1
|
Wu R, Horimoto Y, Oshi M, Benesch MGK, Khoury T, Takabe K, Ishikawa T. Emerging measurements for tumor-infiltrating lymphocytes in breast cancer. Jpn J Clin Oncol 2024:hyae033. [PMID: 38521965 DOI: 10.1093/jjco/hyae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/01/2024] [Indexed: 03/25/2024] Open
Abstract
Tumor-infiltrating lymphocytes are a general term for lymphocytes or immune cells infiltrating the tumor microenvironment. Numerous studies have demonstrated tumor-infiltrating lymphocytes to be robust prognostic and predictive biomarkers in breast cancer. Recently, immune checkpoint inhibitors, which directly target tumor-infiltrating lymphocytes, have become part of standard of care treatment for triple-negative breast cancer. Surprisingly, tumor-infiltrating lymphocytes quantified by conventional methods do not predict response to immune checkpoint inhibitors, which highlights the heterogeneity of tumor-infiltrating lymphocytes and the complexity of the immune network in the tumor microenvironment. Tumor-infiltrating lymphocytes are composed of diverse immune cell populations, including cytotoxic CD8-positive T lymphocytes, B cells and myeloid cells. Traditionally, tumor-infiltrating lymphocytes in tumor stroma have been evaluated by histology. However, the standardization of this approach is limited, necessitating the use of various novel technologies to elucidate the heterogeneity in the tumor microenvironment. This review outlines the evaluation methods for tumor-infiltrating lymphocytes from conventional pathological approaches that evaluate intratumoral and stromal tumor-infiltrating lymphocytes such as immunohistochemistry, to the more recent advancements in computer tissue imaging using artificial intelligence, flow cytometry sorting and multi-omics analyses using high-throughput assays to estimate tumor-infiltrating lymphocytes from bulk tumor using immune signatures or deconvolution tools. We also discuss higher resolution technologies that enable the analysis of tumor-infiltrating lymphocytes heterogeneity such as single-cell analysis and spatial transcriptomics. As we approach the era of personalized medicine, it is important for clinicians to understand these technologies.
Collapse
Affiliation(s)
- Rongrong Wu
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Yoshiya Horimoto
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
- Department of Breast Oncology, Juntendo University Hospital, Tokyo, Japan
| | - Masanori Oshi
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Matthew G K Benesch
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Thaer Khoury
- Department of Pathology & Laboratory Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kazuaki Takabe
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Surgery, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, The State University of New York, Buffalo, NY, USA
- Department of Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Breast Surgery, Fukushima Medical University, Fukushima, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery and Oncology, Tokyo Medical University, Tokyo, Japan
| |
Collapse
|
2
|
Chen H, Song A, Ul Rehman F, Han D. Multidimensional progressive single-cell sequencing reveals cell microenvironment composition and cancer heterogeneity in lung cancer. Environ Toxicol 2024; 39:890-904. [PMID: 37956258 DOI: 10.1002/tox.24018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023]
Abstract
Despite substantial advances in cancer biology and treatment, the clinical outcomes of patients with lung cancer remain unsatisfactory. The tumor microenvironment (TME) is a potential target. Using single-cell RNA sequencing, we could distinguish eight distinct cell types in the lung cancer microenvironment, demonstrating substantial intratumoral heterogeneity in 19 different lung cancer tumor samples. Through the re-dimensional grouping of cancer-associated fibroblasts (CAFs), myeloid cells, epithelial cells, natural killer (NK) cells, and T cells, the difference in the TME of lung cancer was revealed. We discovered SFTPB, SFN, and KRT8 as possible predictive biomarkers for lung cancer by assessing the gene expression patterns in epithelial cells. Examining cell-to-cell communications showed a robust association between the quantity of matrix CAFs, epithelial cells, and macrophages in the thrombospondin signaling pathway. Additionally, we found that the amyloid precursor protein signaling pathway primarily originated from the matrix, and inflammatory cancer-associated endothelial and fibroblast cells showed a co-expression relationship with myeloid cells and B cells. Through cell-to-cell correlation analysis, we found positive regulation between NK cells, regulatory T cells, GZMB-CD8 T cells, and GZMK-CD8 T cells, which could play a role in developing immune TMEs. These findings support studies on cancer heterogeneity and add to our understanding of lung cancer's cellular microenvironment.
Collapse
Affiliation(s)
- Hua Chen
- Department of Research and Development, Qingdao Bioman Biomedical Technology Co., LTD, Qingdao, China
- Department of Research and Development, Shanghai life Biomedical Technology Co., LTD, Shanghai, China
| | - Anqi Song
- Department of Student Affairs, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Faisal Ul Rehman
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dan Han
- Department of Emergency Medicine and Intensive Care, Shanghai Songjiang District Central Hospital, Shanghai, China
| |
Collapse
|
3
|
Kafka A, Ermogenous C, Ombrato L. Isolation of Live Immune Cells from the Tumor Microenvironment by FACS. Methods Mol Biol 2024; 2748:1-12. [PMID: 38070103 DOI: 10.1007/978-1-0716-3593-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Isolation of live cells from the tumor microenvironment (TME) has represented a challenge, particularly from metastatic nodules that need to be identified within the entire metastatic tissue. Cherry-niche, an in vivo labelling technique, allows the isolation of all the different cell populations in the TME without needing to visually locate the metastatic cancer cell colonies. Therefore, neighboring TME cells can be isolated even from the early stages of cancer cell seeding and colonization in the metastatic tissue. Here, we show how to use Cherry-niche to identify and isolate neutrophils from the lung metastatic niche. We also provide examples of downstream analyses to characterize freshly isolated neutrophils ex vivo, such as Giemsa staining, reactive oxygen species (ROS) detection, and phagocytosis assays. Similar strategies can be used to isolate other immune and non-immune cells from the metastatic TME.
Collapse
Affiliation(s)
- Aikaterini Kafka
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University London, John Vane Science Centre, London, UK
| | - Christos Ermogenous
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University London, John Vane Science Centre, London, UK
| | - Luigi Ombrato
- Centre for Tumour Microenvironment, Barts Cancer Institute, Queen Mary University London, John Vane Science Centre, London, UK.
| |
Collapse
|
4
|
Weed DT, Zilio S, McGee C, Marnissi B, Sargi Z, Franzmann E, Thomas G, Leibowitz J, Nicolli E, Arnold D, Bicciato S, Serafini P. The Tumor Immune Microenvironment Architecture Correlates with Risk of Recurrence in Head and Neck Squamous Cell Carcinoma. Cancer Res 2023; 83:3886-3900. [PMID: 37602821 PMCID: PMC10690086 DOI: 10.1158/0008-5472.can-23-0379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/11/2023] [Accepted: 08/15/2023] [Indexed: 08/22/2023]
Abstract
Emerging evidence suggests that not only the frequency and composition of tumor-infiltrating leukocytes but also their spatial organization might be a major determinant of tumor progression and response to therapy. Therefore, mapping and analyzing the fine tumor immune architecture could potentially provide insights for predicting cancer prognosis. Here, we performed an explorative, prospective clinical study to assess whether structures within the tumor microenvironment can predict recurrence after salvage surgery in head and neck squamous cell carcinoma (HNSCC). The major immune subsets were measured using flow cytometry and co-detection by indexing (CODEX) multiparametric imaging. Flow cytometry underestimated the number of PMN-MDSCs and neutrophils in the tumor and overestimated the tumor-infiltrating lymphocyte frequency. An ad hoc computational framework was used to identify and analyze discrete cellular neighborhoods. A high frequency of tertiary lymphoid structures composed of CD31highCD38high plasma cells was associated with reduced recurrence after surgery in HNSCC. These data support the notion that the structural architecture of the tumor immune microenvironment plays an essential role in tumor progression and indicates that type 1 tertiary lymphoid structures and long-lived CD31highCD38high plasma cells are associated with good prognosis in HNSCC. SIGNIFICANCE Imaging the spatial tumor immune microenvironment and evaluating the presence of type 1 tertiary lymphoid structures enables prediction of recurrence after surgery in patients with head and neck squamous cell carcinoma.
