistochemistry
- Immunotherapy
- MES, Mesenchymal transition
- NES, Normalized enrichment score
- Overall survival
- RMA, Robust multiarray average
- RMS, Restricted mean survival
- TPM, Transcripts per kilobase million
- ssGSEA, Single-sample GSEA
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Affiliation(s)
- Zichen Bian
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Jia Chen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Chang Liu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Qintao Ge
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China
| | - Meng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China,Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, China
| | - Jialin Meng
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China,Corresponding authors at: Jixi Road 218, Shushan District, Hefei City 230022, Anhui Province, China.
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Institute of Urology & Anhui Province Key Laboratory of Genitourinary Diseases, Anhui Medical University, Hefei 230022, China,Corresponding authors at: Jixi Road 218, Shushan District, Hefei City 230022, Anhui Province, China.
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Devoy C, Flores Bueso Y, Tangney M. Understanding and harnessing triple-negative breast cancer-related microbiota in oncology. Front Oncol 2022; 12:1020121. [PMID: 36505861 PMCID: PMC9730816 DOI: 10.3389/fonc.2022.1020121] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Bacterial inhabitants of the body have the potential to play a role in various stages of cancer initiation, progression, and treatment. These bacteria may be distal to the primary tumour, such as gut microbiota, or local to the tissue, before or after tumour growth. Breast cancer is well studied in this context. Amongst breast cancer types, Triple Negative Breast Cancer (TNBC) is more aggressive, has fewer treatment options than receptor-positive breast cancers, has an overall worse prognosis and higher rates of reoccurrence. Thus, an in-depth understanding of the bacterial influence on TNBC progression and treatment is of high value. In this regard, the Gut Microbiota (GM) can be involved in various stages of tumour progression. It may suppress or promote carcinogenesis through the release of carcinogenic metabolites, sustenance of proinflammatory environments and/or the promotion of epigenetic changes in our genome. It can also mediate metastasis and reoccurrence through interactions with the immune system and has been recently shown to influence chemo-, radio-, and immune-therapies. Furthermore, bacteria have also been found to reside in normal and malignant breast tissue. Several studies have now described the breast and breast tumour microbiome, with the tumour microbiota of TNBC having the least taxonomic diversity among all breast cancer types. Here, specific conditions of the tumour microenvironment (TME) - low O2, leaky vasculature and immune suppression - are supportive of tumour selective bacterial growth. This innate bacterial ability could enable their use as delivery agents for various therapeutics or as diagnostics. This review aims to examine the current knowledge on bacterial relevance to TNBC and potential uses while examining some of the remaining unanswered questions regarding mechanisms underpinning observed effects.
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Affiliation(s)
- Ciaran Devoy
- Cancer Research@UCC, College of Medicine and Health, University College Cork, Cork, Ireland,SynBio Center, University College Cork, Cork, Ireland,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Yensi Flores Bueso
- Cancer Research@UCC, College of Medicine and Health, University College Cork, Cork, Ireland,SynBio Center, University College Cork, Cork, Ireland,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Mark Tangney
- Cancer Research@UCC, College of Medicine and Health, University College Cork, Cork, Ireland,SynBio Center, University College Cork, Cork, Ireland,APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Pharmacy, College of Medicine and Health, University College Cork, Cork, Ireland,*Correspondence: Mark Tangney,
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19
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Le Bris Y, Normand A, Bouard L, Ménard A, Bossard C, Moreau A, Béné MC. Aggressive, early resistant and relapsed mantle cell lymphoma distinct extrinsic microenvironment highlighted by transcriptome analysis. EJHAEM 2022; 3:1165-1171. [PMID: 36467789 PMCID: PMC9713019 DOI: 10.1002/jha2.549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/03/2022] [Accepted: 08/07/2022] [Indexed: 06/17/2023]
Abstract
Immunotherapy strategies relying on innate or adaptive immune components are increasingly used in onco-haematology. However, little is known about the infiltrated lymph nodes (LN) or bone marrow (BM) landscape of mantle cell lymphoma (MCL). The original transcriptomic approach of reverse transcriptase multiplex ligation-dependent probe amplification (RT-MLPA) was applied here to explore the expression of 24 genes of interest in MCL at diagnosis (21 LN and 15 BM) or relapse (18 LN). This allowed us to identify that at baseline, samples from MCL patients with an aggressive morphology (i.e. blastoid or pleomorphic) or a high proliferative profile, displayed significantly higher monocyte/macrophage-associated transcripts (CD14 and CD163) in LN and BM. Regarding T-cells, aggressive MCL forms had significantly lower amounts of LN CD3E transcripts, yet an increased expression of cytotoxic markers in LN (CD8) and BM (CD94). A very high-risk group with early treatment resistance displayed, at diagnosis, high proliferation (KI67) and high macrophages and cytotoxic transcript levels. Post-immunochemotherapy relapsed samples revealed lower levels of T- and natural killer-cells markers, while monocyte/macrophage markers remained similar to diagnosis. This study suggests that rapid analysis of MCL microenvironment transcriptome signatures by RT-MLPA could allow for an early distinction of patient subgroups candidates for adapted treatment strategies.
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Affiliation(s)
- Yannick Le Bris
- Hematology BiologyNantes University HospitalNantesFrance
- CRCINAINSERMCNRSUniversité d'AngersUniversité de NantesNantesFrance
| | - Adeline Normand
- Department of Pathology, Nantes University HospitalNantesFrance
| | - Louise Bouard
- Hematology ClinicCentre Hospitalier Bretagne AtlantiqueVannesFrance
| | - Audrey Ménard
- Hematology BiologyNantes University HospitalNantesFrance
| | - Céline Bossard
- Department of Pathology, Nantes University HospitalNantesFrance
| | - Anne Moreau
- Department of Pathology, Nantes University HospitalNantesFrance
- Department of PathologyCentre Hospitalier Départemental de VendéeLa Roche sur YonFrance
| | - Marie C. Béné
- Hematology BiologyNantes University HospitalNantesFrance
- CRCINAINSERMCNRSUniversité d'AngersUniversité de NantesNantesFrance
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20
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Otohinoyi D, Kuchi A, Wu J, Hicks C. Integrating Genomic Information with Tumor-Immune Microenvironment in Triple-Negative Breast Cancer. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192113901. [PMID: 36360779 PMCID: PMC9659069 DOI: 10.3390/ijerph192113901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND the development and progression of triple-negative breast cancer (TNBC) is driven by somatic driver mutations and the tumor-immune microenvironment. To date, data on somatic mutations has not been leveraged and integrated with information on the immune microenvironment to elucidate the possible oncogenic interactions and their potential effects on clinical outcomes. Here, we investigated possible oncogenic interactions between somatic mutations and the tumor-immune microenvironment, and their correlation with patient survival in TNBC. METHODS We performed analysis combining data on 7,875 somatic mutated genes with information on 1,751 immune-modulated genes, using gene-expression data as the intermediate phenotype, and correlated the resulting information with survival. We conducted functional analysis to identify immune-modulated molecular networks and signaling pathways enriched for somatic mutations likely to drive clinical outcomes. RESULTS We discovered differences in somatic mutation profiles between patients who died and those who survived, and a signature of somatic mutated immune-modulated genes transcriptionally associated with TNBC, predictive of survival. In addition, we discovered immune-modulated molecular networks and signaling pathways enriched for somatic mutations. CONCLUSIONS The investigation revealed possible oncogenic interactions between somatic mutations and the tumor-immune microenvironment in TNBC, likely to affect clinical outcomes.
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21
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Boudin L, de Nonneville A, Finetti P, Mescam L, Le Cesne A, Italiano A, Blay JY, Birnbaum D, Mamessier E, Bertucci F. CSPG4 expression in soft tissue sarcomas is associated with poor prognosis and low cytotoxic immune response. Lab Invest 2022; 20:464. [PMID: 36221119 PMCID: PMC9552405 DOI: 10.1186/s12967-022-03679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022]
Abstract
Background Soft tissue sarcomas (STS) are heterogeneous and pro-metastatic tumors. Identification of accurate prognostic factors and novel therapeutic targets are crucial. CSPG4 is a cell surface proteoglycan with oncogenic functions. It recently emerged as a potential target for immunotherapy, including cell therapy based on CSPG4-specific chimeric antigen receptor (CAR)-redirected cytokine-induced killer lymphocytes (CSPG4-CAR.CIKs) in STS. However, expression of CSPG4 is poorly known in STS so far. Methods We analyzed CSPG4 gene expression in 1378 localized STS clinical samples, and searched for correlations with clinicopathological data, including disease-free survival (DFS), and with tumor immune features. Results CSPG4 expression was heterogeneous across samples. High expression was associated with younger patients’ age, more frequent undifferentiated pleomorphic sarcoma and myxofibrosarcoma pathological subtypes, more frequent internal trunk tumor site, and more CINSARC high-risk samples. No correlation existed with pathological tumor size and grade, and tumor depth. Patients with high CSPG4 expression displayed 49% (95% CI 42–57) 5-year DFS versus 61% (95% CI 56–68) in patients with low expression (p = 3.17E−03), representing a 49% increased risk of event in the “CSPG4-high” group (HR = 1.49, 95% CI 1.14–1.94). This unfavorable prognostic value persisted in multivariate analysis, independently from other variables. There were significant differences in immune variables between “CSPG4-high” and “CSPG4-low” tumors. The "CSPG4-low" tumors displayed profiles suggesting higher anti-tumor cytotoxic immune response and higher potential vulnerability to immune checkpoint inhibitors (ICI). By contrast, the "CSPG4-high" tumors displayed profiles implying an immune-excluded tumor microenvironment, potentially induced by hypoxia, resulting from an immature chaotic microvasculature, and/or the presence of contractile myofibroblasts. Conclusions Patients with “CSPG4-high” STS, theoretically candidate for CAR.CIKs, display shorter DFS and an immune environment unfavorable to vulnerability to CAR.CIKs, which could be improved by combining anti-angiogenic drugs able to normalize the tumor vasculature. By contrast, “CSPG4-low” STS are better candidates for immune therapy involving ICI. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03679-y.
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Affiliation(s)
- Laurys Boudin
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - A de Nonneville
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France.,Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - Léna Mescam
- French Sarcoma Group, Lyon, France.,Department of Pathology, Institut Paoli-Calmettes, 232 Bd. Sainte-Marguerite, 13009, Marseille, France
| | - A Le Cesne
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Antoine Italiano
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Institut Bergonie, Bordeaux, France
| | - Jean-Yves Blay
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Centre Léon Bérard, UNICANCER &, Université Claude Bernard Lyon I, Lyon, France
| | - Daniel Birnbaum
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - Emilie Mamessier
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - François Bertucci
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France. .,Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France. .,French Sarcoma Group, Lyon, France.
