1
|
Yan H, Ju X, Huang A, Yuan J. Advancements in technology for characterizing the tumor immune microenvironment. Int J Biol Sci 2024; 20:2151-2167. [PMID: 38617534 PMCID: PMC11008272 DOI: 10.7150/ijbs.92525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/12/2024] [Indexed: 04/16/2024] Open
Abstract
Immunotherapy plays a key role in cancer treatment, however, responses are limited to a small number of patients. The biological basis for the success of immunotherapy is the complex interaction between tumor cells and tumor immune microenvironment (TIME). Historically, research on tumor immune constitution was limited to the analysis of one or two markers, more novel technologies are needed to interpret the complex interactions between tumor cells and TIME. In recent years, major advances have already been made in depicting TIME at a considerably elevated degree of throughput, dimensionality and resolution, allowing dozens of markers to be labeled simultaneously, and analyzing the heterogeneity of tumour-immune infiltrates in detail at the single cell level, depicting the spatial landscape of the entire microenvironment, as well as applying artificial intelligence (AI) to interpret a large amount of complex data from TIME. In this review, we summarized emerging technologies that have made contributions to the field of TIME, and provided prospects for future research.
Collapse
Affiliation(s)
- Honglin Yan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | | | | | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| |
Collapse
|
2
|
Feng S, Calinawan A, Pugliese P, Wang P, Ceccarelli M, Petralia F, Gosline SJC. Decomprolute is a benchmarking platform designed for multiomics-based tumor deconvolution. CELL REPORTS METHODS 2024; 4:100708. [PMID: 38412834 PMCID: PMC10921018 DOI: 10.1016/j.crmeth.2024.100708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/29/2024]
Abstract
Tumor deconvolution enables the identification of diverse cell types that comprise solid tumors. To date, however, both the algorithms developed to deconvolve tumor samples, and the gold-standard datasets used to assess the algorithms are geared toward the analysis of gene expression (e.g., RNA sequencing) rather than protein levels. Despite the popularity of gene expression datasets, protein levels often provide a more accurate view of rare cell types. To facilitate the use, development, and reproducibility of multiomic deconvolution algorithms, we introduce Decomprolute, a Common Workflow Language framework that leverages containerization to compare tumor deconvolution algorithms across multiomic datasets. Decomprolute incorporates the large-scale multiomic datasets produced by the Clinical Proteomic Tumor Analysis Consortium (CPTAC), which include matched mRNA expression and proteomic data from thousands of tumors across multiple cancer types to build a fully open-source, containerized proteogenomic tumor deconvolution benchmarking platform. http://pnnl-compbio.github.io/decomprolute.
Collapse
Affiliation(s)
- Song Feng
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Anna Calinawan
- Icahn School of Medicine at Mount Sinai School, New York, NY, USA
| | | | - Pei Wang
- Icahn School of Medicine at Mount Sinai School, New York, NY, USA
| | | | | | | |
Collapse
|
3
|
Adhikary S, Pathak S, Palani V, Acar A, Banerjee A, Al-Dewik NI, Essa MM, Mohammed SGAA, Qoronfleh MW. Current Technologies and Future Perspectives in Immunotherapy towards a Clinical Oncology Approach. Biomedicines 2024; 12:217. [PMID: 38255322 PMCID: PMC10813720 DOI: 10.3390/biomedicines12010217] [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: 12/04/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Immunotherapy is now established as a potent therapeutic paradigm engendering antitumor immune response against a wide range of malignancies and other diseases by modulating the immune system either through the stimulation or suppression of immune components such as CD4+ T cells, CD8+ T cells, B cells, monocytes, macrophages, dendritic cells, and natural killer cells. By targeting several immune checkpoint inhibitors or blockers (e.g., PD-1, PD-L1, PD-L2, CTLA-4, LAG3, and TIM-3) expressed on the surface of immune cells, several monoclonal antibodies and polyclonal antibodies have been developed and already translated clinically. In addition, natural killer cell-based, dendritic cell-based, and CAR T cell therapies have been also shown to be promising and effective immunotherapeutic approaches. In particular, CAR T cell therapy has benefited from advancements in CRISPR-Cas9 genome editing technology, allowing the generation of several modified CAR T cells with enhanced antitumor immunity. However, the emerging SARS-CoV-2 infection could hijack a patient's immune system by releasing pro-inflammatory interleukins and cytokines such as IL-1β, IL-2, IL-6, and IL-10, and IFN-γ and TNF-α, respectively, which can further promote neutrophil extravasation and the vasodilation of blood vessels. Despite the significant development of advanced immunotherapeutic technologies, after a certain period of treatment, cancer relapses due to the development of resistance to immunotherapy. Resistance may be primary (where tumor cells do not respond to the treatment), or secondary or acquired immune resistance (where tumor cells develop resistance gradually to ICIs therapy). In this context, this review aims to address the existing immunotherapeutic technologies against cancer and the resistance mechanisms against immunotherapeutic drugs, and explain the impact of COVID-19 on cancer treatment. In addition, we will discuss what will be the future implementation of these strategies against cancer drug resistance. Finally, we will emphasize the practical steps to lay the groundwork for enlightened policy for intervention and resource allocation to care for cancer patients.
Collapse
Affiliation(s)
- Subhamay Adhikary
- Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Surajit Pathak
- Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Vignesh Palani
- Faculty of Medicine, Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Türkiye;
| | - Antara Banerjee
- Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Nader I. Al-Dewik
- Department of Pediatrics, Women’s Wellness and Research Center, Hamad Medical Corporation, Doha 00974, Qatar;
| | - Musthafa Mohamed Essa
- College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat 123, Oman
| | | | - M. Walid Qoronfleh
- Research & Policy Division, Q3 Research Institute (QRI), Ypsilanti, MI 48917, USA
| |
Collapse
|
4
|
Zecca A, Barili V, Boni C, Fisicaro P, Vecchi A, Rossi M, Reverberi V, Montali A, Pedrazzi G, Ferrari C, Cariani E, Missale G. High CD49a+ NK cell infiltrate is associated with poor clinical outcomes in Hepatocellular Carcinoma. Heliyon 2023; 9:e22680. [PMID: 38107324 PMCID: PMC10724659 DOI: 10.1016/j.heliyon.2023.e22680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/30/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
NK cells infiltrating Hepatocellular Carcinoma (HCC) may express residency markers such as Integrin Subunit Alpha 1 (CD49a) that have been associated with nurturing functions in the decidua, and characterized by the production of angiogenic factors as well as loss of cytotoxicity. CIBERSORT, a computational analysis method for quantifying cell fractions from bulk tissue gene expression profiles, was used to estimate the infiltrating immune cell composition of the tumor microenvironment from gene expression profiles of a large cohort of 225 HCCs in the public GEO database. Decidual-like CD49a+ NK cells, in addition to another 22 immune cell populations, were characterized and thoroughly investigated so that HCC cell heterogeneity in a large cohort of 225 HCCs from the public GEO database could be studied. An inverse correlation of the expression of CD49a+ NK-cells and CD8+ T-cells suggested a negative association with clinical outcomes. This result was confirmed in a further validation cohort of 100 HCC patients from The Cancer Genome Atlas, Liver Hepatocellular Carcinoma (TCGA-LIHC). Cox regression analysis did not identify CD49a+ cells as a variable independently associated with survival. However, a more abundant infiltrate of this subset was present in patients at a more advanced pathological and clinical HCC stage. In conclusion, we found that NK cells, with a decidual-like gene expression profile, are enriched in HCC, and their abundance increases not only in tumor size but also at advanced stages of the disease suggesting that these cells play a role in tumor growth. For this reason, these NK cells may represent a possible new target for immunotherapeutic approaches in HCC.