Collapse
Affiliation(s)
- Donald T. Weed
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Serena Zilio
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Christie McGee
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Boutheina Marnissi
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Zoukaa Sargi
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Elizabeth Franzmann
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Giovana Thomas
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Jason Leibowitz
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Elizabeth Nicolli
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - David Arnold
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paolo Serafini
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida
| |
Collapse
|
5
|
Ivanisevic T, Sewduth RN. Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers. Proteomes 2023; 11:34. [PMID: 37873876 PMCID: PMC10594525 DOI: 10.3390/proteomes11040034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023] Open
Abstract
Multi-omics is a cutting-edge approach that combines data from different biomolecular levels, such as DNA, RNA, proteins, metabolites, and epigenetic marks, to obtain a holistic view of how living systems work and interact. Multi-omics has been used for various purposes in biomedical research, such as identifying new diseases, discovering new drugs, personalizing treatments, and optimizing therapies. This review summarizes the latest progress and challenges of multi-omics for designing new treatments for human diseases, focusing on how to integrate and analyze multiple proteome data and examples of how to use multi-proteomics data to identify new drug targets. We also discussed the future directions and opportunities of multi-omics for developing innovative and effective therapies by deciphering proteome complexity.
Collapse
Affiliation(s)
| | - Raj N. Sewduth
- VIB-KU Leuven Center for Cancer Biology (VIB), 3000 Leuven, Belgium;
| |
Collapse
|
6
|
Ziegler C, Mir A, Anandakrishnan S, Martin P, Contreras E, Slemons I, Witkowski B, DeSilva C, Farmer A, Vranic S, Gatalica Z, Richardson D, Derkach DN. Assay-agnostic spatial profiling detects tumor microenvironment signatures: new diagnostic insights for triple-negative breast cancer. Mol Oncol 2023; 17:1953-1961. [PMID: 37666492 PMCID: PMC10552887 DOI: 10.1002/1878-0261.13515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 09/06/2023] Open
Abstract
The role of the tumor microenvironment (TME) in immuno-oncology has driven demand for technologies that deliver in situ, or spatial, molecular information. Compartmentalized heterogeneity that traditional methods miss is becoming key to predicting both acquired drug resistance to targeted therapies and patient response to immunotherapy. Here, we describe a novel method for assay-agnostic spatial profiling and demonstrate its ability to detect immune microenvironment signatures in breast cancer patients that are unresolved by the immunohistochemical (IHC) assessment of programmed cell death ligand-1 (PD-L1) on immune cells, which represents the only FDA microenvironment-based companion diagnostic test that has been approved for triple-negative breast cancer (TNBC). Two distinct physiological states were found that are uncorrelated to tumor mutational burden (TMB), microsatellite instability (MSI), PD-L1 expression, and intrinsic cancer subtypes.
Collapse
Affiliation(s)
| | - Alain Mir
- Takara Bio USASan FranciscoCaliforniaUSA
| | | | | | | | | | | | | | | | - Semir Vranic
- College of Medicine, QU HealthQatar UniversityDohaQatar
| | | | | | | |
Collapse
|
7
|
Bekeschus S. Medical gas plasma technology: Roadmap on cancer treatment and immunotherapy. Redox Biol 2023; 65:102798. [PMID: 37556976 PMCID: PMC10433236 DOI: 10.1016/j.redox.2023.102798] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 08/11/2023] Open
Abstract
Despite continuous therapeutic progress, cancer remains an often fatal disease. In the early 2010s, first evidence in rodent models suggested promising antitumor action of gas plasma technology. Medical gas plasma is a partially ionized gas depositing multiple physico-chemical effectors onto tissues, especially reactive oxygen and nitrogen species (ROS/RNS). Today, an evergrowing body of experimental evidence suggests multifaceted roles of medical gas plasma-derived therapeutic ROS/RNS in targeting cancer alone or in combination with oncological treatment schemes such as ionizing radiation, chemotherapy, and immunotherapy. Intriguingly, gas plasma technology was recently unraveled to have an immunological dimension by inducing immunogenic cell death, which could ultimately promote existing cancer immunotherapies via in situ or autologous tumor vaccine schemes. Together with first clinical evidence reporting beneficial effects in cancer patients following gas plasma therapy, it is time to summarize the main concepts along with the chances and limitations of medical gas plasma onco-therapy from a biological, immunological, clinical, and technological point of view.
Collapse
Affiliation(s)
- Sander Bekeschus
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany; Clinic and Policlinic for Dermatology and Venerology, Rostock University Medical Center, Strempelstr. 13, 18057, Rostock, Germany.
| |
Collapse
|
8
|
Chang X, Zheng Y, Xu K. Single-Cell RNA Sequencing: Technological Progress and Biomedical Application in Cancer Research. Mol Biotechnol 2023:10.1007/s12033-023-00777-0. [PMID: 37322261 DOI: 10.1007/s12033-023-00777-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023]
Abstract
Single-cell RNA-seq (scRNA-seq) is a revolutionary technology that allows for the genomic investigation of individual cells in a population, allowing for the discovery of unusual cells associated with cancer and metastasis. ScRNA-seq has been used to discover different types of cancers with poor prognosis and medication resistance such as lung cancer, breast cancer, ovarian cancer, and gastric cancer. Besides, scRNA-seq is a promising method that helps us comprehend the biological features and dynamics of cell development, as well as other disorders. This review gives a concise summary of current scRNA-seq technology. We also explain the main technological steps involved in implementing the technology. We highlight the present applications of scRNA-seq in cancer research, including tumor heterogeneity analysis in lung cancer, breast cancer, and ovarian cancer. In addition, this review elucidates potential applications of scRNA-seq in lineage tracing, personalized medicine, illness prediction, and disease diagnosis, which reveals that scRNA-seq facilitates these events by producing genetic variations on the single-cell level.
Collapse
Affiliation(s)
- Xu Chang
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yunxi Zheng
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Kai Xu
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, 330006, Jiangxi, People's Republic of China.
| |
Collapse
|
9
|
Lv S, Tao L, Liao H, Huang Z, Lu Y. Comprehensive analysis of single-cell RNA-seq and bulk RNA-seq revealed the heterogeneity and convergence of the immune microenvironment in renal cell carcinoma. Funct Integr Genomics 2023; 23:193. [PMID: 37264263 DOI: 10.1007/s10142-023-01113-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023]
Abstract
Substantial progress has been made in cancer biology and treatment in recent years, but the clinical outcome of patients with renal cell carcinoma (RCC) remains unsatisfactory. The tumor microenvironment (TME) is a potential target. By analyzing single-cell RNA sequencing (sc-RNAseq) data from six RCC tumor samples, this study identified 11 different cell types in the RCC cellular microenvironment, indicating a high degree of intratumoral heterogeneity. Through re-dimensionality reduction clustering of epithelial cells, neutrophils, macrophages, and T cells, we deeply reveal differences in the RCC tumor microenvironment. By analyzing differentially expressed genes in normal epithelial cells and malignant epithelial cells, we identify RNASET2 and GATM as potential prognostic biomarkers in RCC. In addition, by transcriptional factor analysis, we found significant differences in the expression of GZMK-CD8 T cell and B cell transcription factors between cancer tissues and normal tissues. By cell correlation analysis, we found significant correlations between neutrophils and macrophages and between IL7R-CD4 T cells and T regulatory (Treg) cells in RCC, which may be involved in the formation of immune TMEs. By cell developmental trajectory analysis, we showed that macrophages may be derived from neutrophils, whereas Treg cells may be derived from IL7R-CD4 T cells. By cell communication analysis, we found a clear interaction between macrophages and endothelial cells, neutrophils, and GZMK-CD8 T cells. In addition, we found that ADGRE5 signaling was mainly derived from mast cells and GZMK-CD8 T cells, and had a significant communication effect with neutrophils. The COLLAGEN signaling pathway is mainly derived from fibroblasts and has a significant communication effect with mast cells. Finally, we verified that RNASET2, which is highly expressed in epithelial cells, promotes proliferation and migration of RCC in vitro. RNASET2 is likely to be a potential target for renal cell carcinoma therapy. The results based on sc-RNAseq data analysis help to further elucidate the cellular microenvironment of RCC and provide help for cancer heterogeneity studies. This will help to provide more accurate personalized treatment for patients in clinical diagnosis.