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22
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Wu CG, Casanova R, Mairinger F, Soltermann A. Lung adenocarcinoma patients with malignant pleural effusions in hot adaptive immunity status have a longer overall survival. Front Oncol 2022; 12:1031094. [PMID: 36267973 PMCID: PMC9577289 DOI: 10.3389/fonc.2022.1031094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Malignant pleural effusion (MPE) is a common complication of lung adenocarcinoma (LADC) which is associated with a dismal prognosis. We investigated the prognostic role of PD-L1 and other immunomodulators expression in the immune compartment of MPE immune composition. MPE cytologic cell blocks of 83 LADC patients were analysed for the mRNA expression of 770 cancer-immune genes by the NanoString nCounter platform. The expression of relevant immune cell lineage markers was validated by immunohistochemistry (IHC) using quantitative pathology. The mRNA immune profiling identified four MPE patient clusters (C). C1/2 (adaptive+, hot) showed better overall survival (OS) than C3/4 (adaptive-, cold). Additionally, cold immunity profiles (adaptive-), C4 (innate+) were associated with worse OS than C3 (innate-). High PD-L1 expression was linked to the regulation of T cell activation and interferon signalling pathways. Genes of pattern recognition receptor and type I interferon signalling pathways were specifically upregulated in the long-survival (≥90 days) patient group. Moreover, immunomodulators were co-activated and highly expressed in hot adaptive immunity patient clusters, whereas CD274 (PD-L1), TNFRSF9 (4-1BB), VEGFA (VEGF-A) and CD276 (B7-H3) were upregulated in the groups referred as cold. The patient cluster, age and PD-L1 expression were independent prognosticators for LADC MPE patients (p-value < 0.05). Our study sheds light on the variances of immune contexture regarding different PD-L1 expression and survival conditions. It revealed four distinct prognostic patient clusters with specific immune cell components and immunomodulator expression profiles, which, collectively, is supportive for future therapeutic and prognosis for cancer management.
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Affiliation(s)
- Cheng-Guang Wu
- Institute of Pathology, University Hospital Zurich, Zurich, Switzerland
- *Correspondence: Cheng-Guang Wu, ; Alex Soltermann,
| | - Ruben Casanova
- Institute of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Fabian Mairinger
- Institute of Pathology, University Hospital Essen, Essen, Germany
| | - Alex Soltermann
- Facharzt Foederatio Medicorum Helveticorum (FMH) Pathologie, Pathologie Länggasse, Ittigen, Switzerland
- *Correspondence: Cheng-Guang Wu, ; Alex Soltermann,
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23
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Immune-related 3-lncRNA signature with prognostic connotation in a multi-cancer setting. J Transl Med 2022; 20:442. [PMID: 36180904 PMCID: PMC9523969 DOI: 10.1186/s12967-022-03654-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/19/2022] [Indexed: 11/27/2022] Open
Abstract
Background Advances in our understanding of the tumor microenvironment have radically changed the cancer field, highlighting the emerging need for biomarkers of an active, favorable tumor immune phenotype to aid treatment stratification and clinical prognostication. Numerous immune-related gene signatures have been defined; however, their prognostic value is often limited to one or few cancer types. Moreover, the area of non-coding RNA as biomarkers remains largely unexplored although their number and biological roles are rapidly expanding. Methods We developed a multi-step process to identify immune-related long non-coding RNA signatures with prognostic connotation in multiple TCGA solid cancer datasets. Results Using the breast cancer dataset as a discovery cohort we found 2988 differentially expressed lncRNAs between immune favorable and unfavorable tumors, as defined by the immunologic constant of rejection (ICR) gene signature. Mapping of the lncRNAs to a coding-non-coding network identified 127 proxy protein-coding genes that are enriched in immune-related diseases and functions. Next, we defined two distinct 20-lncRNA prognostic signatures that show a stronger effect on overall survival than the ICR signature in multiple solid cancers. Furthermore, we found a 3 lncRNA signature that demonstrated prognostic significance across 5 solid cancer types with a stronger association with clinical outcome than ICR. Moreover, this 3 lncRNA signature showed additional prognostic significance in uterine corpus endometrial carcinoma and cervical squamous cell carcinoma and endocervical adenocarcinoma as compared to ICR. Conclusion We identified an immune-related 3-lncRNA signature with prognostic connotation in multiple solid cancer types which performed equally well and in some cases better than the 20-gene ICR signature, indicating that it could be used as a minimal informative signature for clinical implementation. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03654-7.
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24
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Ribeiro R, Carvalho MJ, Goncalves J, Moreira JN. Immunotherapy in triple-negative breast cancer: Insights into tumor immune landscape and therapeutic opportunities. Front Mol Biosci 2022; 9:903065. [PMID: 36060249 PMCID: PMC9437219 DOI: 10.3389/fmolb.2022.903065] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/13/2022] [Indexed: 12/24/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a clinically aggressive subtype of breast cancer that represents 15-20% of breast tumors and is more prevalent in young pre-menopausal women. It is the subtype of breast cancers with the highest metastatic potential and recurrence at the first 5 years after diagnosis. In addition, mortality increases when a complete pathological response is not achieved. As TNBC cells lack estrogen, progesterone, and HER2 receptors, patients do not respond well to hormone and anti-HER2 therapies, and conventional chemotherapy remains the standard treatment. Despite efforts to develop targeted therapies, this disease continues to have a high unmet medical need, and there is an urgent demand for customized diagnosis and therapeutics. As immunotherapy is changing the paradigm of anticancer treatment, it arises as an alternative treatment for TNBC patients. TNBC is classified as an immunogenic subtype of breast cancer due to its high levels of tumor mutational burden and presence of immune cell infiltrates. This review addresses the implications of these characteristics for the diagnosis, treatment, and prognosis of the disease. Herein, the role of immune gene signatures and tumor-infiltrating lymphocytes as biomarkers in TNBC is reviewed, identifying their application in patient diagnosis and stratification, as well as predictors of efficacy. The expression of PD-L1 expression is already considered to be predictive of response to checkpoint inhibitor therapy, but the challenges regarding its value as biomarker are described. Moreover, the rationales for different formats of immunotherapy against TNBC currently under clinical research are discussed, and major clinical trials are highlighted. Immune checkpoint inhibitors have demonstrated clinical benefit, particularly in early-stage tumors and when administered in combination with chemotherapy, with several regimens approved by the regulatory authorities. The success of antibody-drug conjugates and research on other emerging approaches, such as vaccines and cell therapies, will also be addressed. These advances give hope on the development of personalized, more effective, and safe treatments, which will improve the survival and quality of life of patients with TNBC.
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Affiliation(s)
- Rita Ribeiro
- CNC—Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Faculty of Medicine (Polo 1), Coimbra, Portugal
- iMed.ULisboa—Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
- Univ Coimbra—University of Coimbra, CIBB, Faculty of Pharmacy, Coimbra, Portugal
| | - Maria João Carvalho
- Univ Coimbra—University of Coimbra, CIBB, Faculty of Pharmacy, Coimbra, Portugal
- CHUC—Coimbra Hospital and University Centre, Department of Gynaecology, Coimbra, Portugal
- Univ Coimbra—University Clinic of Gynaecology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- iCBR—Institute for Clinical and Biomedical Research Area of Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- CACC—Clinical Academic Center of Coimbra, Coimbra, Portugal
| | - João Goncalves
- iMed.ULisboa—Research Institute for Medicines, Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - João Nuno Moreira
- CNC—Center for Neurosciences and Cell Biology, Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Faculty of Medicine (Polo 1), Coimbra, Portugal
- Univ Coimbra—University of Coimbra, CIBB, Faculty of Pharmacy, Coimbra, Portugal
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25
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Zhao W, Jin L, Chen P, Li D, Gao W, Dong G. Colorectal cancer immunotherapy-Recent progress and future directions. Cancer Lett 2022; 545:215816. [PMID: 35810989 DOI: 10.1016/j.canlet.2022.215816] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/12/2022] [Accepted: 07/01/2022] [Indexed: 12/09/2022]
Abstract
Compared with conventional chemotherapy and targeted therapy, immunotherapy has changed the treatment prospects of various solid tumors and has recently become the main treatment method for metastatic or recurrent solid tumors, including malignant melanoma, non-small-cell lung cancer, and renal cell carcinoma. The application of immune checkpoint inhibitor (ICI)-based immunotherapy in patients with colorectal cancer (CRC) has yielded satisfactory results in terms of safety and efficacy, and several immunotherapeutic agents, including pembrolizumab, nivolumab, and ipilimumab, have been approved for the treatment of advanced CRC. The advent of other immunotherapies, such as chimeric antigen receptor-modified T (CAR-T) cells or cancer vaccines, have also contributed to the development of immunotherapy for CRC. Here, we summarize the findings of recent clinical trials on the efficacy of immunotherapy in CRC and briefly describe the mechanisms associated with tumor-intrinsic resistance to ICIs. We then discuss potential biomarkers for predicting the efficacy of immunotherapy.
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Affiliation(s)
- Wen Zhao
- School of Medicine, Nankai University, Tianjin, 300071, China; Department of General Surgery, Chinese PLA General Hospital, Beijing, 100853, China
| | - Lujia Jin
- Department of General Surgery, Chinese PLA General Hospital, Beijing, 100853, China
| | - Peng Chen
- Department of General Surgery, Chinese PLA General Hospital, Beijing, 100853, China
| | - Dingchang Li
- Department of General Surgery, Chinese PLA General Hospital, Beijing, 100853, China
| | - Wenxing Gao
- Department of General Surgery, Chinese PLA General Hospital, Beijing, 100853, China
| | - Guanglong Dong
- School of Medicine, Nankai University, Tianjin, 300071, China; Department of General Surgery, Chinese PLA General Hospital, Beijing, 100853, China.