Collapse
Affiliation(s)
- Alessandra Zecca
- Unit of Infectious Diseases and Hepatology, Laboratory of Viral Immunopathology, Azienda Ospedaliero–Universitaria of Parma, 43126 Parma, Italy
| | - Valeria Barili
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Carolina Boni
- Unit of Infectious Diseases and Hepatology, Laboratory of Viral Immunopathology, Azienda Ospedaliero–Universitaria of Parma, 43126 Parma, Italy
| | - Paola Fisicaro
- Unit of Infectious Diseases and Hepatology, Laboratory of Viral Immunopathology, Azienda Ospedaliero–Universitaria of Parma, 43126 Parma, Italy
| | - Andrea Vecchi
- Unit of Infectious Diseases and Hepatology, Laboratory of Viral Immunopathology, Azienda Ospedaliero–Universitaria of Parma, 43126 Parma, Italy
| | - Marzia Rossi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Valentina Reverberi
- Unit of Infectious Diseases and Hepatology, Laboratory of Viral Immunopathology, Azienda Ospedaliero–Universitaria of Parma, 43126 Parma, Italy
| | - Anna Montali
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Giuseppe Pedrazzi
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Carlo Ferrari
- Unit of Infectious Diseases and Hepatology, Laboratory of Viral Immunopathology, Azienda Ospedaliero–Universitaria of Parma, 43126 Parma, Italy
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Gabriele Missale
- Unit of Infectious Diseases and Hepatology, Laboratory of Viral Immunopathology, Azienda Ospedaliero–Universitaria of Parma, 43126 Parma, Italy
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| |
Collapse
|
5
|
Wang Z, Katsaros D, Wang J, Biglio N, Hernandez BY, Fei P, Lu L, Risch H, Yu H. Machine learning-based cluster analysis of immune cell subtypes and breast cancer survival. Sci Rep 2023; 13:18962. [PMID: 37923775 PMCID: PMC10624674 DOI: 10.1038/s41598-023-45932-4] [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: 12/16/2022] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
Host immunity involves various immune cells working in concert to achieve balanced immune response. Host immunity interacts with tumorigenic process impacting disease outcome. Clusters of different immune cells may reveal unique host immunity in relation to breast cancer progression. CIBERSORT algorithm was used to estimate relative abundances of 22 immune cell types in 3 datasets, METABRIC, TCGA, and our study. The cell type data in METABRIC were analyzed for cluster using unsupervised hierarchical clustering (UHC). The UHC results were employed to train machine learning models. Kaplan-Meier and Cox regression survival analyses were performed to assess cell clusters in association with relapse-free and overall survival. Differentially expressed genes by clusters were interrogated with IPA for molecular signatures. UHC analysis identified two distinct immune cell clusters, clusters A (83.2%) and B (16.8%). Memory B cells, plasma cells, CD8 positive T cells, resting memory CD4 T cells, activated NK cells, monocytes, M1 macrophages, and resting mast cells were more abundant in clusters A than B, whereas regulatory T cells and M0 and M2 macrophages were more in clusters B than A. Patients in cluster A had favorable survival. Similar survival associations were also observed in other independent studies. IPA analysis showed that pathogen-induced cytokine storm signaling pathway, phagosome formation, and T cell receptor signaling were related to the cell type clusters. Our finding suggests that different immune cell clusters may indicate distinct immune responses to tumor growth, suggesting their potential for disease management.
Collapse
Affiliation(s)
- Zhanwei Wang
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Dionyssios Katsaros
- Department of Surgical Sciences, Gynecology, AOU Città della Salute, University of Torino, Turin, Italy
| | - Junlong Wang
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Nicholetta Biglio
- Division of Obstetrics and Gynecology, Department of Surgical Sciences, University of Torino School of Medicine, Mauriziano Hospital, Turin, Italy
| | - Brenda Y Hernandez
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Peiwen Fei
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Harvey Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA.
| |
Collapse
|
6
|
Alonso-Moreda N, Berral-González A, De La Rosa E, González-Velasco O, Sánchez-Santos JM, De Las Rivas J. Comparative Analysis of Cell Mixtures Deconvolution and Gene Signatures Generated for Blood, Immune and Cancer Cells. Int J Mol Sci 2023; 24:10765. [PMID: 37445946 DOI: 10.3390/ijms241310765] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
In the last two decades, many detailed full transcriptomic studies on complex biological samples have been published and included in large gene expression repositories. These studies primarily provide a bulk expression signal for each sample, including multiple cell-types mixed within the global signal. The cellular heterogeneity in these mixtures does not allow the activity of specific genes in specific cell types to be identified. Therefore, inferring relative cellular composition is a very powerful tool to achieve a more accurate molecular profiling of complex biological samples. In recent decades, computational techniques have been developed to solve this problem by applying deconvolution methods, designed to decompose cell mixtures into their cellular components and calculate the relative proportions of these elements. Some of them only calculate the cell proportions (supervised methods), while other deconvolution algorithms can also identify the gene signatures specific for each cell type (unsupervised methods). In these work, five deconvolution methods (CIBERSORT, FARDEEP, DECONICA, LINSEED and ABIS) were implemented and used to analyze blood and immune cells, and also cancer cells, in complex mixture samples (using three bulk expression datasets). Our study provides three analytical tools (corrplots, cell-signature plots and bar-mixture plots) that allow a thorough comparative analysis of the cell mixture data. The work indicates that CIBERSORT is a robust method optimized for the identification of immune cell-types, but not as efficient in the identification of cancer cells. We also found that LINSEED is a very powerful unsupervised method that provides precise and specific gene signatures for each of the main immune cell types tested: neutrophils and monocytes (of the myeloid lineage), B-cells, NK cells and T-cells (of the lymphoid lineage), and also for cancer cells.