Collapse
Affiliation(s)
- Shihui Lv
- Department of Urology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Liping Tao
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Hongbing Liao
- Department of Urology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhiming Huang
- Department of Urology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yongyong Lu
- Department of Urology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| |
Collapse
|
10
|
Christodoulou MI, Zaravinos A. Single-Cell Analysis in Immuno-Oncology. Int J Mol Sci 2023; 24:ijms24098422. [PMID: 37176128 PMCID: PMC10178969 DOI: 10.3390/ijms24098422] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/01/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
The complexity of the cellular and non-cellular milieu surrounding human tumors plays a decisive role in the course and outcome of disease. The high variability in the distribution of the immune and non-immune compartments within the tumor microenvironments (TME) among different patients governs the mode of their response or resistance to current immunotherapeutic approaches. Through deciphering this diversity, one can tailor patients' management to meet an individual's needs. Single-cell (sc) omics technologies have given a great boost towards this direction. This review gathers recent data about how multi-omics profiling, including the utilization of single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin with sequencing (scATAC-seq), T-cell receptor sequencing (scTCR-seq), mass, tissue-based, or microfluidics cytometry, and related bioinformatics tools, contributes to the high-throughput assessment of a large number of analytes at single-cell resolution. Unravelling the exact TCR clonotype of the infiltrating T cells or pinpointing the classical or novel immune checkpoints across various cell subsets of the TME provide a boost to our comprehension of adaptive immune responses, their antigen specificity and dynamics, and grant suggestions for possible therapeutic targets. Future steps are expected to merge high-dimensional data with tissue localization data, which can serve the investigation of novel multi-modal biomarkers for the selection and/or monitoring of the optimal treatment from the current anti-cancer immunotherapeutic armamentarium.
Collapse
Affiliation(s)
- Maria-Ioanna Christodoulou
- Tumor Immunology and Biomarkers Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 2404 Nicosia, Cyprus
- Cancer Genetics, Genomics and Systems Biology Group, Basic and Translational Cancer Research Center (BTCRC), 1516 Nicosia, Cyprus
| |
Collapse
|
11
|
He X, Liu X, Zuo F, Shi H, Jing J. Artificial intelligence-based multi-omics analysis fuels cancer precision medicine. Semin Cancer Biol 2023; 88:187-200. [PMID: 36596352 DOI: 10.1016/j.semcancer.2022.12.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/16/2022] [Accepted: 12/29/2022] [Indexed: 01/02/2023]
Abstract
With biotechnological advancements, innovative omics technologies are constantly emerging that have enabled researchers to access multi-layer information from the genome, epigenome, transcriptome, proteome, metabolome, and more. A wealth of omics technologies, including bulk and single-cell omics approaches, have empowered to characterize different molecular layers at unprecedented scale and resolution, providing a holistic view of tumor behavior. Multi-omics analysis allows systematic interrogation of various molecular information at each biological layer while posing tricky challenges regarding how to extract valuable insights from the exponentially increasing amount of multi-omics data. Therefore, efficient algorithms are needed to reduce the dimensionality of the data while simultaneously dissecting the mysteries behind the complex biological processes of cancer. Artificial intelligence has demonstrated the ability to analyze complementary multi-modal data streams within the oncology realm. The coincident development of multi-omics technologies and artificial intelligence algorithms has fuelled the development of cancer precision medicine. Here, we present state-of-the-art omics technologies and outline a roadmap of multi-omics integration analysis using an artificial intelligence strategy. The advances made using artificial intelligence-based multi-omics approaches are described, especially concerning early cancer screening, diagnosis, response assessment, and prognosis prediction. Finally, we discuss the challenges faced in multi-omics analysis, along with tentative future trends in this field. With the increasing application of artificial intelligence in multi-omics analysis, we anticipate a shifting paradigm in precision medicine becoming driven by artificial intelligence-based multi-omics technologies.
Collapse
Affiliation(s)
- Xiujing He
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Xiaowei Liu
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Fengli Zuo
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Hubing Shi
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China
| | - Jing Jing
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, PR China.
| |
Collapse
|
12
|
Venkatesiah SS, Augustine D, Mishra D, Gujjar N, Haragannavar VC, Awan KH, Patil S. Immunology of Oral Squamous Cell Carcinoma-A Comprehensive Insight with Recent Concepts. Life (Basel) 2022; 12:1807. [PMID: 36362963 PMCID: PMC9695443 DOI: 10.3390/life12111807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 09/28/2023] Open
Abstract
This review aims to understand the concept of oral cancer immunology through the notion of immune profiling, immunoediting and immunotherapy, and to gain knowledge regarding its application for the management of oral cancer patients. Oral cancer is an immunogenic tumor where the cells of the tumor microenvironment play an important role in tumorigenesis. Understanding the mechanism of these modulations can help design immunotherapeutic strategies in oral cancer patients. This article gives an overview of immunomodulation in the oral cancer tumor microenvironment, with concepts of immune profiling, immunoediting and immunotherapy. English literature searches via Google Scholar, Web of Science, EBSCO, Scopus, and PubMed database were performed with the key words immunology, tumor microenvironment, cells, cross talk, immune profiling, biomarkers, inflammation, gene expression, techniques, immunoediting, immunosurveillance, tumor escape, immunotherapy, immune checkpoint inhibitors, vaccines in cancer, oral cancer, and head and neck cancer. Original research articles, reviews, and case reports published from 2016-2021 (n = 81) were included to appraise different topics, and were discussed under the following subsections. Literature published on oral cancer immunology reveals that oral cancer immune profiling with appropriate markers and techniques and knowledge on immunoediting concepts can help design and play an effective role in immunotherapeutic management of oral cancer patients. An evaluation of oral cancer immunology helps to determine its role in tumorigenesis, and immunotherapy could be the emerging drift in the effective management of oral cancer.
Collapse
Affiliation(s)
- Sowmya Samudrala Venkatesiah
- Department of Oral Pathology & Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, MSR Nagar, Bengaluru 560054, India
| | - Dominic Augustine
- Department of Oral Pathology & Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, MSR Nagar, Bengaluru 560054, India
| | - Deepika Mishra
- Department of Oral Pathology & Microbiology, Centre for Dental Education and Research, All India Institute of Medical Sciences (AIIMS), Delhi 110608, India
| | - Neethi Gujjar
- Department of Oral Pathology & Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, MSR Nagar, Bengaluru 560054, India
| | - Vanishri C. Haragannavar
- Department of Oral Pathology & Microbiology, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, MSR Nagar, Bengaluru 560054, India
| | - Kamran Habib Awan
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT 84095, USA
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UT 84095, USA
- Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences University, Chennai 600077, India
| |
Collapse
|
13
|
Zhang L, Ye B, Chen Z, Chen ZS. Progress in the studies on the molecular mechanisms associated with multidrug resistance in cancers. Acta Pharm Sin B 2022; 13:982-997. [PMID: 36970215 PMCID: PMC10031261 DOI: 10.1016/j.apsb.2022.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/28/2022] [Accepted: 08/18/2022] [Indexed: 11/01/2022] Open
Abstract
Chemotherapy is one of the important methods to treat cancer, and the emergence of multidrug resistance (MDR) is one major cause for the failure of cancer chemotherapy. Almost all anti-tumor drugs develop drug resistance over a period of time of application in cancer patients, reducing their effects on killing cancer cells. Chemoresistance can lead to a rapid recurrence of cancers and ultimately patient death. MDR may be induced by multiple mechanisms, which are associated with a complex process of multiple genes, factors, pathways, and multiple steps, and today the MDR-associated mechanisms are largely unknown. In this paper, from the aspects of protein-protein interactions, alternative splicing (AS) in pre-mRNA, non-coding RNA (ncRNA) mediation, genome mutations, variance in cell functions, and influence from the tumor microenvironment, we summarize the molecular mechanisms associated with MDR in cancers. In the end, prospects for the exploration of antitumor drugs that can reverse MDR are briefly discussed from the angle of drug systems with improved targeting properties, biocompatibility, availability, and other advantages.