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26
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Blaye C, Darbo É, Debled M, Brouste V, Vélasco V, Pinard C, Larmonier N, Pellegrin I, Tarricone A, Arnedos M, Commeny J, Bonnefoi H, Larmonier C, MacGrogan G. An immunological signature to predict outcome in patients with triple-negative breast cancer with residual disease after neoadjuvant chemotherapy. ESMO Open 2022; 7:100502. [PMID: 35759853 PMCID: PMC9434232 DOI: 10.1016/j.esmoop.2022.100502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/22/2022] [Indexed: 11/27/2022] Open
Abstract
Background When triple-negative breast cancer (TNBC) patients have residual disease after neoadjuvant chemotherapy (NACT), they have a high risk of metastatic relapse. With immune infiltrate in TNBC being prognostic and predictive of response to treatment, our aim was to develop an immunologic transcriptomic signature using post-NACT samples to predict relapse. Materials and methods We identified 115 samples of residual tumors from post-NACT TNBC patients. We profiled the expression of 770 genes related to cancer microenvironment using the NanoString PanCancer IO360 panel to develop a prognostic transcriptomic signature, and we describe the immune microenvironments of the residual tumors. Results Thirty-eight (33%) patients experienced metastatic relapse. Hierarchical clustering separated patients into five clusters with distinct prognosis based on pathways linked to immune activation, epithelial-to-mesenchymal transition and cell cycle. The immune microenvironment of the residual disease was significantly different between patients who experienced relapse compared to those who did not, the latter having significantly more effector antitumoral immune cells, with significant differences in lymphoid subpopulations. We selected eight genes linked to immunity (BLK, GZMM, CXCR6, LILRA1, SPIB, CCL4, CXCR4, SLAMF7) to develop a transcriptomic signature which could predict relapse in our cohort. This signature was validated in two external cohorts (KMplot and METABRIC). Conclusions Lack of immune activation after NACT is associated with a high risk of distant relapse. We propose a prognostic signature based on immune infiltrate that could lead to targeted therapeutic strategies to improve patient prognosis. Infiltrate of cytotoxic cells is higher in the residual disease of TNBC patients who will not experience metastatic relapse. Underexpression of immune-related pathways is associated with metastatic relapse in residual disease of TNBC patients. An immune gene-based signature can predict metastatic relapse in TNBC patients after NACT.
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Affiliation(s)
- C Blaye
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France; Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, Bordeaux, France
| | - É Darbo
- Univ. Bordeaux, INSERM U1218, ACTION Laboratory, Bordeaux, France
| | - M Debled
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France
| | - V Brouste
- Departments of Clinical Research and Medical Information, Bordeaux, France
| | - V Vélasco
- Biopathology, Institut Bergonié, Bordeaux, France
| | - C Pinard
- Pathology Laboratory, University Hospital of Martinique, Fort de France
| | - N Larmonier
- Univ. Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, Bordeaux, France; Univ. Bordeaux, Bordeaux, France
| | - I Pellegrin
- Service d'Immunologie et Immunogénétique, University Hospital of Bordeaux, Bordeaux, France; Centre de Ressources Biologiques Plurithématique, University Hospital of Bordeaux, Bordeaux, France
| | - A Tarricone
- Service d'Immunologie et Immunogénétique, University Hospital of Bordeaux, Bordeaux, France
| | - M Arnedos
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France
| | - J Commeny
- Department of Surgery, Institut Bergonié, Bordeaux, France
| | - H Bonnefoi
- Department of Medical Oncology, Institut Bergonié, Bordeaux, France; Univ. Bordeaux, INSERM U1218, ACTION Laboratory, Bordeaux, France; Univ. Bordeaux, Bordeaux, France
| | - C Larmonier
- Biopathology, Institut Bergonié, Bordeaux, France
| | - G MacGrogan
- Univ. Bordeaux, INSERM U1218, ACTION Laboratory, Bordeaux, France; Biopathology, Institut Bergonié, Bordeaux, France.
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27
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Uchimiak K, Badowska-Kozakiewicz AM, Sobiborowicz-Sadowska A, Deptała A. Current State of Knowledge on the Immune Checkpoint Inhibitors in Triple-Negative Breast Cancer Treatment: Approaches, Efficacy, and Challenges. Clin Med Insights Oncol 2022; 16:11795549221099869. [PMID: 35721387 PMCID: PMC9201309 DOI: 10.1177/11795549221099869] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype with limited treatment options. Recently, there has been a growing interest in immunotherapy with immune checkpoint inhibitors (ICIs) in TNBC, leading to extensive preclinical and clinical research. This review summarizes the current state of knowledge on ICIs efficacy and their predictive markers in TNBC and highlights the areas where the data are still limited. Currently, the only approved ICI-based regimen for TNBC is pembrolizumab with chemotherapy. Its advantage over chemotherapy alone was confirmed for non-metastatic TNBC regardless of programmed death-ligand 1 (PD-L1) expression (KEYNOTE-522) and for metastatic, PD-L1-positive TNBC (KEYNOTE-355). Pembrolizumab's efficacy was also evaluated in monotherapy, or in combination with niraparib and radiation therapy, showing potential efficacy and acceptable safety profile in phase 2 clinical trials. Atezolizumab + nab-paclitaxel increased the overall survival (OS) over placebo + nab-paclitaxel in early TNBC, regardless of PD-L1 status (IMpassion031). In IMpassion130 (untreated, advanced TNBC), the OS improvement was not statistically significant in the intention-to-treat population but clinically meaningful in the PD-L1 positive cohort. The durvalumab-anthracycline combination showed an increased response durability over placebo anthracycline in early TNBC (GeparNuevo). Several phase 1 clinical trials also showed a potential efficacy of atezolizumab and avelumab monotherapy in metastatic TNBC. ICIs appear to be applicable in both neoadjuvant and adjuvant settings, and are both pretreated and previously untreated patients. Further research is necessary to determine the most beneficial drug combinations and optimize patient selection. It is essential to identify the predictive markers for ICIs and factors affecting their expression.
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Affiliation(s)
- Katarzyna Uchimiak
- Students’ Scientific Organization of
Cancer Cell Biology, Department of Cancer Prevention, Medical University of Warsaw,
Warsaw, Poland
| | | | - Aleksandra Sobiborowicz-Sadowska
- Students’ Scientific Organization of
Cancer Cell Biology, Department of Cancer Prevention, Medical University of Warsaw,
Warsaw, Poland
| | - Andrzej Deptała
- Department of Cancer Prevention,
Medical University of Warsaw, Warsaw, Poland
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28
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Sun J, Yan C, Xu D, Zhang Z, Li K, Li X, Zhou M, Hao D. Immuno-genomic characterisation of high-grade serous ovarian cancer reveals immune evasion mechanisms and identifies an immunological subtype with a favourable prognosis and improved therapeutic efficacy. Br J Cancer 2022; 126:1570-1580. [PMID: 35017656 PMCID: PMC9130248 DOI: 10.1038/s41416-021-01692-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 12/07/2021] [Accepted: 12/23/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Immunotherapy has revolutionised the field of cancer therapy and immunology, but has demonstrated limited therapeutic efficacy in high-grade serous ovarian cancer (HGSOC). METHODS Multi-omics data of 495 TCGA HGSOC tumours and RNA-seq data of 1708 HGSOC tumours were analyzed. Multivariate Cox regression analysis and meta-analyses were used to identify prognostic genes. The immune microenvironment was characterised using the ssGSEA methods for 28 immune cell types. Immunohistochemistry staining of tumour tissues of 14 patients was used to validate the key findings further. RESULTS A total of 1142 genes were identified as favourable prognostic genes, which are prevailing in immune-related pathways and the infiltration of most immune subpopulations was observed to be associated with a favourable prognosis suggesting that tumour immunogenicity was the most prominent factor associated with improved clinical outcomes and response to chemotherapy of HGSOC. We identified multiple genomic and transcriptomic determinants of immunogenicity, including the copy loss of chromosome 4q and deficiencies of the homologous recombination pathway. Finally, an immunological subtype characterised by increased infiltration of activated CD8 T cells and decreased Tregs was associated with favourable prognosis and improved therapeutic efficacy. CONCLUSIONS Our study characterised the immunogenomic landscape and refined the immunological classifications of HGSOC. This may improve the selection of patients with HGSOC who are suitable candidates for immunotherapy.
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Affiliation(s)
- Jie Sun
- grid.268099.c0000 0001 0348 3990School of Biomedical Engineering, Wenzhou Medical University, 325027 Wenzhou, P. R. China
| | - Congcong Yan
- grid.268099.c0000 0001 0348 3990School of Biomedical Engineering, Wenzhou Medical University, 325027 Wenzhou, P. R. China
| | - Dandan Xu
- grid.155956.b0000 0000 8793 5925Centre for Addiction and Mental Health, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Psychiatry, University of Toronto, Toronto, ON Canada
| | - Zicheng Zhang
- grid.268099.c0000 0001 0348 3990School of Biomedical Engineering, Wenzhou Medical University, 325027 Wenzhou, P. R. China
| | - Ke Li
- grid.268099.c0000 0001 0348 3990School of Biomedical Engineering, Wenzhou Medical University, 325027 Wenzhou, P. R. China
| | - Xiaobo Li
- grid.410736.70000 0001 2204 9268Department of Pathology, Harbin Medical University, 150081 Harbin, P. R. China
| | - Meng Zhou
- grid.268099.c0000 0001 0348 3990School of Biomedical Engineering, Wenzhou Medical University, 325027 Wenzhou, P. R. China
| | - Dapeng Hao
- grid.410736.70000 0001 2204 9268Department of Pathology, Harbin Medical University, 150081 Harbin, P. R. China
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Lambert SL, Zhang C, Guo C, Turan T, Masica DL, Englert S, Fang Y, Sheridan J, McLaughlin RT, Tribouley C, Vosganian G, Afar D. Association of Baseline and Pharmacodynamic Biomarkers With Outcomes in Patients Treated With the PD-1 Inhibitor Budigalimab. J Immunother 2022; 45:167-179. [PMID: 35034046 PMCID: PMC8906246 DOI: 10.1097/cji.0000000000000408] [Citation(s) in RCA: 6] [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: 01/04/2021] [Accepted: 10/22/2021] [Indexed: 11/25/2022]
Abstract
Budigalimab, a novel anti-PD-1 monoclonal antibody, demonstrated efficacy and biomarker pharmacodynamics in patients with head and neck squamous cell carcinoma (HNSCC) or non-small cell lung cancer (NSCLC) consistent with those reported by other PD-1 inhibitors. Herein are presented additional outcomes of biomarker analyses from the phase 1 study of budigalimab monotherapy in patients with HNSCC and NSCLC (NCT03000257). PD-1 inhibitor naive patients with advanced HNSCC (n=41) or NSCLC (n=40) received budigalimab intravenously at 250 mg every 2 weeks (Q2W) or 500 mg Q4W until progression. Archival tumor specimens were evaluated by immunohistochemistry for CD8 and tumor PD-1 ligand 1 (PD-L1) expression, RNA, and whole-exome sequencing. Serum and whole blood samples were acquired at baseline and at select on-treatment time points. As of October 2019, best overall response of 15% in HNSCC and 18% in NSCLC was observed in all treated patients; both cohorts reported responses in PD-L1+ and PD-L1- tumors. Treatment with budigalimab was associated with increases in multiple soluble biomarkers including interferon gamma-induced chemokines. Expanded overall T-cell counts, total CD8 T-cell counts, and percentages of CD8+CD45RA-CD62L- effector memory T cells were observed at cycle 1, day 15 in responders. Univariate analysis demonstrated an association between prolonged progression-free survival and higher tumor mutational burden/neoantigen load, smaller tumor size, lower platelet-lymphocyte ratios, lower CCL23, lower colony-stimulating factor 1, and lower interleukin-6 levels at baseline. The biomarker analysis presented herein identified additional early pharmacodynamic biomarkers associated with anti-PD-1 activity and improved clinical responses to budigalimab in patients with advanced HNSCC and NSCLC.