Collapse
Affiliation(s)
- Natalia Alonso-Moreda
- Cancer Research Center (CiC-IBMCC, CSIC/USAL & IBSAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), & Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Alberto Berral-González
- Cancer Research Center (CiC-IBMCC, CSIC/USAL & IBSAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), & Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Enrique De La Rosa
- Cancer Research Center (CiC-IBMCC, CSIC/USAL & IBSAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), & Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Oscar González-Velasco
- Cancer Research Center (CiC-IBMCC, CSIC/USAL & IBSAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), & Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - José Manuel Sánchez-Santos
- Cancer Research Center (CiC-IBMCC, CSIC/USAL & IBSAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), & Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
- Department of Statistics, University of Salamanca (USAL), 37008 Salamanca, Spain
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL & IBSAL), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), & Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain
| |
Collapse
|
7
|
Tiwari A, Trivedi R, Lin SY. Tumor microenvironment: barrier or opportunity towards effective cancer therapy. J Biomed Sci 2022; 29:83. [PMID: 36253762 PMCID: PMC9575280 DOI: 10.1186/s12929-022-00866-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/01/2022] [Indexed: 12/24/2022] Open
Abstract
Tumor microenvironment (TME) is a specialized ecosystem of host components, designed by tumor cells for successful development and metastasis of tumor. With the advent of 3D culture and advanced bioinformatic methodologies, it is now possible to study TME’s individual components and their interplay at higher resolution. Deeper understanding of the immune cell’s diversity, stromal constituents, repertoire profiling, neoantigen prediction of TMEs has provided the opportunity to explore the spatial and temporal regulation of immune therapeutic interventions. The variation of TME composition among patients plays an important role in determining responders and non-responders towards cancer immunotherapy. Therefore, there could be a possibility of reprogramming of TME components to overcome the widely prevailing issue of immunotherapeutic resistance. The focus of the present review is to understand the complexity of TME and comprehending future perspective of its components as potential therapeutic targets. The later part of the review describes the sophisticated 3D models emerging as valuable means to study TME components and an extensive account of advanced bioinformatic tools to profile TME components and predict neoantigens. Overall, this review provides a comprehensive account of the current knowledge available to target TME.
Collapse
Affiliation(s)
- Aadhya Tiwari
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
8
|
Zaitsev A, Chelushkin M, Dyikanov D, Cheremushkin I, Shpak B, Nomie K, Zyrin V, Nuzhdina E, Lozinsky Y, Zotova A, Degryse S, Kotlov N, Baisangurov A, Shatsky V, Afenteva D, Kuznetsov A, Paul SR, Davies DL, Reeves PM, Lanuti M, Goldberg MF, Tazearslan C, Chasse M, Wang I, Abdou M, Aslanian SM, Andrewes S, Hsieh JJ, Ramachandran A, Lyu Y, Galkin I, Svekolkin V, Cerchietti L, Poznansky MC, Ataullakhanov R, Fowler N, Bagaev A. Precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes. Cancer Cell 2022; 40:879-894.e16. [PMID: 35944503 DOI: 10.1016/j.ccell.2022.07.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/10/2022] [Accepted: 07/12/2022] [Indexed: 12/21/2022]
Abstract
Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues. We present the decision tree machine learning algorithm, Kassandra, trained on a broad collection of >9,400 tissue and blood sorted cell RNA profiles incorporated into millions of artificial transcriptomes to accurately reconstruct the tumor microenvironment (TME). Bioinformatics correction for technical and biological variability, aberrant cancer cell expression inclusion, and accurate quantification and normalization of transcript expression increased Kassandra stability and robustness. Performance was validated on 4,000 H&E slides and 1,000 tissues by comparison with cytometric, immunohistochemical, or single-cell RNA-seq measurements. Kassandra accurately deconvolved TME elements, showing the role of these populations in tumor pathogenesis and other biological processes. Digital TME reconstruction revealed that the presence of PD-1-positive CD8+ T cells strongly correlated with immunotherapy response and increased the predictive potential of established biomarkers, indicating that Kassandra could potentially be utilized in future clinical applications.
Collapse
Affiliation(s)
| | | | | | | | - Boris Shpak
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | - Krystle Nomie
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | - Vladimir Zyrin
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | | | | | | | - Nikita Kotlov
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | | | - Daria Afenteva
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | - Susan Raju Paul
- The Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Diane L Davies
- Division of Thoracic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick M Reeves
- The Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Lanuti
- Division of Thoracic Surgery, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Madison Chasse
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | - Iris Wang
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | - Mary Abdou
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | | | - James J Hsieh
- Molecular Oncology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Akshaya Ramachandran
- Molecular Oncology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Yang Lyu
- Molecular Oncology, Division of Oncology, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Ilia Galkin
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA
| | | | - Leandro Cerchietti
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Mark C Poznansky
- The Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | | | - Nathan Fowler
- BostonGene, Corp., 95 Sawyer Road, Waltham, MA 02453, USA; Department of Lymphoma and Myeloma, MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 429, Houston, TX 77030, USA.
| | | |
Collapse
|
9
|
Xu C, Song L, Yang Y, Liu Y, Pei D, Liu J, Guo J, Liu N, Li X, Liu Y, Li X, Yao L, Kang Z. Clinical M2 Macrophage-Related Genes Can Serve as a Reliable Predictor of Lung Adenocarcinoma. Front Oncol 2022; 12:919899. [PMID: 35936688 PMCID: PMC9352953 DOI: 10.3389/fonc.2022.919899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022] Open
Abstract
BackgroundNumerous studies have found that infiltrating M2 macrophages play an important role in the tumor progression of lung adenocarcinoma (LUAD). However, the roles of M2 macrophage infiltration and M2 macrophage-related genes in immunotherapy and clinical outcomes remain obscure.MethodsSample information was extracted from TCGA and GEO databases. The TIME landscape was revealed using the CIBERSORT algorithm. Weighted gene co-expression network analysis (WGCNA) was used to find M2 macrophage-related gene modules. Through univariate Cox regression, lasso regression analysis, and multivariate Cox regression, the genes strongly associated with the prognosis of LUAD were screened out. Risk score (RS) was calculated, and all samples were divided into high-risk group (HRG) and low-risk group (LRG) according to the median RS. External validation of RS was performed using GSE68571 data information. Prognostic nomogram based on risk signatures and other clinical information were constructed and validated with calibration curves. Potential associations of tumor mutational burden (TMB) and risk signatures were analyzed. Finally, the potential association of risk signatures with chemotherapy efficacy was investigated using the pRRophetic algorithm.ResultsBased on 504 samples extracted from TCGA database, 183 core genes were identified using WGCNA. Through a series of screening, two M2 macrophage-related genes (GRIA1 and CLEC3B) strongly correlated with LUAD prognosis were finally selected. RS was calculated, and prognostic risk nomogram including gender, age, T, N, M stage, clinical stage, and RS were constructed. The calibration curve shows that our constructed model has good performance. HRG patients were suitable for new ICI immunotherapy, while LRG was more suitable for CTLA4-immunosuppressive therapy alone. The half-maximal inhibitory concentrations (IC50) of the four chemotherapeutic drugs (metformin, cisplatin, paclitaxel, and gemcitabine) showed significant differences in HRG/LRG.ConclusionsIn conclusion, a comprehensive analysis of the role of M2 macrophages in tumor progression will help predict prognosis and facilitate the advancement of therapeutic techniques.