Collapse
|
14
|
Caligola S, De Sanctis F, Canè S, Ugel S. Breaking the Immune Complexity of the Tumor Microenvironment Using Single-Cell Technologies. Front Genet 2022; 13:867880. [PMID: 35651929 PMCID: PMC9149246 DOI: 10.3389/fgene.2022.867880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/27/2022] [Indexed: 12/31/2022] Open
Abstract
Tumors are not a simple aggregate of transformed cells but rather a complicated ecosystem containing various components, including infiltrating immune cells, tumor-related stromal cells, endothelial cells, soluble factors, and extracellular matrix proteins. Profiling the immune contexture of this intricate framework is now mandatory to develop more effective cancer therapies and precise immunotherapeutic approaches by identifying exact targets or predictive biomarkers, respectively. Conventional technologies are limited in reaching this goal because they lack high resolution. Recent developments in single-cell technologies, such as single-cell RNA transcriptomics, mass cytometry, and multiparameter immunofluorescence, have revolutionized the cancer immunology field, capturing the heterogeneity of tumor-infiltrating immune cells and the dynamic complexity of tenets that regulate cell networks in the tumor microenvironment. In this review, we describe some of the current single-cell technologies and computational techniques applied for immune-profiling the cancer landscape and discuss future directions of how integrating multi-omics data can guide a new "precision oncology" advancement.
Collapse
Affiliation(s)
- Simone Caligola
- Immunology Section, Department of Medicine, University of Verona, Verona, Italy
| | | | - Stefania Canè
- Immunology Section, Department of Medicine, University of Verona, Verona, Italy
| | - Stefano Ugel
- Immunology Section, Department of Medicine, University of Verona, Verona, Italy
| |
Collapse
|
15
|
Kiuru M, Kriner MA, Wong S, Zhu G, Terrell JR, Li Q, Hoang M, Beechem J, McPherson JD. High-Plex Spatial RNA Profiling Reveals Cell Type‒Specific Biomarker Expression during Melanoma Development. J Invest Dermatol 2022; 142:1401-1412.e20. [PMID: 34699906 PMCID: PMC9714472 DOI: 10.1016/j.jid.2021.06.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/15/2021] [Accepted: 06/23/2021] [Indexed: 01/26/2023]
Abstract
Early diagnosis of melanoma is critical for improved survival. However, the biomarkers of early melanoma evolution and their origin within the tumor and its microenvironment, including the keratinocytes, are poorly defined. To address this, we used spatial transcript profiling that maintains the morphological tumor context to measure the expression of >1,000 RNAs in situ in patient-derived formalin-fixed, paraffin-embedded tissue sections in primary melanoma and melanocytic nevi. We profiled 134 regions of interest (each 200 μm in diameter) enriched in melanocytes, neighboring keratinocytes, or immune cells. This approach captured distinct expression patterns across cell types and tumor types during melanoma development. Unexpectedly, we discovered that S100A8 is expressed by keratinocytes within the tumor microenvironment during melanoma growth. Immunohistochemistry of 252 tumors showed prominent keratinocyte-derived S100A8 expression in melanoma but not in benign tumors and confirmed the same pattern for S100A8's binding partner S100A9, suggesting that injury to the epidermis may be an early and readily detectable indicator of melanoma development. Together, our results establish a framework for high-plex, spatial, and cell type‒specific resolution of gene expression in archival tissue applicable to the development of biomarkers and characterization of tumor microenvironment interactions in tumor evolution.
Collapse
Affiliation(s)
- Maija Kiuru
- Department of Dermatology, University of California Davis, Sacramento, California, USA,Department of Pathology & Laboratory Medicine, University of California Davis, Sacramento, California, USA
| | | | - Samantha Wong
- Department of Dermatology, University of California Davis, Sacramento, California, USA
| | - Guannan Zhu
- Department of Dermatology, University of California Davis, Sacramento, California, USA,Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Jessica R. Terrell
- Department of Dermatology, University of California Davis, Sacramento, California, USA
| | - Qian Li
- Center for Oncology Hematology Outcomes Research and Training (COHORT) and Division of Hematology and Oncology, University of California, Davis, Sacramento, CA
| | | | | | - John D. McPherson
- Department of Biochemistry & Molecular Medicine, University of California Davis, Sacramento, California, USA
| |
Collapse
|
16
|
Yin H, Guo R, Zhang H, Liu S, Gong Y, Yuan Y. A Dynamic Transcriptome Map of Different Tissue Microenvironment Cells Identified During Gastric Cancer Development Using Single-Cell RNA Sequencing. Front Immunol 2021; 12:728169. [PMID: 34745098 PMCID: PMC8566821 DOI: 10.3389/fimmu.2021.728169] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022] Open
Abstract
Gastric cancer (GC) development trends have identified multiple processes ranging from inflammation to carcinogenesis, however, key pathogenic mechanisms remain unclear. Tissue microenvironment (TME) cells are critical for the progression of malignant tumors. Here, we generated a dynamic transcriptome map of various TME cells during multi-disease stages using single-cell sequencing analysis. We observed a set of key transition markers related to TME cell carcinogenic evolution, and delineated landmark dynamic carcinogenic trajectories of these cells. Of these, macrophages, fibroblasts, and endothelial cells exerted considerable effects toward epithelial cells, suggesting these cells may be key TME factors promoting GC occurrence and development. Our results suggest a phenotypic convergence of different TME cell types toward tumor formation processes in GC. We believe our data would pave the way for early GC detection, diagnosis, and treatment therapies.
Collapse
Affiliation(s)
- Honghao Yin
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Rui Guo
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Huanyu Zhang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Songyi Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, China
| |
Collapse
|
17
|
Ganini C, Amelio I, Bertolo R, Bove P, Buonomo OC, Candi E, Cipriani C, Di Daniele N, Juhl H, Mauriello A, Marani C, Marshall J, Melino S, Marchetti P, Montanaro M, Natale ME, Novelli F, Palmieri G, Piacentini M, Rendina EA, Roselli M, Sica G, Tesauro M, Rovella V, Tisone G, Shi Y, Wang Y, Melino G. Global mapping of cancers: The Cancer Genome Atlas and beyond. Mol Oncol 2021; 15:2823-2840. [PMID: 34245122 PMCID: PMC8564642 DOI: 10.1002/1878-0261.13056] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/04/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Cancer genomes have been explored from the early 2000s through massive exome sequencing efforts, leading to the publication of The Cancer Genome Atlas in 2013. Sequencing techniques have been developed alongside this project and have allowed scientists to bypass the limitation of costs for whole-genome sequencing (WGS) of single specimens by developing more accurate and extensive cancer sequencing projects, such as deep sequencing of whole genomes and transcriptomic analysis. The Pan-Cancer Analysis of Whole Genomes recently published WGS data from more than 2600 human cancers together with almost 1200 related transcriptomes. The application of WGS on a large database allowed, for the first time in history, a global analysis of features such as molecular signatures, large structural variations and noncoding regions of the genome, as well as the evaluation of RNA alterations in the absence of underlying DNA mutations. The vast amount of data generated still needs to be thoroughly deciphered, and the advent of machine-learning approaches will be the next step towards the generation of personalized approaches for cancer medicine. The present manuscript wants to give a broad perspective on some of the biological evidence derived from the largest sequencing attempts on human cancers so far, discussing advantages and limitations of this approach and its power in the era of machine learning.