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Affiliation(s)
| | | | | | | | | | - Stefan Englert
- Data and Statistical Sciences, AbbVie Deutschland GmbH & Co KG, Ludwigshafen, Germany
| | - Yuni Fang
- Drug Metabolism, Pharmacokinetics, AbbVie Inc, Redwood City, CA
| | - James Sheridan
- Drug Metabolism, Pharmacokinetics, AbbVie Inc, Redwood City, CA
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de Nonneville A, Finetti P, Picard M, Monneur A, Pantaleo MA, Astolfi A, Ostrowski J, Birnbaum D, Mamessier E, Bertucci F. CSPG4 Expression in GIST Is Associated with Better Prognosis and Strong Cytotoxic Immune Response. Cancers (Basel) 2022; 14:cancers14051306. [PMID: 35267618 PMCID: PMC8909029 DOI: 10.3390/cancers14051306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Gastrointestinal stromal tumors (GIST) are the most frequent sarcomas of the gastrointestinal tract. Identification of novel prognostic and/or therapeutic targets is a major issue to overcome tyrosine kinase inhibitors resistances. CSPG4, a cell surface proteoglycan, emerged as a potential therapeutic target for immune therapy in different cancers, including sarcomas. CSPG4 expression has never been studied in GIST. In this work we analyzed CSPG4 mRNA expression in a large series of clinical GIST samples given the scarcity of disease (n = 309 patients). We find that high CSPG4 expression is independently associated with disease-free survival, and with an immune landscape favorable to induce strong cytotoxic immune response after NK cell stimulation. Our results suggest the potential value of CSPG4-specific chimeric antigen receptor-redirected cytokine-induced killer lymphocytes treatment in GIST, notably “CSPG4-high” tumors, and calls for preclinical validation, drug testing in vivo, then in clinical trials. Abstract The treatment of gastrointestinal stromal tumors (GIST) must be improved through the development of more reliable prognostic factors and of therapies able to overcome imatinib resistance. The immune system represents an attractive tool. CSPG4, a cell surface proteoglycan, emerged as a potential therapeutic target for immune therapy in different cancers, including cell therapy based on CSPG4-specific chimeric antigen receptor (CAR)-redirected cytokine-induced killer lymphocytes (CSPG4-CAR.CIKs) in sarcomas. CSPG4 expression has never been studied in GIST. We analyzed CSPG4 mRNA expression data of 309 clinical GIST samples profiled using DNA microarrays and searched for correlations with clinicopathological and immune features. CSPG4 expression, higher in tumors than normal digestive tissues, was heterogeneous across tumors. High expression was associated with AFIP low-risk, gastric site, and localized stage, and independently with longer postoperative disease-free survival (DFS) in localized stage. The correlations between CSPG4 expression and immune signatures highlighted a higher anti-tumor immune response in “CSPG4-high” tumors, relying on both the adaptive and innate immune system, in which the boost of NK cells by CSPG4-CAR.CIKs might be instrumental, eventually combined with immune checkpoint inhibitors. In conclusion, high CSPG4 expression in GIST is associated with better DFS and offers an immune environment favorable to a vulnerability to CAR.CIKs.
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Affiliation(s)
- Alexandre de Nonneville
- Predictive Oncology Laboratory, Equipe Labellisée Ligue Nationale Contre Le Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University, 13009 Marseille, France; (A.d.N.); (P.F.); (M.P.); (D.B.); (E.M.)
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille University, CNRS, INSERM, 13009 Marseille, France;
| | - Pascal Finetti
- Predictive Oncology Laboratory, Equipe Labellisée Ligue Nationale Contre Le Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University, 13009 Marseille, France; (A.d.N.); (P.F.); (M.P.); (D.B.); (E.M.)
| | - Maelle Picard
- Predictive Oncology Laboratory, Equipe Labellisée Ligue Nationale Contre Le Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University, 13009 Marseille, France; (A.d.N.); (P.F.); (M.P.); (D.B.); (E.M.)
| | - Audrey Monneur
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille University, CNRS, INSERM, 13009 Marseille, France;
| | - Maria Abbondanza Pantaleo
- Department of Specialized, Experimental and Diagnostic Medicine, Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (M.A.P.); (A.A.)
| | - Annalisa Astolfi
- Department of Specialized, Experimental and Diagnostic Medicine, Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (M.A.P.); (A.A.)
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center of Postgraduate Education, 01-813 Warsaw, Poland;
- Department of Genetics, Maria Sklodowska-Curie National Institute of Oncology, 02-781 Warsaw, Poland
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Equipe Labellisée Ligue Nationale Contre Le Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University, 13009 Marseille, France; (A.d.N.); (P.F.); (M.P.); (D.B.); (E.M.)
| | - Emilie Mamessier
- Predictive Oncology Laboratory, Equipe Labellisée Ligue Nationale Contre Le Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University, 13009 Marseille, France; (A.d.N.); (P.F.); (M.P.); (D.B.); (E.M.)
| | - François Bertucci
- Predictive Oncology Laboratory, Equipe Labellisée Ligue Nationale Contre Le Cancer, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University, 13009 Marseille, France; (A.d.N.); (P.F.); (M.P.); (D.B.); (E.M.)
- Department of Medical Oncology, Institut Paoli-Calmettes, Aix-Marseille University, CNRS, INSERM, 13009 Marseille, France;
- Correspondence: ; Tel.: +33-4-91-22-35-37; Fax: +33-4-91-22-36-70
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Jiang C, Schaafsma E, Hong W, Zhao Y, Zhu K, Chao CC, Cheng C. Influence of T Cell-Mediated Immune Surveillance on Somatic Mutation Occurrences in Melanoma. Front Immunol 2022; 12:703821. [PMID: 35111147 PMCID: PMC8801458 DOI: 10.3389/fimmu.2021.703821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/16/2021] [Indexed: 01/09/2023] Open
Abstract
Background Neoantigens are presented on the cancer cell surface by peptide-restricted human leukocyte antigen (HLA) proteins and can subsequently activate cognate T cells. It has been hypothesized that the observed somatic mutations in tumors are shaped by immunosurveillance. Methods We investigated all somatic mutations identified in The Cancer Genome Atlas (TCGA) Skin Cutaneous Melanoma (SKCM) samples. By applying a computational algorithm, we calculated the binding affinity of the resulting neo-peptides and their corresponding wild-type peptides with the major histocompatibility complex (MHC) Class I complex. We then examined the relationship between binding affinity alterations and mutation frequency. Results Our results show that neoantigens derived from recurrent mutations tend to have lower binding affinities with the MHC Class I complex compared to peptides from non-recurrent mutations. Tumor samples harboring recurrent SKCM mutations exhibited lower immune infiltration levels, indicating a relatively colder immune microenvironment. Conclusions These results suggested that the occurrences of somatic mutations in melanoma have been shaped by immunosurveillance. Mutations that lead to neoantigens with high MHC class I binding affinity are more likely to be eliminated and thus are less likely to be present in tumors.
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Affiliation(s)
- Chongming Jiang
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Evelien Schaafsma
- Department of Molecular and Systems Biology, Dartmouth College, Hanover, NH, United States
| | - Wei Hong
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Yanding Zhao
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Ken Zhu
- Medical School, UT Southwestern Medical Center, Dallas, TX, United States
| | - Cheng-Chi Chao
- Antibody Discovery, Chempartner Corporation, South San Francisco, CA, United States
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, United States
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, United States
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, United States
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Bertucci F, Niziers V, de Nonneville A, Finetti P, Mescam L, Mir O, Italiano A, Le Cesne A, Blay JY, Ceccarelli M, Bedognetti D, Birnbaum D, Mamessier E. Immunologic constant of rejection signature is prognostic in soft-tissue sarcoma and refines the CINSARC signature. J Immunother Cancer 2022; 10:jitc-2021-003687. [PMID: 35017155 PMCID: PMC8753443 DOI: 10.1136/jitc-2021-003687] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Soft-tissue sarcomas (STSs) are heterogeneous and aggressive tumors, with high metastatic risk. The immunologic constant of rejection (ICR) 20-gene signature is a signature of cytotoxic immune response. We hypothesized that ICR might improve the prognostic assessment of early-stage STS. METHODS We retrospectively applied ICR to 1455 non-metastatic STS and searched for correlations between ICR classes and clinicopathological and biological variables, including metastasis-free survival (MFS). RESULTS Thirty-four per cent of tumors were classified as ICR1, 27% ICR2, 24% ICR3, and 15% ICR4. These classes were associated with patients' age, pathological type, and tumor depth, and an enrichment from ICR1 to ICR4 of quantitative/qualitative scores of immune response. ICR1 class was associated with a 59% increased risk of metastatic relapse when compared with ICR2-4 class. In multivariate analysis, ICR classification remained associated with MFS, as well as pathological type and Complexity Index in Sarcomas (CINSARC) classification, suggesting independent prognostic value. A prognostic clinicogenomic model, including the three variables, was built in a learning set (n=339) and validated in an independent set (n=339), showing greater prognostic precision than each variable alone or in doublet. Finally, connectivity mapping analysis identified drug classes potentially able to reverse the expression profile of poor-prognosis tumors, such as chemotherapy and targeted therapies. CONCLUSION ICR signature is independently associated with postoperative MFS in early-stage STS, independently from other prognostic features, including CINSARC. We built a robust prognostic clinicogenomic model integrating ICR, CINSARC, and pathological type, and suggested differential vulnerability of each prognostic group to different systemic therapies.