Collapse
Affiliation(s)
- Chaojie Xu
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Lishan Song
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yubin Yang
- Peking University First Hospital, Peking University, Beijing, China
| | - Yi Liu
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Dongchen Pei
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Jiabang Liu
- Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Jianhua Guo
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Nan Liu
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xiaoyong Li
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yuchen Liu
- Shenzhen Institute of Translational Medicine, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- *Correspondence: Zhengjun Kang,
- Lin Yao,
- Xuesong Li,
- Yuchen Liu,
- Xiaoyong Li,
| | - Xuesong Li
- College of Pharmacy, Shantou University School of Medicine, Shantou, China
| | - Lin Yao
- College of Pharmacy, Shantou University School of Medicine, Shantou, China
| | - Zhengjun Kang
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
10
|
Abou Khouzam R, Zaarour RF, Brodaczewska K, Azakir B, Venkatesh GH, Thiery J, Terry S, Chouaib S. The Effect of Hypoxia and Hypoxia-Associated Pathways in the Regulation of Antitumor Response: Friends or Foes? Front Immunol 2022; 13:828875. [PMID: 35211123 PMCID: PMC8861358 DOI: 10.3389/fimmu.2022.828875] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022] Open
Abstract
Hypoxia is an environmental stressor that is instigated by low oxygen availability. It fuels the progression of solid tumors by driving tumor plasticity, heterogeneity, stemness and genomic instability. Hypoxia metabolically reprograms the tumor microenvironment (TME), adding insult to injury to the acidic, nutrient deprived and poorly vascularized conditions that act to dampen immune cell function. Through its impact on key cancer hallmarks and by creating a physical barrier conducive to tumor survival, hypoxia modulates tumor cell escape from the mounted immune response. The tumor cell-immune cell crosstalk in the context of a hypoxic TME tips the balance towards a cold and immunosuppressed microenvironment that is resistant to immune checkpoint inhibitors (ICI). Nonetheless, evidence is emerging that could make hypoxia an asset for improving response to ICI. Tackling the tumor immune contexture has taken on an in silico, digitalized approach with an increasing number of studies applying bioinformatics to deconvolute the cellular and non-cellular elements of the TME. Such approaches have additionally been combined with signature-based proxies of hypoxia to further dissect the turbulent hypoxia-immune relationship. In this review we will be highlighting the mechanisms by which hypoxia impacts immune cell functions and how that could translate to predicting response to immunotherapy in an era of machine learning and computational biology.
Collapse
Affiliation(s)
- Raefa Abou Khouzam
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Rania Faouzi Zaarour
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Klaudia Brodaczewska
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
| | - Bilal Azakir
- Faculty of Medicine, Beirut Arab University, Beirut, Lebanon
| | - Goutham Hassan Venkatesh
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Jerome Thiery
- INSERM U1186, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Faculty of Medicine, University Paris Sud, Le Kremlin Bicêtre, France
| | - Stéphane Terry
- INSERM U1186, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Faculty of Medicine, University Paris Sud, Le Kremlin Bicêtre, France.,Research Department, Inovarion, Paris, France
| | - Salem Chouaib
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates.,INSERM U1186, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| |
Collapse
|
11
|
Fonseca M, Macedo AS, Lima SAC, Reis S, Soares R, Fonte P. Evaluation of the Antitumour and Antiproliferative Effect of Xanthohumol-Loaded PLGA Nanoparticles on Melanoma. MATERIALS (BASEL, SWITZERLAND) 2021; 14:6421. [PMID: 34771946 PMCID: PMC8585140 DOI: 10.3390/ma14216421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022]
Abstract
Cutaneous melanoma is the deadliest type of skin cancer and current treatment is still inadequate, with low patient survival rates. The polyphenol xanthohumol has been shown to inhibit tumourigenesis and metastasization, however its physicochemical properties restrict its application. In this work, we developed PLGA nanoparticles encapsulating xanthohumol and tested its antiproliferative, antitumour, and migration effect on B16F10, malignant cutaneous melanoma, and RAW 264.7, macrophagic, mouse cell lines. PLGA nanoparticles had a size of 312 ± 41 nm and a PdI of 0.259, while achieving a xanthohumol loading of about 90%. The viability study showed similar cytoxicity between the xanthohumol and xanthohumol-loaded PLGA nanoparticles at 48 h with the IC50 established at 10 µM. Similar antimigration effects were observed for free and the encapsulated xanthohumol. It was also observed that the M1 antitumor phenotype was stimulated on macrophages. The ultimate anti-melanoma effect emerges from an association between the viability, migration and macrophagic phenotype modulation. These results display the remarkable antitumour effect of the xanthohumol-loaded PLGA nanoparticles and are the first advance towards the application of a nanoformulation to deliver xanthohumol to reduce adverse effects by currently employed chemotherapeutics.
Collapse
Affiliation(s)
- Magda Fonseca
- Department of Biomedicine, Faculty of Medicine, University of Porto, Al Prof Hernani Monteiro, 4200-319 Porto, Portugal; (M.F.); (R.S.)
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Ana S. Macedo
- LAQV, REQUIMTE, Department of Chemical Sciences-Applied Chemistry Lab, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; (A.S.M.); (S.A.C.L.); (S.R.)
| | - Sofia A. Costa Lima
- LAQV, REQUIMTE, Department of Chemical Sciences-Applied Chemistry Lab, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; (A.S.M.); (S.A.C.L.); (S.R.)
| | - Salette Reis
- LAQV, REQUIMTE, Department of Chemical Sciences-Applied Chemistry Lab, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal; (A.S.M.); (S.A.C.L.); (S.R.)
| | - Raquel Soares
- Department of Biomedicine, Faculty of Medicine, University of Porto, Al Prof Hernani Monteiro, 4200-319 Porto, Portugal; (M.F.); (R.S.)