Collapse
Affiliation(s)
- Carlo Ganini
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- IDI‐IRCCSRomeItaly
| | - Ivano Amelio
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Riccardo Bertolo
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Pierluigi Bove
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Oreste Claudio Buonomo
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Eleonora Candi
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- IDI‐IRCCSRomeItaly
| | - Chiara Cipriani
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Nicola Di Daniele
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Alessandro Mauriello
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Carla Marani
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - John Marshall
- Medstar Georgetown University HospitalGeorgetown UniversityWashingtonDCUSA
| | - Sonia Melino
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Manuela Montanaro
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Maria Emanuela Natale
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- San Carlo di Nancy HospitalRomeItaly
| | - Flavia Novelli
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giampiero Palmieri
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Mauro Piacentini
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | | | - Mario Roselli
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giuseppe Sica
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Manfredi Tesauro
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Valentina Rovella
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Giuseppe Tisone
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| | - Yufang Shi
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
- CAS Key Laboratory of Tissue Microenvironment and TumorShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina
- The First Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and ProtectionInstitutes for Translational MedicineSoochow UniversityChina
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and TumorShanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghaiChina
| | - Gerry Melino
- Department of Experimental MedicineTorvergata Oncoscience Research Centre of Excellence, TORUniversity of Rome Tor VergataItaly
| |
Collapse
|
18
|
Guerrisi A, Russillo M, Loi E, Ganeshan B, Ungania S, Desiderio F, Bruzzaniti V, Falcone I, Renna D, Ferraresi V, Caterino M, Solivetti FM, Cognetti F, Morrone A. Exploring CT Texture Parameters as Predictive and Response Imaging Biomarkers of Survival in Patients With Metastatic Melanoma Treated With PD-1 Inhibitor Nivolumab: A Pilot Study Using a Delta-Radiomics Approach. Front Oncol 2021; 11:704607. [PMID: 34692481 PMCID: PMC8529867 DOI: 10.3389/fonc.2021.704607] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/08/2021] [Indexed: 01/08/2023] Open
Abstract
In the era of artificial intelligence and precision medicine, the use of quantitative imaging methodological approaches could improve the cancer patient’s therapeutic approaches. Specifically, our pilot study aims to explore whether CT texture features on both baseline and first post-treatment contrast-enhanced CT may act as a predictor of overall survival (OS) and progression-free survival (PFS) in metastatic melanoma (MM) patients treated with the PD-1 inhibitor Nivolumab. Ninety-four lesions from 32 patients treated with Nivolumab were analyzed. Manual segmentation was performed using a free-hand polygon approach by drawing a region of interest (ROI) around each target lesion (up to five lesions were selected per patient according to RECIST 1.1). Filtration-histogram-based texture analysis was employed using a commercially available research software called TexRAD (Feedback Medical Ltd, London, UK; https://fbkmed.com/texrad-landing-2/) Percentage changes in texture features were calculated to perform delta-radiomics analysis. Texture feature kurtosis at fine and medium filter scale predicted OS and PFS. A higher kurtosis is correlated with good prognosis; kurtosis values greater than 1.11 for SSF = 2 and 1.20 for SSF = 3 were indicators of higher OS (fine texture: 192 HR = 0.56, 95% CI = 0.32–0.96, p = 0.03; medium texture: HR = 0.54, 95% CI = 0.29–0.99, p = 0.04) and PFS (fine texture: HR = 0.53, 95% CI = 0.29–0.95, p = 0.03; medium texture: HR = 0.49, 209 95% CI = 0.25–0.96, p = 0.03). In delta-radiomics analysis, the entropy percentage variation correlated with OS and PFS. Increasing entropy indicates a worse outcome. An entropy variation greater than 5% was an indicator of bad prognosis. CT delta-texture analysis quantified as entropy predicted OS and PFS. Baseline CT texture quantified as kurtosis also predicted survival baseline. Further studies with larger cohorts are mandatory to confirm these promising exploratory results.
Collapse
Affiliation(s)
- Antonino Guerrisi
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Michelangelo Russillo
- Medical Oncology Unit 1, Department of Clinical and Cancer Research IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Emiliano Loi
- Medical Physics and Expert Systems Laboratory, 3 Department of Research and Advanced Technologies, Istituti Fisioterapici Ospitalieri - IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Balaji Ganeshan
- Institute of Nuclear Medicine, Imaging Department, University College Hospital, London, United Kingdom
| | - Sara Ungania
- Medical Physics and Expert Systems Laboratory, 3 Department of Research and Advanced Technologies, Istituti Fisioterapici Ospitalieri - IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Flora Desiderio
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Vicente Bruzzaniti
- Medical Physics and Expert Systems Laboratory, 3 Department of Research and Advanced Technologies, Istituti Fisioterapici Ospitalieri - IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Italia Falcone
- Medical Oncology Unit 1, Department of Clinical and Cancer Research IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Davide Renna
- Medical Oncology 1, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Virginia Ferraresi
- Medical Oncology Unit 1, Department of Clinical and Cancer Research IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Mauro Caterino
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Francesco Maria Solivetti
- Radiology and Diagnostic Imaging Unit, Department of Clinical and Dermatological Research, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Francesco Cognetti
- Medical Oncology Unit 1, Department of Clinical and Cancer Research IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Aldo Morrone
- Scientific Director, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| |
Collapse
|
19
|
Abstract
From genomics to transcriptomics to proteomics, microfluidic tools underpin recent advances in single-cell biology. Detection of specific proteoforms-with single-cell resolution-presents challenges in detection specificity and sensitivity. Miniaturization of protein immunoblots to single-cell resolution mitigates these challenges. For example, in microfluidic western blotting, protein targets are separated by electrophoresis and subsequently detected using fluorescently labeled antibody probes. To quantify the expression level of each protein target, the fluorescent protein bands are fit to Gaussians; yet, this method is difficult to use with noisy, low-abundance, or low-SNR protein bands, and with significant band skew or dispersion. In this study, we investigate segmentation-based approaches to robustly quantify protein bands from single-cell protein immunoblots. As compared to a Gaussian fitting pipeline, the segmentation pipeline detects >1.5× more protein bands for downstream quantification as well as more of the low-abundance protein bands (i.e., with SNR ∼3). Utilizing deep learning-based segmentation approaches increases the recovery of low-SNR protein bands by an additional 50%. However, we find that segmentation-based approaches are less robust at quantifying poorly resolved protein bands (separation resolution, Rs < 0.6). With burgeoning needs for more single-cell protein analysis tools, we see microfluidic separations as benefitting substantially from segmentation-based analysis approaches.
Collapse
Affiliation(s)
- Anjali Gopal
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
| | - Amy E. Herr
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
| |
Collapse
|
20
|
Jia L, Wang T, Zhao Y, Zhang S, Ba T, Kuai X, Wang B, Zhang N, Zhao W, Yang Z, Qiao H. Single-cell profiling of infiltrating B cells and tertiary lymphoid structures in the TME of gastric adenocarcinomas. Oncoimmunology 2021; 10:1969767. [PMID: 34513317 PMCID: PMC8425751 DOI: 10.1080/2162402x.2021.1969767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The occurrence and development of gastric adenocarcinoma (gADC) is closely related to the interaction between tumor cells and immune cells in the tumor microenvironment (TME). Our objective was to characterize the repertoire of immune cells in the TME of gADC. To analyze the transcriptomic, immune, and spatial information of TME in gADC, we constructed single-cell RNA sequencing, 10 × Genomics V(D)J analysis, multiple immunofluorescence techniques, and OSCmap analysis of 49,765 single cells in seven samples from four gADC patients. Our integrative analysis of B cells demonstrated that a large number of mucosal associated lymphoid tissue (MALT)-B cells were detected in the gADC tissues, which have mature tertiary lymphatic structures (mTLSs), and almost no MALT-B cells in peripheral blood sample. Moreover, MALT-B cells are a class of IgA+ plasma cells, which are characterized with high expression of complement pathway activation-related genes. Next, natural killer T (NKT) cells mainly exist in gADC tissues accompanied by mTLSs. This study also classified monocytes/macrophages and epithelial cells into benign and malignant types. Interestingly, CSOmap (q < .05) and multiple immunofluorescence (p < .05) results indicated more types of immune cells can be enriched in tissues with mTLSs than normal TLSs, and the density of mTLSs were higher than normal TLSs. Our findings provide novel insights for the signature of immune cells and tumor cells in the TME of gADC with TLSs and highlight the potential importance of IgA-mediated humoral immunity in gADC patients with TLSs.
Collapse
Affiliation(s)
- Lizhou Jia
- Cancer Center, Bayannur Hospital, Bayannur, China
| | - Tengqi Wang
- Cancer Center, Bayannur Hospital, Bayannur, China
| | - Youcai Zhao
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Shuyu Zhang
- International Department, Huhhot NO.2 High School, Huhhot, Inner Mongolia, China
| | - Teer Ba
- School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Xingwang Kuai
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Bin Wang
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ning Zhang
- Cancer Center, Bayannur Hospital, Bayannur, China
| | - Wei Zhao
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Research Center for the Prevention and Treatment of Drug Resistant Microbial Infecting, Youjiang Medical University for Nationalities, Baise, China
| | - Zhiping Yang
- Cancer Center, Bayannur Hospital, Bayannur, China
| | - Haishi Qiao
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
21
|
Lapuente-Santana Ó, van Genderen M, Hilbers PA, Finotello F, Eduati F. Interpretable systems biomarkers predict response to immune-checkpoint inhibitors. Patterns (N Y) 2021; 2:100293. [PMID: 34430923 PMCID: PMC8369166 DOI: 10.1016/j.patter.2021.100293] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/22/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Cancer cells can leverage several cell-intrinsic and -extrinsic mechanisms to escape immune system recognition. The inherent complexity of the tumor microenvironment, with its multicellular and dynamic nature, poses great challenges for the extraction of biomarkers of immune response and immunotherapy efficacy. Here, we use RNA-sequencing (RNA-seq) data combined with different sources of prior knowledge to derive system-based signatures of the tumor microenvironment, quantifying immune-cell composition and intra- and intercellular communications. We applied multi-task learning to these signatures to predict different hallmarks of immune responses and derive cancer-type-specific models based on interpretable systems biomarkers. By applying our models to independent RNA-seq data from cancer patients treated with PD-1/PD-L1 inhibitors, we demonstrated that our method to Estimate Systems Immune Response (EaSIeR) accurately predicts therapeutic outcome. We anticipate that EaSIeR will be a valuable tool to provide a holistic description of immune responses in complex and dynamic systems such as tumors using available RNA-seq data.