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Affiliation(s)
- Francois Bertucci
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France .,Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France.,French Sarcoma Group, Lyon, France
| | - Vincent Niziers
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France.,Department of Surgery, Institut Paoli-Calmettes, Marseille, France
| | - Alexandre de Nonneville
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France.,Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Pascal Finetti
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - Léna Mescam
- French Sarcoma Group, Lyon, France.,Department of Pathology, Institut Paoli-Calmettes, Marseille, France
| | - Olivier Mir
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Antoine Italiano
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Institut Bergonie, Bordeaux, France
| | - Axel Le Cesne
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Jean-Yves Blay
- French Sarcoma Group, Lyon, France.,Department of Medical Oncology, Centre Leon Berard, Lyon, France
| | - Michele Ceccarelli
- DIETI, University of Naples Federico II Faculty of Engineering, Naples, Italy
| | - Davide Bedognetti
- Cancer Research, Sidra Medicine, Doha, Qatar.,Department of Internal Medicine and Medical Specialties, University of Genova, Genova, Italy
| | - Daniel Birnbaum
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
| | - Emilie Mamessier
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Institut Paoli-Calmettes, Aix-Marseille Université, INSERM UMR1068, CNRS UMR725, Marseille, France
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Pullikuth AK, Routh ED, Zimmerman KD, Chifman J, Chou JW, Soike MH, Jin G, Su J, Song Q, Black MA, Print C, Bedognetti D, Howard-McNatt M, O’Neill SS, Thomas A, Langefeld CD, Sigalov AB, Lu Y, Miller LD. Bulk and Single-Cell Profiling of Breast Tumors Identifies TREM-1 as a Dominant Immune Suppressive Marker Associated With Poor Outcomes. Front Oncol 2021; 11:734959. [PMID: 34956864 PMCID: PMC8692779 DOI: 10.3389/fonc.2021.734959] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
BackgroundTriggering receptor expressed on myeloid cells (TREM)-1 is a key mediator of innate immunity previously associated with the severity of inflammatory disorders, and more recently, the inferior survival of lung and liver cancer patients. Here, we investigated the prognostic impact and immunological correlates of TREM1 expression in breast tumors.MethodsBreast tumor microarray and RNAseq expression profiles (n=4,364 tumors) were analyzed for associations between gene expression, tumor immune subtypes, distant metastasis-free survival (DMFS) and clinical response to neoadjuvant chemotherapy (NAC). Single-cell (sc)RNAseq was performed using the 10X Genomics platform. Statistical associations were assessed by logistic regression, Cox regression, Kaplan-Meier analysis, Spearman correlation, Student’s t-test and Chi-square test.ResultsIn pre-treatment biopsies, TREM1 and known TREM-1 inducible cytokines (IL1B, IL8) were discovered by a statistical ranking procedure as top genes for which high expression was associated with reduced response to NAC, but only in the context of immunologically “hot” tumors otherwise associated with a high NAC response rate. In surgical specimens, TREM1 expression varied among tumor molecular subtypes, with highest expression in the more aggressive subtypes (Basal-like, HER2-E). High TREM1 significantly and reproducibly associated with inferior distant metastasis-free survival (DMFS), independent of conventional prognostic markers. Notably, the association between high TREM1 and inferior DMFS was most prominent in the subset of immunogenic tumors that exhibited the immunologically hot phenotype and otherwise associated with superior DMFS. Further observations from bulk and single-cell RNAseq analyses indicated that TREM1 expression was significantly enriched in polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) and M2-like macrophages, and correlated with downstream transcriptional targets of TREM-1 (IL8, IL-1B, IL6, MCP-1, SPP1, IL1RN, INHBA) which have been previously associated with pro-tumorigenic and immunosuppressive functions.ConclusionsTogether, these findings indicate that increased TREM1 expression is prognostic of inferior breast cancer outcomes and may contribute to myeloid-mediated breast cancer progression and immune suppression.
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Affiliation(s)
- Ashok K. Pullikuth
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Eric D. Routh
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Julia Chifman
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- Department of Mathematics and Statistics, American University, Washington, DC, United States
| | - Jeff W. Chou
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, United States
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
| | - Michael H. Soike
- Department of Radiation Oncology, University of Alabama-Birmingham, Birmingham, AL, United States
| | - Guangxu Jin
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
| | - Jing Su
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, United States
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Qianqian Song
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- Center for Cancer Genomics and Precision Oncology, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Michael A. Black
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin, New Zealand
| | - Cristin Print
- Department of Molecular Medicine and Pathology and Maurice Wilkins Institute, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Davide Bedognetti
- Cancer Program, Sidra Medicine, Doha, Qatar & Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Marissa Howard-McNatt
- Surgical Oncology Service, Department of Surgery, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Stacey S. O’Neill
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
- Department of Pathology, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Alexandra Thomas
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
- Section of Hematology and Oncology, Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, NC, United States
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston Salem, NC, United States
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
| | | | - Yong Lu
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
- Department of Microbiology & Immunology, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Lance D. Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston Salem, NC, United States
- The Comprehensive Cancer Center of Wake Forest University, Winston Salem, NC, United States
- *Correspondence: Lance D. Miller,
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Terp MG, Gammelgaard OL, Vever H, Gjerstorff MF, Ditzel HJ. Sustained compensatory p38 MAPK signaling following treatment with MAPK inhibitors induces the immunosuppressive protein CD73 in cancer: combined targeting could improve outcomes. Mol Oncol 2021; 15:3299-3316. [PMID: 34165921 PMCID: PMC8637576 DOI: 10.1002/1878-0261.13046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/23/2021] [Accepted: 06/23/2021] [Indexed: 11/25/2022] Open
Abstract
RAS-MAPK signaling promotes immune evasion and cancer cell survival, and MAPK inhibitors (MAPKis) are frequently used as cancer therapies. Despite progress elucidating the direct effects of MAPKi on immune cells, their indirect effect on the tumor microenvironment (TME) through changes in tumor cells remains incompletely understood. Here, we present evidence of a rapid compensatory response to MAPKi that is driven by sustained p38 MAPK signaling and by which cancer cells can upregulate the immunosuppressive protein CD73 to reduce the antitumor immune response. This compensatory response also results in decreased sensitivity toward MAPKi, and, accordingly, combining anti-CD73 antibodies and MAPKi significantly enhances the antitumor effect compared to single-agent treatment in vivo. Combining MAPKi and anti-CD73 was accompanied by significant alterations in intratumor immune cell composition, supporting the effect of MAPKi-induced CD73 expression on the TME. We show that high CD73 expression significantly correlates with worse outcome in MAPKi-treated colorectal cancer patients, highlighting the potential clinical importance of increased CD73 expression following MAPKi treatment. Our findings may explain the diminished effect of MAPKi in cancer patients and provides further rationale for combined anti-CD73 and MAPKi treatment.
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Affiliation(s)
- Mikkel G. Terp
- Department of Cancer and Inflammation ResearchInstitute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Odd L. Gammelgaard
- Department of Cancer and Inflammation ResearchInstitute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Henriette Vever
- Department of Cancer and Inflammation ResearchInstitute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
| | - Morten F. Gjerstorff
- Department of Cancer and Inflammation ResearchInstitute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
- Department of OncologyOdense University HospitalDenmark
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Academy of Geriatric Cancer Research (AgeCare)Odense University HospitalDenmark
| | - Henrik J. Ditzel
- Department of Cancer and Inflammation ResearchInstitute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark
- Department of OncologyOdense University HospitalDenmark
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
- Academy of Geriatric Cancer Research (AgeCare)Odense University HospitalDenmark
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Ye T, Feng J, Cui M, Yang J, Wan X, Xie D, Liu J. LncRNA MIAT Services as a Noninvasive Biomarker for Diagnosis and Correlated with Immune Infiltrates in Breast Cancer. Int J Womens Health 2021; 13:991-1004. [PMID: 34712062 PMCID: PMC8548061 DOI: 10.2147/ijwh.s312714] [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] [Received: 03/25/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Background Myocardial infarction associated transcript (MIAT) is identified as a long chain non-coding RNA (lncRNA), which was associated with myocardial infarction susceptibility. While intense efforts have been made to elucidate the relationship between MIAT and carcinogenesis, the tumor immunoreaction of MIAT remains elusive. Thus, this study aimed to investigate the role of MIAT in the immunoregulation of breast cancer (BC) and further explore the better clinical significance. Methods The differential expression of MIAT between BC and normal/adjacent tissues was compared using Wilcoxon rank sum test. The diagnostic and prognostic values of elevated MIAT expression in BC tissues were unveiled via receiver operating characteristic (ROC) analysis and KM-plotter analysis. Limma and edgeR package were used to identify differentially expressed genes (DEGs) and microRNAs (DEMs) from TCGA database respectively. A co-expression dataset was constructed to comprehensively understand the relationship between MIAT and DEGs based on the Pearson correlation coefficient. Furthermore, GO and KEGG analyses were conducted to predict the potential functions of MIAT. We next intersected immune-related genes (IRGs) from ImmPort database with MIAT-co-expressed genes to obtain MIAT-co-expressed IRGs, in order to construct MIAT-microRNA (miRNA)-mRNA network. And the correlation between MIAT and tumor-infiltrating immune cells (TICs) and immunophenoscore (IPS) analysis was analyzed by TIMER and CIBERSORT. Finally, the reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was used to detect the expression profiles of MIAT in serum samples. Results The expression levels of MIAT were notably higher in BC than in normal or adjacent tissues. And MIAT expression could be used as a prognostic indicator of mortality risk in patients with BC in different aspects. Moreover, the enrichment analyses suggested that MIAT was strongly involved in BC immune response. In addition, TIMER database and CIBERSORT analyses indicated that MIAT was significantly correlated with 13 types of TICs (B cells, dendritic cells, neutrophils, CD8 T cells, CD4 memory resting T cells, CD4 memory activated T cells, gamma delta T cells, M1 macrophages, plasma cells, activated NK cells, monocytes, M2 macrophages, activated mast cells). Simultaneously, the IPS analysis implied that the higher the MIAT expression, the better the immunotherapy effect. The ROC curve analysis showed that the area under the curve (AUC) value of MIAT was 0.86 (sensitivity = 87.80%, specificity = 75.61%). And the high MIAT expression in serum was positive related to TNM stage (P = 0.032) and lymph node metastasis (P = 0.028). Conclusion MIAT may be a valuable noninvasive diagnostic biomarker for BC and is associated with tumor-infiltrating immune cells in tumor microenvironment, suggesting MIAT as a potential target for future treatment of BC.