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Pedro Fonte
- Center for Marine Sciences (CCMAR), University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal
- Department of Chemistry and Pharmacy, Faculty of Sciences and Technology, University of Algarve, Gambelas Campus, 8005-139 Faro, Portugal
- iBB—Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisboa, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| |
Collapse
|
12
|
Steen CB, Luca BA, Esfahani MS, Azizi A, Sworder BJ, Nabet BY, Kurtz DM, Liu CL, Khameneh F, Advani RH, Natkunam Y, Myklebust JH, Diehn M, Gentles AJ, Newman AM, Alizadeh AA. The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Cancer Cell 2021; 39:1422-1437.e10. [PMID: 34597589 PMCID: PMC9205168 DOI: 10.1016/j.ccell.2021.08.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by diverse cell types and cell states in the tumor microenvironment (TME). However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine-learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL cell states and ecosystems. Using this approach, we identified five cell states of malignant B cells that vary in prognostic associations and differentiation status. We also identified striking variation in cell states for 12 other lineages comprising the TME and forming cell state interactions in stereotyped ecosystems. While cell-of-origin subtypes have distinct TME composition, DLBCL ecosystems capture clinical heterogeneity within existing subtypes and extend beyond cell-of-origin and genotypic classes. These results resolve the DLBCL microenvironment at systems-level resolution and identify opportunities for therapeutic targeting (https://ecotyper.stanford.edu/lymphoma).
Collapse
Affiliation(s)
- Chloé B Steen
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Bogdan A Luca
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mohammad S Esfahani
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Armon Azizi
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Brian J Sworder
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - David M Kurtz
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Chih Long Liu
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Farnaz Khameneh
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ranjana H Advani
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - June H Myklebust
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
| | - Ash A Alizadeh
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
13
|
Wu SY, Lin KC, Lawal B, Wu ATH, Wu CZ. MXD3 as an onco-immunological biomarker encompassing the tumor microenvironment, disease staging, prognoses, and therapeutic responses in multiple cancer types. Comput Struct Biotechnol J 2021; 19:4970-4983. [PMID: 34584637 PMCID: PMC8441106 DOI: 10.1016/j.csbj.2021.08.047] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023] Open
Abstract
MAX dimerization (MXD) protein 3 (MXD3) is a member of the MXD family of basic-helix-loop-helix-leucine-zipper (bHLHZ) transcription factors that plays pivotal roles in cell cycle progression and cell proliferation. However, there is insufficient scientific evidence on the pathogenic roles of MXD3 in various cancers and whether MXD3 plays a role in the immuno-oncology context of the tumor microenvironment, pathogenesis, prognosis, and therapeutic response of different tumors through certain common molecular mechanisms; thus, we saw a need to conduct the present in silico pan-cancer study. Using various computational tools, we interrogated the role of MXD3 in tumor immune infiltration, immune evasion, tumor progression, therapy response, and prognosis of cohorts from various cancer types. Our results indicated that MXD3 was aberrantly expressed in almost all The Cancer Genome Atlas (TCGA) cancer types and subtypes and was associated with the tumor stage, metastasis, and worse prognoses of various cohorts. Our results also suggested that MXD3 is associated with tumor immune evasion via different mechanisms involving T-cell exclusion in different cancer types and by tumor infiltration of immune cells in thymoma (THYM), liver hepatocellular carcinoma (LIHC), and head and neck squamous cell carcinoma (HNSC). Methylation of MXD3 was inversely associated with messenger (m)RNA expression levels and mediated dysfunctional T-cell phenotypes and worse prognoses of cohorts from different cancer types. Finally, we found that genetic alterations and oncogenic features of MXD3 were concomitantly associated with deregulation of the DBN1, RAB24, SLC34A1, PRELID1, LMAN2, F12, GRK6, RGS14, PRR7, and PFN3 genes and were connected to phospholipid transport and ion homeostasis. Our results also suggested that MXD3 expression is associated with immune or chemotherapeutic outcomes in various cancers. In addition, higher MXD3 expression levels were associated with decreased sensitivity of cancer cell lines to several mitogen-activated protein kinase kinase (MEK) inhibitors but led to increased activities of other kinase inhibitors, including Akt inhibitors. Interestingly, MXD3 exhibited higher predictive power for response outcomes and overall survival of immune checkpoint blockade sub-cohorts than three of seven standardized biomarkers. Altogether, our study strongly suggests that MXD3 is an immune-oncogenic molecule and could serve as a biomarker for cancer detection, prognosis, therapeutic design, and follow-up.
Collapse
Affiliation(s)
- Szu-Yuan Wu
- Department of Food Nutrition and Health Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan.,Big Data Center, Lo-Hsu Medical Foundation, Lotung Poh-Ai Hospital, Yilan, Taiwan.,Division of Radiation Oncology, Lo-Hsu Medical Foundation, Lotung Poh-Ai Hospital, Yilan, Taiwan.,Department of Healthcare Administration, College of Medical and Health Science, Asia University, Taichung, Taiwan.,Graduate Institute of Business Administration, Fu Jen Catholic University, New Taipei City, Taiwan.,Centers for Regional Anesthesia and Pain Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Cancer Center, Lo-Hsu Medical Foundation, Lotung Poh-Ai Hospital, Yilan, Taiwan
| | - Kuan-Chou Lin
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Oral and Maxillofacial Surgery, Department of Dentistry, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Bashir Lawal
- Graduate Institute for Cancer Biology & Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
| | - Alexander T H Wu
- The PhD Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan.,Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan.,Taipei Heart Institute (THI), Taipei Medical University, Taipei, Taiwan
| | - Ching-Zong Wu
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Dentistry, Taipei Medical University Hospital, Taipei, Taiwan.,Department of Dentistry, Lotung Poh-Ai hospital, Yilan, Taiwan
| |
Collapse
|
14
|
Xu Y, Su GH, Ma D, Xiao Y, Shao ZM, Jiang YZ. Technological advances in cancer immunity: from immunogenomics to single-cell analysis and artificial intelligence. Signal Transduct Target Ther 2021; 6:312. [PMID: 34417437 PMCID: PMC8377461 DOI: 10.1038/s41392-021-00729-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/06/2021] [Accepted: 07/18/2021] [Indexed: 02/07/2023] Open
Abstract
Immunotherapies play critical roles in cancer treatment. However, given that only a few patients respond to immune checkpoint blockades and other immunotherapeutic strategies, more novel technologies are needed to decipher the complicated interplay between tumor cells and the components of the tumor immune microenvironment (TIME). Tumor immunomics refers to the integrated study of the TIME using immunogenomics, immunoproteomics, immune-bioinformatics, and other multi-omics data reflecting the immune states of tumors, which has relied on the rapid development of next-generation sequencing. High-throughput genomic and transcriptomic data may be utilized for calculating the abundance of immune cells and predicting tumor antigens, referring to immunogenomics. However, as bulk sequencing represents the average characteristics of a heterogeneous cell population, it fails to distinguish distinct cell subtypes. Single-cell-based technologies enable better dissection of the TIME through precise immune cell subpopulation and spatial architecture investigations. In addition, radiomics and digital pathology-based deep learning models largely contribute to research on cancer immunity. These artificial intelligence technologies have performed well in predicting response to immunotherapy, with profound significance in cancer therapy. In this review, we briefly summarize conventional and state-of-the-art technologies in the field of immunogenomics, single-cell and artificial intelligence, and present prospects for future research.