Collapse
Affiliation(s)
- Óscar Lapuente-Santana
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Maisa van Genderen
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Peter A.J. Hilbers
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612 AZ Eindhoven, the Netherlands
| |
Collapse
|
22
|
Gohil SH, Iorgulescu JB, Braun DA, Keskin DB, Livak KJ. Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy. Nat Rev Clin Oncol 2021; 18:244-256. [PMID: 33277626 PMCID: PMC8415132 DOI: 10.1038/s41571-020-00449-x] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Advances in molecular biology, microfluidics and bioinformatics have empowered the study of thousands or even millions of individual cells from malignant tumours at the single-cell level of resolution. This high-dimensional, multi-faceted characterization of the genomic, transcriptomic, epigenomic and proteomic features of the tumour and/or the associated immune and stromal cells enables the dissection of tumour heterogeneity, the complex interactions between tumour cells and their microenvironment, and the details of the evolutionary trajectory of each tumour. Single-cell transcriptomics, the ability to track individual T cell clones through paired sequencing of the T cell receptor genes and high-dimensional single-cell spatial analysis are all areas of particular relevance to immuno-oncology. Multidimensional biomarker signatures will increasingly be crucial to guiding clinical decision-making in each patient with cancer. High-dimensional single-cell technologies are likely to provide the resolution and richness of data required to generate such clinically relevant signatures in immuno-oncology. In this Perspective, we describe advances made using transformative single-cell analysis technologies, especially in relation to clinical response and resistance to immunotherapy, and discuss the growing utility of single-cell approaches for answering important research questions.
Collapse
Affiliation(s)
- Satyen H Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Academic Haematology, University College London Cancer Institute, London, UK
| | - J Bryan Iorgulescu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA.
| |
Collapse
|
23
|
Mezawa Y, Orimo A. Phenotypic heterogeneity, stability and plasticity in tumor-promoting carcinoma-associated fibroblasts. FEBS J 2021; 289:2429-2447. [PMID: 33786982 DOI: 10.1111/febs.15851] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/15/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022]
Abstract
Reciprocal interactions between cancer cells and stromal cells in the tumor microenvironment (TME) are essential for full-blown tumor development. Carcinoma-associated fibroblasts (CAFs) are a key component of the TME together with a wide variety of stromal cell types including vascular, inflammatory, and immune cells in the extracellular matrix. CAFs not only promote tumor growth, invasion, and metastasis, but also dampen the efficacy of various therapies including immune checkpoint inhibitors. CAFs are composed of distinct fibroblast populations presumably with diverse activated fibroblastic states and tumor-promoting phenotypes in a tumor, indicating intratumor heterogeneity in these fibroblasts. Given that CAFs have been implicated in both disease progression and therapeutic responses, elucidating the functional roles of each fibroblast population in CAFs and the molecular mechanisms mediating their phenotypic stability and plasticity in the TME would be crucial for understanding tumor biology. We herein discuss how distinct fibroblast populations comprising CAFs establish their cell identities, in terms of cells-of-origin, stimuli from the TME, and the phenotypes characteristic of activated states.
Collapse
Affiliation(s)
- Yoshihiro Mezawa
- Department of Pathology and Oncology, Juntendo University School of Medicine, Tokyo, Japan
| | - Akira Orimo
- Department of Pathology and Oncology, Juntendo University School of Medicine, Tokyo, Japan
| |
Collapse
|
24
|
Abstract
Introduction: Tumor immune microenvironment (TIME) promotes immune escape, allowing for tumor progression and metastasis. In spite of the current evidence of the complicated role of immune cells in promoting or suppressing cancer progression, the heterogeneity of TIME according to the tumor site has been scarcely investigated. Here, we analyzed transcriptomic profiles of metastatic breast cancer to understand how TIME varies according to tumor sites. Methods: Two gene expression datasets from metastatic breast cancer of various sites and a single-cell RNA sequencing dataset of primary breast cancer and metastatic lymph nodes were analyzed. The immune cell-type enrichment of each tumor was estimated. Immune cell types were identified by clustering analysis, and the proportions of cell types in TIME were assessed according to the tumor site. Results: Metastatic bone lesions showed more neutrophils than breast lesions. Tumors clustered according to immune cell type were significantly associated with tumor site. In single-cell analyses, the TIMEs of metastatic lymph nodes showed fewer macrophages than those of primary tumors. Differentially expressed gene signatures in the primary tumor and metastatic lymph nodes were associated with macrophage activation. Conclusion: We conclude that metastatic sites show variable enrichment patterns of immune cells, and that the TIME of metastatic lesions should be considered in precise immuno-oncology treatments.
Collapse
Affiliation(s)
- Hyunjong Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, South Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Kwon Joong Na
- Department of Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul, South Korea
| | - Hongyoon Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul, South Korea
| |
Collapse
|
25
|
Hajiran A, Chakiryan N, Aydin AM, Zemp L, Nguyen J, Laborde JM, Chahoud J, Spiess PE, Zaman S, Falasiri S, Fournier M, Teer JK, Dhillon J, McCarthy S, Moran-Segura C, Katende EN, Sexton WJ, Koomen JM, Mulé J, Kim Y, Manley B. Reconnaissance of tumor immune microenvironment spatial heterogeneity in metastatic renal cell carcinoma and correlation with immunotherapy response. Clin Exp Immunol 2021; 204:96-106. [PMID: 33346915 DOI: 10.1111/cei.13567] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/22/2020] [Accepted: 12/02/2020] [Indexed: 12/24/2022] Open
Abstract
A clearer understanding of the tumor immune microenvironment (TIME) in metastatic clear cell renal cell carcinoma (ccRCC) may help to inform precision treatment strategies. We sought to identify clinically meaningful TIME signatures in ccRCC. We studied tumors from 39 patients with metastatic ccRCC using quantitative multiplexed immunofluorescence and relevant immune marker panels. Cell densities were analyzed in three regions of interest (ROIs): tumor core, tumor-stroma interface and stroma. Patients were stratified into low- and high-marker density groups using median values as thresholds. Log-rank and Cox regression analyses while controlling for clinical variables were used to compare survival outcomes to patterns of immune cell distributions. There were significant associations with increased macrophage (CD68+ CD163+ CD206+ ) density and poor outcomes across multiple ROIs in primary and metastatic tumors. In primary tumors, T-bet+ T helper type 1 (Th1) cell density was highest at the tumor-stromal interface (P = 0·0021), and increased co-expression of CD3 and T-bet was associated with improved overall survival (P = 0·015) and survival after immunotherapy (P = 0·014). In metastatic tumor samples, decreased forkhead box protein 3 (FoxP3)+ T regulatory cell density correlated with improved survival after immunotherapy (P = 0·016). Increased macrophage markers and decreased Th1 T cell markers within the TIME correlated with poor overall survival and treatment outcomes. Immune markers such as FoxP3 showed consistent levels across the TIME, whereas others, such as T-bet, demonstrated significant variance across the distinct ROIs. These findings suggest that TIME profiling outside the tumor core may identify clinically relevant associations for patients with metastatic ccRCC.