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Affiliation(s)
- Ting Ye
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, People's Republic of China
| | - Jia Feng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, People's Republic of China
| | - Meng Cui
- Department of Laboratory Medicine, The Leshan People's Hospital, Luzhou, Sichuan, 614000, People's Republic of China
| | - Jia Yang
- Department of Laboratory Medicine, The Leshan People's Hospital, Luzhou, Sichuan, 614000, People's Republic of China
| | - Xue Wan
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, People's Republic of China
| | - Dan Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, People's Republic of China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, People's Republic of China
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Nanomedicine for Immunotherapy Targeting Hematological Malignancies: Current Approaches and Perspective. NANOMATERIALS 2021; 11:nano11112792. [PMID: 34835555 PMCID: PMC8619332 DOI: 10.3390/nano11112792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/04/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022]
Abstract
Conventional chemotherapy has partial therapeutic effects against hematological malignancies and is correlated with serious side effects and great risk of relapse. Recently, immunotherapeutic drugs have provided encouraging results in the treatment of hematological malignancies. Several immunotherapeutic antibodies and cell therapeutics are in dynamic development such as immune checkpoint blockades and CAR-T treatment. However, numerous problems restrain the therapeutic effectiveness of tumor immunotherapy as an insufficient anti-tumor immune response, the interference of an immune-suppressive bone marrow, or tumoral milieu with the discharge of immunosuppressive components, access of myeloid-derived suppressor cells, monocyte intrusion, macrophage modifications, all factors facilitating the tumor to escape the anti-cancer immune response, finally reducing the efficiency of the immunotherapy. Nanotechnology can be employed to overcome each of these aspects, therefore having the possibility to successfully produce anti-cancer immune responses. Here, we review recent findings on the use of biomaterial-based nanoparticles in hematological malignancies immunotherapy. In the future, a deeper understanding of tumor immunology and of the implications of nanomedicine will allow nanoparticles to revolutionize tumor immunotherapy, and nanomedicine approaches will reveal their great potential for clinical translation.
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Ma X, Chen H, Yang M, Ke Z, Wang M, Huang T, Li L. Classification of Estrogen Receptor-Positive Breast Cancer Based on Immunogenomic Profiling and Validation at Single-Cell Resolution. Front Cell Dev Biol 2021; 9:722841. [PMID: 34621742 PMCID: PMC8490889 DOI: 10.3389/fcell.2021.722841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The aim of this paper was to identify an immunotherapy-sensitive subtype for estrogen receptor-positive breast cancer (ER+ BC) patients by exploring the relationship between cancer genetic programs and antitumor immunity via multidimensional genome-scale analyses. Methods: Multidimensional ER+ BC high-throughput data (raw count data) including gene expression profiles, copy number variation (CNV) data, single-nucleotide polymorphism mutation data, and relevant clinical information were downloaded from The Cancer Genome Atlas to explore an immune subtype sensitive to immunotherapy using the Consensus Cluster Plus algorithm based on multidimensional genome-scale analyses. One ArrayExpress dataset and eight Gene Expression Omnibus (GEO) datasets (GEO-meta dataset) as well as the Molecular Taxonomy of Breast Cancer International Consortium dataset were used as validation sets to confirm the findings regarding the immune profiles, mutational features, and survival outcomes of the three identified immune subtypes. Moreover, the development trajectory of ER+ BC patients from the single-cell resolution level was also explored. Results: Through comprehensive bioinformatics analysis, three immune subtypes of ER+ BC (C1, C2, and C3, designated the immune suppressive, activation, and neutral subtypes, respectively) were identified. C2 was associated with up-regulated immune cell signatures and immune checkpoint genes. Additionally, five tumor-related pathways (transforming growth factor, epithelial-mesenchymal transition, extracellular matrix, interferon-γ, and WNT signaling) tended to be more activated in C2 than in C1 and C3. Moreover, C2 was associated with a lower tumor mutation burden, a decreased neoantigen load, and fewer CNVs. Drug sensitivity analysis further showed that C2 may be more sensitive to immunosuppressive agents. Conclusion: C2 (the immune activation subtype) may be sensitive to immunotherapy, which provides new insights into effective treatment approaches for ER+ BC.
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Affiliation(s)
- Xianxiong Ma
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hengyu Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Ming Yang
- Department of Pancreatic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zunxiang Ke
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengyi Wang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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38
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Naik A, Thomas R, Al-Khadairi G, Bacha R, Hendrickx W, Decock J. Cancer testis antigen PRAME: An anti-cancer target with immunomodulatory potential. J Cell Mol Med 2021; 25:10376-10388. [PMID: 34612587 PMCID: PMC8581324 DOI: 10.1111/jcmm.16967] [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: 05/25/2021] [Revised: 08/29/2021] [Accepted: 09/20/2021] [Indexed: 12/17/2022] Open
Abstract
PReferentially expressed Antigen in Melanoma (PRAME) is a cancer testis antigen with restricted expression in somatic tissues and re‐expression in poor prognostic solid tumours. PRAME has been extensively investigated as a target for immunotherapy, however, its role in modulating the anti‐tumour immune response remains largely unknown. Here, we show that PRAME tumour expression is associated with worse survival in the TCGA breast cancer cohort, particularly in immune‐unfavourable tumours. Using direct and indirect co‐culture models, we found that PRAME overexpressing MDA‐MB‐468 breast cancer cells inhibit T cell activation and cytolytic potential, which could be partly restored by silencing of PRAME. Furthermore, silencing of PRAME reduced expression of several immune checkpoints and their ligands, including PD‐1, LAG3, PD‐L1, CD86, Gal‐9 and VISTA. Interestingly, silencing of PRAME induced cancer cell killing to levels similar to anti‐PD‐L1 atezolizumab treatment. Comprehensive analysis of soluble inflammatory mediators and cancer cell expression of immune‐related genes showed that PRAME tumour expression can suppress the expression and secretion of multiple pro‐inflammatory cytokines, and mediators of T cell activation, differentiation and cytolysis. Together, our data indicate that targeting of PRAME offers a potential, novel dual therapeutic approach to specifically target tumour cells and regulate immune activation in the tumour microenvironment.
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Affiliation(s)
- Adviti Naik
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Remy Thomas
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Ghaneya Al-Khadairi
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Rim Bacha
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Wouter Hendrickx
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,Cancer Department, Research Branch, Sidra Medicine, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.,College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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39
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Zhang H, Wang Z, Dai Z, Wu W, Cao H, Li S, Zhang N, Cheng Q. Novel Immune Infiltrating Cell Signature Based on Cell Pair Algorithm Is a Prognostic Marker in Cancer. Front Immunol 2021; 12:694490. [PMID: 34594324 PMCID: PMC8476752 DOI: 10.3389/fimmu.2021.694490] [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] [Received: 04/13/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022] Open
Abstract
Tumor-infiltrating immune cells (TIICs) have become an important source of markers for predicting the clinical outcomes of cancer patients. However, measurements of cellular heterogeneity vary due to the frequently updated reference genomes and gene annotations. In this study, we systematically collected and evaluated the infiltration pattern of 65 immune cells. We constructed the Immune Cell Pair (ICP) score based on the cell pair algorithm in 3,715 samples and across 12 independent cancer types, among which, the ICP score from six cancer types was further validated in 2,228 GEO samples. An extensive tumorigenic and immunogenomic analysis was subsequently conducted. As a result, the ICP score showed a robust reliability and efficacy in predicting the survival of patients with gliomas, in pan-cancer samples, and six independent cancer types. Notably, the ICP score was correlated with the genomic alteration features in gliomas. Moreover, the ICP score exhibited a remarkable association with multiple immunomodulators that could potentially mediate immune escape. Finally, the ICP score predicted immunotherapeutic responses with a high sensitivity, allowing a useful tool for predicting the overall survival and guiding immunotherapy for cancer patients.
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Affiliation(s)
- Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wantao Wu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Cao
- Department of Psychiatry, The Second People's Hospital of Hunan Province, The Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Shuyu Li
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Nan Zhang
- One-third Lab, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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40
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Yu QY, Lu TP, Hsiao TH, Lin CH, Wu CY, Tzeng JY, Hsiao CK. An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data. Front Genet 2021; 12:709555. [PMID: 34567069 PMCID: PMC8456116 DOI: 10.3389/fgene.2021.709555] [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: 05/14/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic studies have been a major approach to elucidating disease etiology and to exploring potential targets for treatments of many complex diseases. Statistical analyses in these studies often face the challenges of multiplicity, weak signals, and the nature of dependence among genetic markers. This situation becomes even more complicated when multi-omics data are available. To integrate the data from different platforms, various integrative analyses have been adopted, ranging from the direct union or intersection operation on sets derived from different single-platform analysis to complex hierarchical multi-level models. The former ignores the biological relationship between molecules while the latter can be hard to interpret. We propose in this study an integrative approach that combines both single nucleotide variants (SNVs) and copy number variations (CNVs) in the same genomic unit to co-localize the concurrent effect and to deal with the sparsity due to rare variants. This approach is illustrated with simulation studies to evaluate its performance and is applied to low-density lipoprotein cholesterol and triglyceride measurements from Taiwan Biobank. The results show that the proposed method can more effectively detect the collective effect from both SNVs and CNVs compared to traditional methods. For the biobank analysis, the identified genetic regions including the gene VNN2 could be novel and deserve further investigation.
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Affiliation(s)
- Qi-You Yu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ching-Heng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Yun Wu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, United States.,Department of Statistics, University of Pennsylvania, Philadelphia, PA, United States
| | - Jung-Ying Tzeng
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States
| | - Chuhsing Kate Hsiao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
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Winkler C, King M, Berthe J, Ferraioli D, Garuti A, Grillo F, Rodriguez-Canales J, Ferrando L, Chopin N, Ray-Coquard I, Delpuech O, Rinchai D, Bedognetti D, Ballestrero A, Leo E, Zoppoli G. SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in high-grade serous ovarian cancer. JCI Insight 2021; 6:146098. [PMID: 34549724 PMCID: PMC8492341 DOI: 10.1172/jci.insight.146098] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/28/2021] [Indexed: 01/30/2023] Open
Abstract
Large independent analyses on cancer cell lines followed by functional studies have identified Schlafen 11 (SLFN11), a putative helicase, as the strongest predictor of sensitivity to DNA-damaging agents (DDAs), including platinum. However, its role as a prognostic biomarker is undefined, partially due to the lack of validated methods to score SLFN11 in human tissues. Here, we implemented a pipeline to quantify SLFN11 in human cancer samples. By analyzing a cohort of high-grade serous ovarian carcinoma (HGSOC) specimens before platinum-based chemotherapy treatment, we show, for the first time to our knowledge, that SLFN11 density in both the neoplastic and microenvironmental components was independently associated with favorable outcome. We observed SLFN11 expression in both infiltrating innate and adaptive immune cells, and analyses in a second, independent, cohort revealed that SLFN11 was associated with immune activation in HGSOC. We found that platinum treatments activated immune-related pathways in ovarian cancer cells in an SLFN11-dependent manner, representative of tumor-immune transactivation. Moreover, SLFN11 expression was induced in activated, isolated immune cell subpopulations, hinting that SLFN11 in the immune compartment may be an indicator of immune transactivation. In summary, we propose SLFN11 is a dual biomarker capturing simultaneously interconnected immunological and cancer cell–intrinsic functional dispositions associated with sensitivity to DDA treatment.