Collapse
Affiliation(s)
- Ying Xu
- grid.452404.30000 0004 1808 0942Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guan-Hua Su
- grid.452404.30000 0004 1808 0942Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ding Ma
- grid.452404.30000 0004 1808 0942Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi Xiao
- grid.452404.30000 0004 1808 0942Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi-Ming Shao
- grid.452404.30000 0004 1808 0942Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China ,grid.8547.e0000 0001 0125 2443Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yi-Zhou Jiang
- grid.452404.30000 0004 1808 0942Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China ,grid.11841.3d0000 0004 0619 8943Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
15
|
Patwa A, Yamashita R, Long J, Risom T, Angelo M, Keren L, Rubin DL. Multiplexed imaging analysis of the tumor-immune microenvironment reveals predictors of outcome in triple-negative breast cancer. Commun Biol 2021; 4:852. [PMID: 34244605 PMCID: PMC8271023 DOI: 10.1038/s42003-021-02361-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/10/2021] [Indexed: 12/18/2022] Open
Abstract
Triple-negative breast cancer, the poorest-prognosis breast cancer subtype, lacks clinically approved biomarkers for patient risk stratification and treatment management. Prior literature has shown that interrogation of the tumor-immune microenvironment may be a promising approach to fill these gaps. Recently developed high-dimensional tissue imaging technology, such as multiplexed ion beam imaging, provide spatial context to protein expression in the microenvironment, allowing in-depth characterization of cellular processes. We demonstrate that profiling the functional proteins involved in cell-to-cell interactions in the microenvironment can predict recurrence and overall survival. We highlight the immunological relevance of the immunoregulatory proteins PD-1, PD-L1, IDO, and Lag3 by tying interactions involving them to recurrence and survival. Multivariate analysis reveals that our methods provide additional prognostic information compared to clinical variables. In this work, we present a computational pipeline for the examination of the tumor-immune microenvironment using multiplexed ion beam imaging that produces interpretable results, and is generalizable to other cancer types.
Collapse
Affiliation(s)
- Aalok Patwa
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Archbishop Mitty High School, San Jose, CA, USA
| | - Rikiya Yamashita
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA
| | - Jin Long
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA
| | - Tyler Risom
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel L Rubin
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA.
| |
Collapse
|
16
|
Combinatorial therapy in tumor microenvironment: Where do we stand? Biochim Biophys Acta Rev Cancer 2021; 1876:188585. [PMID: 34224836 DOI: 10.1016/j.bbcan.2021.188585] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/28/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023]
Abstract
The tumor microenvironment plays a pivotal role in tumor initiation and progression by creating a dynamic interaction with cancer cells. The tumor microenvironment consists of various cellular components, including endothelial cells, fibroblasts, pericytes, adipocytes, immune cells, cancer stem cells and vasculature, which provide a sustained environment for cancer cell proliferation. Currently, targeting tumor microenvironment is increasingly being explored as a novel approach to improve cancer therapeutics, as it influences the growth and expansion of malignant cells in various ways. Despite continuous advancements in targeted therapies for cancer treatment, drug resistance, toxicity and immune escape mechanisms are the basis of treatment failure and cancer escape. Targeting tumor microenvironment efficiently with approved drugs and combination therapy is the solution to this enduring challenge that involves combining more than one treatment modality such as chemotherapy, surgery, radiotherapy, immunotherapy and nanotherapy that can effectively and synergistically target the critical pathways associated with disease pathogenesis. This review shed light on the composition of the tumor microenvironment, interaction of different components within tumor microenvironment with tumor cells and associated hallmarks, the current status of combinatorial therapies being developed, and various growing advancements. Furthermore, computational tools can also be used to monitor the significance and outcome of therapies being developed. We addressed the perceived barriers and regulatory hurdles in developing a combinatorial regimen and evaluated the present status of these therapies in the clinic. The accumulating depth of knowledge about the tumor microenvironment in cancer may facilitate further development of effective treatment modalities. This review presents the tumor microenvironment as a sweeping landscape for developing novel cancer therapies.
Collapse
|
17
|
An integrated framework for quantifying immune-tumour interactions in a 3D co-culture model. Commun Biol 2021; 4:781. [PMID: 34168276 PMCID: PMC8225809 DOI: 10.1038/s42003-021-02296-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/03/2021] [Indexed: 02/05/2023] Open
Abstract
Investigational in vitro models that reflect the complexity of the interaction between the immune system and tumours are limited and difficult to establish. Herein, we present a platform to study the tumour-immune interaction using a co-culture between cancer spheroids and activated immune cells. An algorithm was developed for analysis of confocal images of the co-culture to evaluate the following quantitatively; immune cell infiltration, spheroid roundness and spheroid growth. As a proof of concept, the effect of the glucocorticoid stress hormone, cortisol was tested on 66CL4 co-culture model. Results were comparable to 66CL4 syngeneic in vivo mouse model undergoing psychological stress. Furthermore, administration of glucocorticoid receptor antagonists demonstrated the use of this model to determine the effect of treatments on the immune-tumour interplay. In conclusion, we provide a method of quantifying the interaction between the immune system and cancer, which can become a screening tool in immunotherapy design.
Collapse
|
18
|
Mattei F, Andreone S, Mencattini A, De Ninno A, Businaro L, Martinelli E, Schiavoni G. Oncoimmunology Meets Organs-on-Chip. Front Mol Biosci 2021; 8:627454. [PMID: 33842539 PMCID: PMC8032996 DOI: 10.3389/fmolb.2021.627454] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/04/2021] [Indexed: 01/04/2023] Open
Abstract
Oncoimmunology represents a biomedical research discipline coined to study the roles of immune system in cancer progression with the aim of discovering novel strategies to arm it against the malignancy. Infiltration of immune cells within the tumor microenvironment is an early event that results in the establishment of a dynamic cross-talk. Here, immune cells sense antigenic cues to mount a specific anti-tumor response while cancer cells emanate inhibitory signals to dampen it. Animals models have led to giant steps in this research context, and several tools to investigate the effect of immune infiltration in the tumor microenvironment are currently available. However, the use of animals represents a challenge due to ethical issues and long duration of experiments. Organs-on-chip are innovative tools not only to study how cells derived from different organs interact with each other, but also to investigate on the crosstalk between immune cells and different types of cancer cells. In this review, we describe the state-of-the-art of microfluidics and the impact of OOC in the field of oncoimmunology underlining the importance of this system in the advancements on the complexity of tumor microenvironment.