Collapse
Affiliation(s)
- A Hajiran
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - N Chakiryan
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - A M Aydin
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - L Zemp
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Nguyen
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - J M Laborde
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Chahoud
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - P E Spiess
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - S Zaman
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - S Falasiri
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - M Fournier
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Dhillon
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - S McCarthy
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - C Moran-Segura
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - E N Katende
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - W J Sexton
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J M Koomen
- Department of Proteomics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - J Mulé
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Y Kim
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - B Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.,Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| |
Collapse
|
26
|
Liu Q, Zhang R, Zhang X, Liu J, Wu H, Li Y, Cui M, Li T, Song H, Gao J, Zhang Y, Yang S, Liao Q. Dopamine improves chemotherapeutic efficacy for pancreatic cancer by regulating macrophage-derived inflammations. Cancer Immunol Immunother 2021; 70:2165-2177. [PMID: 33454798 DOI: 10.1007/s00262-020-02816-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 12/01/2020] [Indexed: 12/22/2022]
Abstract
Pancreatic cancer is an inflammatory malignancy, and tumor-associated macrophages (TAMs) are the predominant inflammatory cells in tumor tissue. TAMs have complicated interactions with pancreatic cancer cells, however, the details and mechanisms remain largely unknown. In this study, transcriptomics and proteomics analyses were performed to explore the interactions between murine pancreatic cancer cells and TAMs. Dopamine (DA) has been reported to suppress inflammations. However, its roles in TAMs of pancreatic cancer have not been reported. Herein, the roles and mechanisms of DA to affect the chemotherapeutic efficacy for pancreatic cancer were studied. Multi-omics results revealed that there was a tumor-promoting vicious cycle involving murine pancreatic cancer cells and TAMs. DA substantially improved the chemotherapeutic efficacy both in vitro study and in immunocompetent murine pancreatic cancer models by suppression of the M2 characters of TAMs. Further studies found that activation of DRD4 by DA led to the decrease of cAMP, and then inhibited the activation of PKA/p38 signal pathway, which suppressed the tumor-promoting inflammation of TAMs. This study uncovers the reciprocal interactions between TAMs and pancreatic cancer cells using multi-omics techniques and presents that DA has synergistic roles with chemotherapy for pancreatic cancer by suppressing of TAM-derived inflammations.
Collapse
Affiliation(s)
- Qiaofei Liu
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Ronghua Zhang
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.,Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China
| | - Xiang Zhang
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Jingkai Liu
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Huanwen Wu
- Department of Pathology, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, 100730, China
| | - Yuan Li
- Department of Pathology, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Beijing, 100730, China
| | - Ming Cui
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Tong Li
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Huixin Song
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Junyi Gao
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Yalu Zhang
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Sen Yang
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China
| | - Quan Liao
- Department of General Surgery, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, 1# Shuai Fu Yuan, Dongcheng District, Beijing, 100730, China.
| |
Collapse
|
27
|
Shafran Y, Deutsch M, Afrimzon E, Ravid-Hermesh O, Sobolev M, Bar-On-Eizig Z, Shainberg A, Zurgil N. Co-culture hydrogel micro-chamber array-based plate for anti-tumor drug development at single-element resolution. Toxicol In Vitro 2020; 71:105067. [PMID: 33301902 DOI: 10.1016/j.tiv.2020.105067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/19/2020] [Accepted: 12/06/2020] [Indexed: 12/14/2022]
Abstract
In response to the need for reliable cellular models that reflect complex tumor microenvironmental properties, and enable more precise testing of anti-cancer therapeutics effects on humans, a co-culture platform for in-vitro model that enhances the physiology of breast cancer (BC) microenvironment is presented. A six well imaging plate wherein each macro-well contains several separate compartments was designed. Three-dimensional (3D) cancer spheroids are generated and cultured in the inner compartment which is embossed with an array of nano-liter micro-chambers made of hydrogel. Stromal cells are cultured in the outer chambers. The two cell types are cultured side-by-side, sharing a common space, thus enabling extra-cellular communication via secreted molecules. As proof of concept, a model of BC tumor microenvironment was recapitulated by co-cultivating 3D MCF7 spheroids in the presence of tumor-associated macrophages (TAMs). The presence of TAMs induced an aggressive phenotype by promoting spheroid growth, enhancing survivin expression levels and enabling invasive behavior. Moreover, TAMs influenced the response of BC spheroids to cytotoxic treatment as well as hormonal drug therapy, and enhanced the effects of nitric oxide donor. The platform enables time-lapse imaging and treatment without losing spatial location of the measured spheroids, thereby allowing measurements and analysis at individual-object resolution in an easy and efficient manner.
Collapse
Affiliation(s)
- Yana Shafran
- The Biophysical Interdisciplinary Jerome Schottenstein Center for the Research and Technology of the Cellome, Physics Department, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Mordechai Deutsch
- The Biophysical Interdisciplinary Jerome Schottenstein Center for the Research and Technology of the Cellome, Physics Department, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Elena Afrimzon
- The Biophysical Interdisciplinary Jerome Schottenstein Center for the Research and Technology of the Cellome, Physics Department, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Orit Ravid-Hermesh
- The Biophysical Interdisciplinary Jerome Schottenstein Center for the Research and Technology of the Cellome, Physics Department, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Maria Sobolev
- The Biophysical Interdisciplinary Jerome Schottenstein Center for the Research and Technology of the Cellome, Physics Department, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Zehavit Bar-On-Eizig
- The Biophysical Interdisciplinary Jerome Schottenstein Center for the Research and Technology of the Cellome, Physics Department, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Asher Shainberg
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Naomi Zurgil
- The Biophysical Interdisciplinary Jerome Schottenstein Center for the Research and Technology of the Cellome, Physics Department, Bar-Ilan University, Ramat-Gan 52900, Israel.
| |
Collapse
|
28
|
Biswas N, Chakrabarti S. Artificial Intelligence (AI)-Based Systems Biology Approaches in Multi-Omics Data Analysis of Cancer. Front Oncol 2020; 10:588221. [PMID: 33154949 PMCID: PMC7591760 DOI: 10.3389/fonc.2020.588221] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer is the manifestation of abnormalities of different physiological processes involving genes, DNAs, RNAs, proteins, and other biomolecules whose profiles are reflected in different omics data types. As these bio-entities are very much correlated, integrative analysis of different types of omics data, multi-omics data, is required to understanding the disease from the tumorigenesis to the disease progression. Artificial intelligence (AI), specifically machine learning algorithms, has the ability to make decisive interpretation of "big"-sized complex data and, hence, appears as the most effective tool for the analysis and understanding of multi-omics data for patient-specific observations. In this review, we have discussed about the recent outcomes of employing AI in multi-omics data analysis of different types of cancer. Based on the research trends and significance in patient treatment, we have primarily focused on the AI-based analysis for determining cancer subtypes, disease prognosis, and therapeutic targets. We have also discussed about AI analysis of some non-canonical types of omics data as they have the capability of playing the determiner role in cancer patient care. Additionally, we have briefly discussed about the data repositories because of their pivotal role in multi-omics data storing, processing, and analysis.
Collapse
Affiliation(s)
- Nupur Biswas
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, IICB TRUE Campus, Kolkata, India
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, IICB TRUE Campus, Kolkata, India
| |
Collapse
|
29
|
Finotello F, Calura E, Risso D, Hautaniemi S, Romualdi C. Editorial: Multi-omic Data Integration in Oncology. Front Oncol 2020; 10:1768. [PMID: 33042824 PMCID: PMC7522593 DOI: 10.3389/fonc.2020.01768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 01/22/2023] Open
Affiliation(s)
- Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Enrica Calura
- Department of Biology, University of Padua, Padua, Italy
| | - Davide Risso
- Department of Statistical Sciences, University of Padua, Padua, Italy
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | |
Collapse
|
30
|
Abstract
Breast cancer is projected to be the most common cancer in women in 2020 in the USA. Despite high remission rates treatment side effects remain an issue, hence the interest in novel approaches such as immunotherapies which aim to utilize patients' immune systems to target cancer cells. This review summarizes the basics of breast cancer including staging and treatment options, followed by a discussion on immunotherapy, including immune checkpoint blockade. After this, examples of the role of omics-type data and computational biology/bioinformatics in breast cancer are explored. Ultimately, there are several promising areas to investigate such as the prediction of neoantigens and the use of multi-omics data to direct research, with noted appropriate in clinical trial design in terms of end points.