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Affiliation(s)
| | | | - Julie Berthe
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, United Kingdom
| | | | - Anna Garuti
- Department of Internal Medicine and Medical Specialties and
| | - Federica Grillo
- Department of Integrated Surgical and Diagnostic Sciences, University of Genova, Genova, Italy.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | | | | | | | | | | | - Davide Bedognetti
- Department of Internal Medicine and Medical Specialties and.,Cancer Research Department, Sidra Medicine, Doha, Qatar.,Hamad Bin Khalifa University, Doha, Qatar
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties and.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties and.,IRCCS Ospedale Policlinico San Martino, Genova, Italy
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42
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Xie P, An R, Yu S, He J, Zhang H. A novel immune subtype classification of ER-positive, PR-negative and HER2-negative breast cancer based on the genomic and transcriptomic landscape. J Transl Med 2021; 19:398. [PMID: 34544424 PMCID: PMC8454077 DOI: 10.1186/s12967-021-03076-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/10/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The diversity and plasticity behind ER+/PR-/HER2- breast cancer have not been widely explored. It is essential to identify heterogeneous microenvironment phenotypes and investigate specific genomic events driving the formation of these phenotypes. METHODS Based on the immune-related gene expression profiles of 411 ER+/PR-/HER2- breast cancers in the METABRIC cohort, we used consensus clustering to identify heterogeneous immune subtypes and assessed their reproducibility in an independent meta-cohort including 135 patients collected from GEO database. We further analyzed the differences of cellular and molecular characteristics, and potential immune escape mechanism among immune subtypes. In addition, we constructed a transcriptional trajectory to visualize the distribution of individual patient. RESULTS Our analysis identified and validated five reproducible immune subtypes with distinct cellular and molecular characteristics, potential immune escape mechanisms, genomic drivers, as well as clinical outcomes. An immune-cold subtype, with the least amount of lymphocyte infiltration, had a poorer prognosis. By contrast, an immune-hot subtype, which demonstrated the highest infiltration of CD8+ T cells, DCs and NK cells, and elevated IFN-γ response, had a comparatively favorable prognosis. Other subtypes showed more diverse gene expression and immune infiltration patterns with distinct clinical outcomes. Finally, our analysis revealed a complex immune landscape consisting of both discrete cluster and continuous spectrum. CONCLUSION Overall, this study revealed five heterogeneous immune subtypes among ER+/PR-/HER2- breast cancer, also provided important implications for clinical translations.
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Affiliation(s)
- Peiling Xie
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China
| | - Rui An
- Department of Hepatological Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China
| | - Shibo Yu
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China.
| | - Huimin Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, 710061, Xi'an, People's Republic of China.
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Kossai M, Radosevic-Robin N, Penault-Llorca F. Refining patient selection for breast cancer immunotherapy: beyond PD-L1. ESMO Open 2021; 6:100257. [PMID: 34487970 PMCID: PMC8426207 DOI: 10.1016/j.esmoop.2021.100257] [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: 03/22/2021] [Revised: 07/27/2021] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
Therapies that modulate immune response to cancer, such as immune checkpoint inhibitors, began an intense development a few years ago; however, in breast cancer (BC), the results have been relatively disappointing so far. Finding biomarkers for better selection of BC patients for various immunotherapies remains a significant unmet medical need. At present, only tumour tissue programmed death-ligand 1 (PD-L1) and mismatch repair deficiency status are approved as theranostic biomarkers for programmed cell death-1 (PD-1)/PD-L1 inhibitors in BC. However, due to the complexity of tumour microenvironment (TME) and cancer response to immunomodulators, none of them is a perfect selector. Therefore, an intense quest is ongoing for complementary tumour- or host-related predictive biomarkers in breast immuno-oncology. Among the upcoming biomarkers, quantity, immunophenotype and spatial distribution of tumour-infiltrating lymphocytes and other TME cells as well as immune gene signatures emerge as most promising and are being increasingly tested in clinical trials. Biomarkers or strategies allowing dynamic assessment of BC response to immunotherapy, such as circulating/exosomal PD-L1, quantity of white/immune blood cell subpopulations and molecular imaging are particularly suitable for immunotreatment monitoring. Finally, host-related factors, such as microbiome and lifestyle, should also be taken into account when planning integration of immunomodulating therapies into BC management. As none of the biomarkers taken separately is accurate enough, the solution could come from composite biomarkers, which would combine clinical, molecular and immunological features of the disease, possibly powered by artificial intelligence. At present, immune checkpoint inhibitors (ICIs) are the only approved immunotherapy drugs in BC. Tumour PD-L1 and microsatellite status are current companion biomarkers for ICIs in BC; however, these need improvement. Evaluation of tumour immune contexture and the dynamics of circulating immune cell counts are promising novel approaches. Development of noninvasive monitoring and composite biomarkers will facilitate cancer immunotherapy, including in BC.
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Affiliation(s)
- M Kossai
- Department of Pathology, University Clermont Auvergne, INSERM U1240, Centre Jean Perrin, Clermont-Ferrand, France
| | - N Radosevic-Robin
- Department of Pathology, University Clermont Auvergne, INSERM U1240, Centre Jean Perrin, Clermont-Ferrand, France.
| | - F Penault-Llorca
- Department of Pathology, University Clermont Auvergne, INSERM U1240, Centre Jean Perrin, Clermont-Ferrand, France
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Can the New and Old Drugs Exert an Immunomodulatory Effect in Acute Myeloid Leukemia? Cancers (Basel) 2021; 13:cancers13164121. [PMID: 34439275 PMCID: PMC8393879 DOI: 10.3390/cancers13164121] [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: 07/08/2021] [Revised: 08/11/2021] [Accepted: 08/14/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary The advent of novel immunotherapeutic strategies has revealed the importance of immune dysregulation and of a tolerogenic microenvironment for acute myeloid leukemia (AML) fitness. We reviewed the “off-target” effects on the immune system of different drugs used in the treatment of AML to explore the advantages of this unexpected interaction. Abstract Acute myeloid leukemia (AML) is considered an immune-suppressive neoplasm capable of evading immune surveillance through cellular and environmental players. Increasing knowledge of the immune system (IS) status at diagnosis seems to suggest ever more attention of the crosstalk between the leukemic clone and its immunologic counterpart. During the last years, the advent of novel immunotherapeutic strategies has revealed the importance of immune dysregulation and suppression for leukemia fitness. Considering all these premises, we reviewed the “off-target” effects on the IS of different drugs used in the treatment of AML, focusing on the main advantages of this interaction. The data reported support the idea that a successful therapeutic strategy should consider tailored approaches for performing leukemia eradication by both direct blasts killing and the engagement of the IS.
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45
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Heeke AL, Tan AR. Checkpoint inhibitor therapy for metastatic triple-negative breast cancer. Cancer Metastasis Rev 2021; 40:537-547. [PMID: 34101053 PMCID: PMC8184866 DOI: 10.1007/s10555-021-09972-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/27/2021] [Indexed: 12/03/2022]
Abstract
Immunotherapy has become a mainstay of cancer treatment in many malignancies, though its application in breast cancer remains limited. Of the breast cancer subtypes, triple-negative breast cancers (TNBCs) are characterized by immune activation and infiltration and more commonly express biomarkers associated with response to immunotherapy. Checkpoint inhibitor therapy has shown promising activity in metastatic TNBC. In 2019, the US FDA granted accelerated approval of atezolizumab, a programmed death-ligand 1 (PD-L1) inhibitor, in combination with nab-paclitaxel for unresectable locally advanced or metastatic PD-L1-positive TNBC, based on the results of the phase III IMpassion130 trial. In 2020, the FDA also granted accelerated approval of pembrolizumab, a PD-1 inhibitor, in combination with chemotherapy for locally recurrent unresectable and metastatic PD-L1-positive TNBC, based on results of the phase III KEYNOTE-355 trial. Additional combination strategies are being explored in the treatment of metastatic TNBC, with the goal of augmenting antitumor activity. In this review, the clinical development of checkpoint inhibitors in the treatment of metastatic TNBC will be discussed, including clinical outcomes with monotherapy and combination therapy regimens, biomarkers that may predict for benefit, and future directions in the field.
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Torii Y, Nanjo K, Toubai T, Hosokawa M, Sato R, Yamada A, Aizawa K, Himuro M, Ito S, Yamamoto M, Magenau J, Wilcox R, Ishizawa K. A unique three-way Philadelphia chromosome variant t(4;9;22)(q21;q34;q11.2) in a newly diagnosed patient with chronic phase chronic myeloid leukemia: a case report and review of the literature. J Med Case Rep 2021; 15:285. [PMID: 34030730 PMCID: PMC8146239 DOI: 10.1186/s13256-021-02885-4] [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: 02/04/2021] [Accepted: 04/28/2021] [Indexed: 12/04/2022] Open
Abstract
Background Chronic myeloid leukemia is a hematologic malignancy associated with the fusion of two genes: BCR and ABL1. This fusion results from a translocation between chromosomes 9 and 22, which is called the Philadelphia chromosome. Although the Philadelphia chromosome is present in more than 90% of patients with chronic myeloid leukemia, 5–8% of patients with chronic myeloid leukemia show complex variant translocations. Herein, we report a unique case of a three-way translocation variant in chronic phase chronic myeloid leukemia. Case presentation A 40-year-old Asian male who presented with leukocytosis was diagnosed with chronic phase chronic myeloid leukemia. Cytogenetic karyotyping analysis showed 46,XY,t(4;9;22)(q21;q34;q11.2). He was treated with bosutinib and then changed to dasatinib because of intolerance, and MR4.5 (BCR-ABL/ABL ≦ 0.0032%, international scale) was achieved after 17 months of continuous treatment. Conclusion This was the 14th case of t(4;9;22), in particular, a new variant Ph translocation involved in chromosome 4q21 and the first successful case treated with tyrosine kinase inhibitors in the world. We summarize previous case reports regarding three-way variant chromosome translocation, t(4;9;22) and discuss how this rare translocation is linked to prognosis.