Collapse
Affiliation(s)
- Fabrizio Mattei
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Sara Andreone
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Arianna Mencattini
- Department of Electronic Engineering, University of Rome Tor Vergata, Rome, Italy.,Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), University of Rome Tor Vergata, Rome, Italy
| | - Adele De Ninno
- Institute for Photonics and Nanotechnologies, Italian National Research Council, Rome, Italy
| | - Luca Businaro
- Institute for Photonics and Nanotechnologies, Italian National Research Council, Rome, Italy
| | - Eugenio Martinelli
- Department of Electronic Engineering, University of Rome Tor Vergata, Rome, Italy.,Interdisciplinary Center for Advanced Studies on Lab-on-Chip and Organ-on-Chip Applications (ICLOC), University of Rome Tor Vergata, Rome, Italy
| | - Giovanna Schiavoni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| |
Collapse
|
19
|
Ichimiya S, Onishi H, Nagao S, Koga S, Sakihama K, Nakayama K, Fujimura A, Oyama Y, Imaizumi A, Oda Y, Nakamura M. GLI2 but not GLI1/GLI3 plays a central role in the induction of malignant phenotype of gallbladder cancer. Oncol Rep 2021; 45:997-1010. [PMID: 33650666 PMCID: PMC7860001 DOI: 10.3892/or.2021.7947] [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: 08/10/2020] [Accepted: 12/07/2020] [Indexed: 12/24/2022] Open
Abstract
We previously reported that Hedgehog (Hh) signal was enhanced in gallbladder cancer (GBC) and was involved in the induction of malignant phenotype of GBC. In recent years, therapeutics that target Hh signaling have focused on molecules downstream of smoothened (SMO). The three transcription factors in the Hh signal pathway, glioma‑associated oncogene homolog 1 (GLI1), GLI2, and GLI3, function downstream of SMO, but their biological role in GBC remains unclear. In the present study, the biological significance of GLI1, GLI2, and GLI3 were analyzed with the aim of developing novel treatments for GBC. It was revealed that GLI2, but not GLI1 or GLI3, was involved in the cell cycle‑mediated proliferative capacity in GBC and that GLI2, but not GLI1 or GLI3, was involved in the enhanced invasive capacity through epithelial‑mesenchymal transition. Further analyses revealed that GLI2 may function in mediating gemcitabine sensitivity and that GLI2 was involved in the promotion of fibrosis in a mouse xenograft model. Immunohistochemical staining of 66 surgically resected GBC tissues revealed that GLI2‑high expression patients had fewer numbers of CD3+ and CD8+ tumor‑infiltrating lymphocytes (TILs) and increased programmed cell death ligand 1 (PD‑L1) expression in cancer cells. These results suggest that GLI2, but not GLI1 or GLI3, is involved in proliferation, invasion, fibrosis, PD‑L1 expression, and TILs in GBC and could be a novel therapeutic target. The results of this study provide a significant contribution to the development of a new treatment for refractory GBC, which has few therapeutic options.
Collapse
Affiliation(s)
- Shu Ichimiya
- Department of Cancer Therapy and Research, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Hideya Onishi
- Department of Cancer Therapy and Research, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Shinjiro Nagao
- Department of Cancer Therapy and Research, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Satoko Koga
- Department of Cancer Therapy and Research, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Kukiko Sakihama
- Department of Anatomical Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Kazunori Nakayama
- Department of Cancer Therapy and Research, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Akiko Fujimura
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Yasuhiro Oyama
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Akira Imaizumi
- Department of Cancer Therapy and Research, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Yoshinao Oda
- Department of Anatomical Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| | - Masafumi Nakamura
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812‑8582, Japan
| |
Collapse
|
20
|
Tsatsakis A, Calina D, Falzone L, Petrakis D, Mitrut R, Siokas V, Pennisi M, Lanza G, Libra M, Doukas SG, Doukas PG, Kavali L, Bukhari A, Gadiparthi C, Vageli DP, Kofteridis DP, Spandidos DA, Paoliello MMB, Aschner M, Docea AO. SARS-CoV-2 pathophysiology and its clinical implications: An integrative overview of the pharmacotherapeutic management of COVID-19. Food Chem Toxicol 2020; 146:111769. [PMID: 32979398 PMCID: PMC7833750 DOI: 10.1016/j.fct.2020.111769] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023]
Abstract
Common manifestations of COVID-19 are respiratory and can extend from mild symptoms to severe acute respiratory distress. The severity of the illness can also extend from mild disease to life-threatening acute respiratory distress syndrome (ARDS). SARS-CoV-2 infection can also affect the gastrointestinal tract, liver and pancreatic functions, leading to gastrointestinal symptoms. Moreover, SARS-CoV-2 can cause central and peripheral neurological manifestations, affect the cardiovascular system and promote renal dysfunction. Epidemiological data have indicated that cancer patients are at a higher risk of contracting the SARS-CoV-2 virus. Considering the multitude of clinical symptoms of COVID-19, the objective of the present review was to summarize their pathophysiology in previously healthy patients, as well as in those with comorbidities. The present review summarizes the current, though admittedly fluid knowledge on the pathophysiology and symptoms of COVID-19 infection. Although unclear issues still remain, the present study contributes to a more complete understanding of the disease, and may drive the direction of new research. The recognition of the severity of the clinical symptoms of COVID-19 is crucial for the specific therapeutic management of affected patients.
Collapse
Affiliation(s)
- Aristides Tsatsakis
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, 71003, Heraklion, Greece; I.M. Sechenov First Moscow State Medical University (Sechenov University), 119146, Moscow, Russia.
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori "Fondazione G. Pascale", 80131, Naples, Italy.
| | - Dimitrios Petrakis
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, 71003, Heraklion, Greece.
| | - Radu Mitrut
- Department of Cardiology, University and Emergency Hospital, 050098, Bucharest, Romania.
| | - Vasileios Siokas
- Department of Neurology, University of Thessaly, University Hospital of Larissa, 41221, Larissa, Greece.
| | - Manuela Pennisi
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy.
| | - Giuseppe Lanza
- Department of Surgery and Medical-Surgical Specialties, University of Catania, 95123, Catania, Italy; Department of Neurology IC, Oasi Research Institute-IRCCS, 94018, Troina, Italy.
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123, Catania, Italy; Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, 95123, Catania, Italy.
| | - Sotirios G Doukas
- Department of Forensic Sciences and Toxicology, Faculty of Medicine, University of Crete, 71003, Heraklion, Greece; Department of Internal Medicine, Saint Peter's University Hospital, 254 Easton Ave, New Brunswick, NJ, 08901, USA.
| | - Panagiotis G Doukas
- University of Pavol Josef Safarik University, Faculty of Medicine, Kosice, Slovakia.
| | - Leena Kavali
- Department of Internal Medicine, Saint Peter's University Hospital, 254 Easton Ave, New Brunswick, NJ, 08901, USA.
| | - Amar Bukhari
- Department of Medicine, Division of Pulmonary and Critical Care 240 Easton Ave, Adult Ambulatory at Cares Building 4th Floor, New Brunswick, NJ, 08901, USA.
| | - Chiranjeevi Gadiparthi
- Division of Gastroenterology, Hepatology and Clinical Nutrition, Saint Peter's University Hospital, New Brunswick, NJ, USA.
| | - Dimitra P Vageli
- Department of Surgery, The Yale Larynx Laboratory, New Haven, CT, 06510, USA.
| | - Diamantis P Kofteridis
- Department of Internal Medicine, University Hospital of Heraklion, 71110, Heraklion, Crete, Greece.
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion, 71003, Greece.
| | - Monica M B Paoliello
- Department of Molecular Pharmacology, Albert Eisntein College of Medicine, 1300 Morris Park Avenue Bronx, NY, 10461, USA.
| | - Michael Aschner
- I.M. Sechenov First Moscow State Medical University (Sechenov University), 119146, Moscow, Russia; Department of Molecular Pharmacology, Albert Eisntein College of Medicine, 1300 Morris Park Avenue Bronx, NY, 10461, USA.
| | - Anca Oana Docea
- Department of Toxicology, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
| |
Collapse
|
21
|
Valous NA, Moraleda RR, Jäger D, Zörnig I, Halama N. Interrogating the microenvironmental landscape of tumors with computational image analysis approaches. Semin Immunol 2020; 48:101411. [PMID: 33168423 DOI: 10.1016/j.smim.2020.101411] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/13/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
The tumor microenvironment is an interacting heterogeneous collection of cancer cells, resident as well as infiltrating host cells, secreted factors, and extracellular matrix proteins. With the growing importance of immunotherapies, it has become crucial to be able to characterize the composition and the functional orientation of the microenvironment. The development of novel computational image analysis methodologies may enable the robust quantification and localization of immune and related biomarker-expressing cells within the microenvironment. The aim of the review is to concisely highlight a selection of current and significant contributions pertinent to methodological advances coupled with biomedical or translational applications. A further aim is to concisely present computational advances that, to our knowledge, have currently very limited use for the assessment of the microenvironment but have the potential to enhance image analysis pipelines; on this basis, an example is shown for the detection and segmentation of cells of the microenvironment using a published pipeline and a public dataset. Finally, a general proposal is presented on the conceptual design of automation-optimized computational image analysis workflows in the biomedical and clinical domain.
Collapse
Affiliation(s)
- Nektarios A Valous
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.
| | - Rodrigo Rojas Moraleda
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.
| | - Dirk Jäger
- Applied Tumor Immunity Clinical Cooperation Unit, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Inka Zörnig
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor Diseases (NCT), Heidelberg University Hospital (UKHD), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany; Division of Translational Immunotherapy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| |
Collapse
|
22
|
Zhao Y, Pu C, Liu Z. Exploration the Significance of a Novel Immune-Related Gene Signature in Prognosis and Immune Microenvironment of Breast Cancer. Front Oncol 2020; 10:1211. [PMID: 32850356 PMCID: PMC7396707 DOI: 10.3389/fonc.2020.01211] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/15/2020] [Indexed: 12/18/2022] Open
Abstract
This study was designed to identify an immune-related gene signature (IRGS) associated with breast cancer (BC) patient outcomes. Transcriptomic data from 1411 BC patients in the TCGA and GEO databases were used to identify differentially expressed immune-related genes (DEIGs) when comparing BC tumor and normal tissue samples. We were able to construct a 27-gene IRGS that was able to effectively separate BC patients into high- and low-risk groups that corresponded to significant differences in overall and recurrence-free survival (OS and RFS, respectively). Besides, the relevance of this signature to immune response and immune cell infiltration of BC tumors was evaluated. These high- and low-risk BC patients were found to exhibit significantly different immune responses and functional enrichment. We also identified patients in the high-risk group exhibited significantly reduced immune cell infiltration of tumors relative to low-risk patients. Together, the results of this analysis offer a novel overview of the immune microenvironment within BC tumors and highlight key immunological genes associated with patient survival outcomes.
Collapse
Affiliation(s)
- Yajie Zhao
- Department of Breast, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Chunrui Pu
- Department of Breast, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Zhenzhen Liu
- Department of Breast, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| |
Collapse
|
23
|
Zhang L, Chen J, Cheng T, Yang H, Li H, Pan C. Identification of the key genes and characterizations of Tumor Immune Microenvironment in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC). J Cancer 2020; 11:4965-4979. [PMID: 32742444 PMCID: PMC7378909 DOI: 10.7150/jca.42531] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/29/2020] [Indexed: 12/13/2022] Open
Abstract
This study aimed to investigate the key genes and immune microenvironment involved in different TNM stages of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). The gene expression and clinical characteristics data were downloaded from the genomic data commons (GDC) database. After initial data processing, the characteristics of the immune microenvironment were analyzed. The differentially expressed genes (DEGs) in tumor vs. normal, and in early vs. advanced stages were screened, followed by Spearman correlation test for tumor infiltrating immune cells (TIICs) to identify immune-related genes. Finally, functional enrichment, protein-protein interaction, and survival analyses were performed. In LUAD, early stage was with higher immune scores, greater number of memory B cells and M0 macrophages compared to advanced stage. M0 and M2 macrophages, and resting memory CD4+ T cells accounted for a large proportion of TIICs in LUAD. The abundance of M0 macrophage infiltration was significantly correlated with the TNM stage and survival. In LUSC, early stage was with higher cytolytic activity and neoantigen burden compared to advanced stage. M0 and M2 macrophages, and plasma cells accounted for a large proportion of TIICs in LUSC. The abundance of resting and activated mast cells was significantly correlated with TNM stage, while resting dendritic cells, eosinophils, activated memory CD4 T cells, and mast cells were significantly correlated with prognosis. Tumor mutation burden analysis revealed that the median of variants per sample decreased from stage I to IV in LUAD, while it increased in LUSC. Further, 83 and 9 immune-related DEGs were identified in LUAD and LUSC, respectively, of which 23 genes in LUAD and 2 genes in LUSC correlated with survival. In conclusion, we identified the key genes, and characterized the tumor immune microenvironment in LUAD and LUSC which may provide therapeutic targets for the treatment of NSCLC.
Collapse
Affiliation(s)
| | - Jianhua Chen
- Thoracic Medicine Department 1, Hunan Cancer Hospital, Changsha, Hunan Province, P.R. China, 410013
| | | | | | | | | |
Collapse
|