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Affiliation(s)
- Yuka Torii
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
| | - Kana Nanjo
- Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Tomomi Toubai
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan.
| | - Masashi Hosokawa
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
| | - Ryo Sato
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
| | - Akane Yamada
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
| | - Keiko Aizawa
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
| | - Masahito Himuro
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
| | - Satoshi Ito
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
| | - Masakazu Yamamoto
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
| | - John Magenau
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ryan Wilcox
- Department of Internal Medicine, Division of Hematology and Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kenichi Ishizawa
- Department of Internal Medicine III, Division of Hematology and Cell Therapy, Yamagata University faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata, 990-9585, Japan
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Tolba MF, Elghazaly H, Bousoik E, Elmazar MMA, Tolaney SM. Novel combinatorial strategies for boosting the efficacy of immune checkpoint inhibitors in advanced breast cancers. Clin Transl Oncol 2021; 23:1979-1994. [PMID: 33871826 DOI: 10.1007/s12094-021-02613-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022]
Abstract
The year 2019 witnessed the first approval of an immune checkpoint inhibitor (ICI) for the management of triple negative breast cancers (TNBC) that are metastatic and programmed death ligand (PD)-L1 positive. Extensive research has focused on testing ICI-based combinatorial strategies, with the ultimate goal of enhancing the response of breast tumors to immunotherapy to increase the number of breast cancer patients benefiting from this transformative treatment. The promising investigational strategies included immunotherapy combinations with monoclonal antibodies (mAbs) against human epidermal growth factor receptor (HER)-2 for the HER2 + tumors versus cyclin-dependent kinase (CDK)4/6 inhibitors in the estrogen receptor (ER) + disease. Multiple approaches are showing signals of success in advanced TNBC include employing Poly (ADP-ribose) polymerase (PARP) inhibitors, tyrosine kinase inhibitors, MEK inhibitors, phosphatidylinositol 3‑kinase (PI3K)/protein kinase B (AKT) signaling inhibitors or inhibitors of adenosine receptor, in combination with the classical PD-1/PD-L1 immune checkpoint inhibitors. Co-treatment with chemotherapy, high intensity focused ultrasound (HIFU) or interleukin-2-βɣ agonist have also produced promising outcomes. This review highlights the latest combinatorial strategies under development for overcoming cancer immune evasion and enhancing the percentage of immunotherapy responders in the different subsets of advanced breast cancers.
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Affiliation(s)
- M F Tolba
- Department of Pharmacology and Toxicology, Faculty of Pharmacy and Center of Drug Discovery Research and Development, Ain Shams University, Cairo, 11566, Egypt.
- School of Life and Medical Sciences, University of Hertfordshire-Hosted By Global Academic Foundation, New Capital City, Egypt.
| | - H Elghazaly
- Clinical Oncology Department, and Medical Research Center (MASRI), Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - E Bousoik
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Chapman University, Irvine, CA, USA
- School of Pharmacy, Omar-Al-Mukhtar University, Derna, Libya
| | - M M A Elmazar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, The British University in Egypt (BUE), 11837, El Sherouk City, Egypt
| | - S M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Harvard Medical School, Boston, MA, USA
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Ghidini M, Petrillo A, Botticelli A, Trapani D, Parisi A, La Salvia A, Sajjadi E, Piciotti R, Fusco N, Khakoo S. How to Best Exploit Immunotherapeutics in Advanced Gastric Cancer: Between Biomarkers and Novel Cell-Based Approaches. J Clin Med 2021; 10:1412. [PMID: 33915839 PMCID: PMC8037391 DOI: 10.3390/jcm10071412] [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: 02/14/2021] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Despite extensive research efforts, advanced gastric cancer still has a dismal prognosis with conventional treatment options. Immune checkpoint inhibitors have revolutionized the treatment landscape for many solid tumors. Amongst gastric cancer subtypes, tumors with microsatellite instability and Epstein Barr Virus positive tumors provide the strongest rationale for responding to immunotherapy. Various predictive biomarkers such as mismatch repair status, programmed death ligand 1 expression, tumor mutational burden, assessment of tumor infiltrating lymphocytes and circulating biomarkers have been evaluated. However, results have been inconsistent due to different methodologies and thresholds used. Clinical implementation therefore remains a challenge. The role of immune checkpoint inhibitors in gastric cancer is emerging with data from monotherapy in the heavily pre-treated population already available and studies in earlier disease settings with different combinatorial approaches in progress. Immune checkpoint inhibitor combinations with chemotherapy (CT), anti-angiogenics, tyrosine kinase inhibitors, anti-Her2 directed therapy, poly (ADP-ribose) polymerase inhibitors or dual checkpoint inhibitor strategies are being explored. Moreover, novel strategies including vaccines and CAR T cell therapy are also being trialed. Here we provide an update on predictive biomarkers for response to immunotherapy with an overview of their strengths and limitations. We discuss clinical trials that have been reported and trials in progress whilst providing an account of future steps needed to improve outcome in this lethal disease.
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Affiliation(s)
- Michele Ghidini
- Medical Oncology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | | | - Andrea Botticelli
- Department of Clinical and Molecular Medicine, Sapienza University, 00189 Rome, Italy;
- Medical Oncology (B), Policlinico Umberto I, 00161 Rome, Italy
| | - Dario Trapani
- Division of Early Drug Development for innovative therapies, European Institute of Oncology, IRCCS, 20141 Milan, Italy;
| | - Alessandro Parisi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
- Medical Oncology Unit, St. Salvatore Hospital, 67100 L’Aquila, Italy
| | - Anna La Salvia
- Department of Oncology, University Hospital 12 De Octubre, 28041 Madrid, Spain;
| | - Elham Sajjadi
- Division of Pathology, European Institute of Oncology, IRCCS, 20141 Milan, Italy; (E.S.); (R.P.); (N.F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Roberto Piciotti
- Division of Pathology, European Institute of Oncology, IRCCS, 20141 Milan, Italy; (E.S.); (R.P.); (N.F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Nicola Fusco
- Division of Pathology, European Institute of Oncology, IRCCS, 20141 Milan, Italy; (E.S.); (R.P.); (N.F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Shelize Khakoo
- Department of Medicine, Royal Marsden Hospital, London and Surrey, Sutton SM25PT, UK;
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Xu FF, Zheng SF, Xu C, Cai G, Wang SB, Qi WX, Wang CF, Chen JY, Lu C. Prognostic and predictive significance of tumor infiltrating lymphocytes for ductal carcinoma in situ. Oncoimmunology 2021; 10:1875637. [PMID: 33796401 PMCID: PMC7993193 DOI: 10.1080/2162402x.2021.1875637] [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] [Indexed: 11/08/2022] Open
Abstract
This study aims to identify the density of TILs in ductal carcinoma in situ (DCIS) in terms of prognostic significance with recurrence and the benefit of whole breast irradiation (WBI). The clinicopathological data of DCIS patients from Jan 2009 to Dec 2016 who received breast-conserving surgery (BCS) were retrospectively reviewed. Cox regression analysis was used to confirm independent prognostic factors of ipsilateral breast tumor recurrence (IBTR). Kaplan–Meier method was utilized to analyze IBTR and values of WBI. Touching-tumor-infiltrating lymphocytes (TILs) were defined by TILs touching or within one lymphocyte cell thickness from the malignant ducts’ basement membrane. In total, 129 patients were enrolled in this analysis with 98 patients who received WBI. After a median follow-up of 53.0 months, there were 16 IBTR events with five invasive IBTRs. Univariate and multivariate analyses showed that touching-TILs >5 were an independent prognostic factor for higher IBTR (HR = 6.17, 95%CI 1.95–19.56, p < .01). The whole cohort was classified into two subgroups: dense group (>5 touching-TILs per duct) and sparse group (≤5 touching-TILs per duct). Dense touching-TILs were associated with unfavorable biologic characteristics. The 5-y rate of IBTR between dense and sparse group was 29.0% versus 4.5% (p < .01). For the sparse group, WBI significantly reduced the rate of 5-y-IBTR risk from 13.2% to 1.7% (p = .02), but there was no benefit of WBI in the dense group. Touching-TILs density was heterogeneous in patients with DCIS. Sparse touching-TILs were associated with better prognosis and benefit from WBI. Dense touching-TILs not only were associated with a higher risk of IBTR but also lack of benefit from WBI.
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Affiliation(s)
- Fei-Fei Xu
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Sai-Fang Zheng
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Cheng Xu
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Gang Cai
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shu-Bei Wang
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Wei-Xiang Qi
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Chao-Fu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jia-Yi Chen
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Cao Lu
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Thomas R, Al-Khadairi G, Decock J. Immune Checkpoint Inhibitors in Triple Negative Breast Cancer Treatment: Promising Future Prospects. Front Oncol 2021; 10:600573. [PMID: 33718107 PMCID: PMC7947906 DOI: 10.3389/fonc.2020.600573] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
Immunotherapy has emerged as the fifth pillar of cancer treatment alongside surgery, radiotherapy, chemotherapy, and targeted therapy. Immune checkpoint inhibitors are the current superheroes of immunotherapy, unleashing a patient's own immune cells to kill tumors and revolutionizing cancer treatment in a variety of cancers. Although breast cancer was historically believed to be immunologically silent, treatment with immune checkpoint inhibitors has been shown to induce modest responses in metastatic breast cancer. Given the inherent heterogeneity of breast tumors, this raised the question whether certain breast tumors might benefit more from immune-based interventions and which cancer cell-intrinsic and/or microenvironmental factors define the likelihood of inducing a potent and durable anti-tumor immune response. In this review, we will focus on triple negative breast cancer as immunogenic breast cancer subtype, and specifically discuss the relevance of tumor mutational burden, the plethora and diversity of tumor infiltrating immune cells in addition to the immunoscore, the presence of immune checkpoint expression, and the microbiome in defining immune checkpoint blockade response. We will highlight the current immune checkpoint inhibitor treatment options, either as monotherapy or in combination with standard-of-care treatment modalities such as chemotherapy and targeted therapy. In addition, we will look into the potential of immunotherapy-based combination strategies using immune checkpoint inhibitors to enhance both innate and adaptive immune responses, or to establish a more immune favorable environment for cancer vaccines. Finally, the review will address the need for unambiguous predictive biomarkers as one of the main challenges of immune checkpoint blockade. To conclude, the potential of immune checkpoint blockade for triple negative breast cancer treatment could be enhanced by exploration of aforementioned factors and treatment strategies thereby providing promising future prospects.
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Affiliation(s)
- Remy Thomas
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Ghaneya Al-Khadairi
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Julie Decock
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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