Collapse
Affiliation(s)
- Ka Lun Leung
- School of Medicine, The University of Central Lancashire, Preston, UK
| | - Devika Verma
- School of Medicine, The University of Central Lancashire, Preston, UK
| | | | - Emyr Bakker
- School of Medicine, The University of Central Lancashire, Preston, UK
| |
Collapse
|
31
|
Abstract
Immunotherapy with checkpoint blockers (ICBs), aimed at unleashing the immune response toward tumor cells, has shown a great improvement in overall patient survival compared to standard therapy, but only in a subset of patients. While a number of recent studies have significantly improved our understanding of mechanisms playing an important role in the tumor microenvironment (TME), we still have an incomplete view of how the TME works as a whole. This hampers our ability to effectively predict the large heterogeneity of patients' response to ICBs. Systems approaches could overcome this limitation by adopting a holistic perspective to analyze the complexity of tumors. In this Mini Review, we focus on how an integrative view of the increasingly available multi-omics experimental data and computational approaches enables the definition of new systems-based predictive biomarkers. In particular, we will focus on three facets of the TME toward the definition of new systems biomarkers. First, we will review how different types of immune cells influence the efficacy of ICBs, not only in terms of their quantification, but also considering their localization and functional state. Second, we will focus on how different cells in the TME interact, analyzing how inter- and intra-cellular networks play an important role in shaping the immune response and are responsible for resistance to immunotherapy. Finally, we will describe the potential of looking at these networks as dynamic systems and how mathematical models can be used to study the rewiring of the complex interactions taking place in the TME.
Collapse
Affiliation(s)
- Óscar Lapuente-Santana
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| |
Collapse
|
32
|
Roy S, Sethi TK, Taylor D, Kim YJ, Johnson DB. Breakthrough concepts in immune-oncology: Cancer vaccines at the bedside. J Leukoc Biol 2020; 108:1455-1489. [PMID: 32557857 DOI: 10.1002/jlb.5bt0420-585rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/15/2020] [Accepted: 04/18/2020] [Indexed: 12/11/2022] Open
Abstract
Clinical approval of the immune checkpoint blockade (ICB) agents for multiple cancer types has reinvigorated the long-standing work on cancer vaccines. In the pre-ICB era, clinical efforts focused on the Ag, the adjuvants, the formulation, and the mode of delivery. These translational efforts on therapeutic vaccines range from cell-based (e.g., dendritic cells vaccine Sipuleucel-T) to DNA/RNA-based platforms with various formulations (liposome), vectors (Listeria monocytogenes), or modes of delivery (intratumoral, gene gun, etc.). Despite promising preclinical results, cancer vaccine trials without ICB have historically shown little clinical activity. With the anticipation and expansion of combinatorial immunotherapeutic trials with ICB, the cancer vaccine field has entered the personalized medicine arena with recent advances in immunogenic neoantigen-based vaccines. In this article, we review the literature to organize the different cancer vaccines in the clinical space, and we will discuss their advantages, limits, and recent progress to overcome their challenges. Furthermore, we will also discuss recent preclinical advances and clinical strategies to combine vaccines with checkpoint blockade to improve therapeutic outcome and present a translational perspective on future directions.
Collapse
Affiliation(s)
- Sohini Roy
- Department of Otolaryngology - Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tarsheen K Sethi
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David Taylor
- Department of Otolaryngology - Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Young J Kim
- Department of Otolaryngology - Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
33
|
Bortolomeazzi M, Keddar MR, Ciccarelli FD, Benedetti L. Identification of non-cancer cells from cancer transcriptomic data. Biochim Biophys Acta Gene Regul Mech 2020; 1863:194445. [PMID: 31654804 PMCID: PMC7346884 DOI: 10.1016/j.bbagrm.2019.194445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/20/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Interactions between cancer cells and non-cancer cells composing the tumour microenvironment play a primary role in determining cancer progression and shaping the response to therapy. The qualitative and quantitative characterisation of the different cell populations in the tumour microenvironment is therefore crucial to understand its role in cancer. In recent years, many experimental and computational approaches have been developed to identify the cell populations composing heterogeneous tissue samples, such as cancer. In this review, we describe the state-of-the-art approaches for the quantification of non-cancer cells from bulk and single-cell cancer transcriptomic data, with a focus on immune cells. We illustrate the main features of these approaches and highlight their applications for the analysis of the tumour microenvironment in solid cancers. We also discuss techniques that are complementary and alternative to RNA sequencing, particularly focusing on approaches that can provide spatial information on the distribution of the cells within the tumour in addition to their qualitative and quantitative measurements. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
Collapse
Affiliation(s)
- Michele Bortolomeazzi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK
| | - Mohamed Reda Keddar
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK
| | - Francesca D Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK.
| | - Lorena Benedetti
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; School of Cancer and Pharmaceutical Sciences, King's College London, London SE11UL, UK.
| |
Collapse
|
34
|
Reichl B, Niederstaetter L, Boegl T, Neuditschko B, Bileck A, Gojo J, Buchberger W, Peyrl A, Gerner C. Determination of a Tumor-Promoting Microenvironment in Recurrent Medulloblastoma: A Multi-Omics Study of Cerebrospinal Fluid. Cancers (Basel) 2020; 12:E1350. [PMID: 32466393 DOI: 10.3390/cancers12061350] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/07/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022] Open
Abstract
Molecular classification of medulloblastoma (MB) is well-established and reflects the cell origin and biological properties of tumor cells. However, limited data is available regarding the MB tumor microenvironment. Here, we present a mass spectrometry-based multi-omics pilot study of cerebrospinal fluid (CSF) from recurrent MB patients. A group of age-matched patients without a neoplastic disease was used as control cohort. Proteome profiling identified characteristic tumor markers, including FSTL5, ART3, and FMOD, and revealed a strong prevalence of anti-inflammatory and tumor-promoting proteins characteristic for alternatively polarized myeloid cells in MB samples. The up-regulation of ADAMTS1, GAP43 and GPR37 indicated hypoxic conditions in the CSF of MB patients. This notion was independently supported by metabolomics, demonstrating the up-regulation of tryptophan, methionine, serine and lysine, which have all been described to be induced upon hypoxia in CSF. While cyclooxygenase products were hardly detectable, the epoxygenase product and beta-oxidation promoting lipid hormone 12,13-DiHOME was found to be strongly up-regulated. Taken together, the data suggest a vicious cycle driven by autophagy, the formation of 12,13-DiHOME and increased beta-oxidation, thus promoting a metabolic shift supporting the formation of drug resistance and stem cell properties of MB cells. In conclusion, the different omics-techniques clearly synergized and mutually supported a novel model for a specific pathomechanism.
Collapse
|
35
|
Abstract
Cancer is the quintessential complex disease. As technologies evolve faster each day, we are able to quantify the different layers of biological elements that contribute to the emergence and development of malignancies. In this multi-omics context, the use of integrative approaches is mandatory in order to gain further insights on oncological phenomena, and to move forward toward the precision medicine paradigm. In this review, we will focus on computational oncology as an integrative discipline that incorporates knowledge from the mathematical, physical, and computational fields to further the biomedical understanding of cancer. We will discuss the current roles of computation in oncology in the context of multi-omic technologies, which include: data acquisition and processing; data management in the clinical and research settings; classification, diagnosis, and prognosis; and the development of models in the research setting, including their use for therapeutic target identification. We will discuss the machine learning and network approaches as two of the most promising emerging paradigms, in computational oncology. These approaches provide a foundation on how to integrate different layers of biological description into coherent frameworks that allow advances both in the basic and clinical settings.
Collapse
Affiliation(s)
- Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Cátedras Conacyt Para Jóvenes Investigadores, National Council on Science and Technology, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
| |
Collapse
|
36
|
Brancato V, Oliveira JM, Correlo VM, Reis RL, Kundu SC. Could 3D models of cancer enhance drug screening? Biomaterials 2019; 232:119744. [PMID: 31918229 DOI: 10.1016/j.biomaterials.2019.119744] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/29/2019] [Accepted: 12/25/2019] [Indexed: 02/06/2023]
Abstract
Cancer is a multifaceted pathology, where cellular and acellular players interact to drive cancer progression and, in the worst-case, metastasis. The current methods to investigate the heterogeneous nature of cancer are inadequate, since they rely on 2D cell cultures and animal models. The cell line-based drug efficacy and toxicity assays are not able to predict the tumor response to anti-cancer agents and it is already widely discussed how molecular pathway are not recapitulated in vitro so called flat biology. On the other side, animal models often fail to detect the side-effects of drugs, mimic the metastatic progression or the interaction between cancer and immune system, due to biologic difference in human and animals. Moreover, ethical and regulatory issues limit animal experimentation. Every year pharma/biotech companies lose resources in drug discovery and testing processes that are successful only in 5% of the cases. There is an urgent need to validate accurate and predictive platforms in order to enhance drug-testing process taking into account the physiopathology of the tumor microenvironment. Three dimensional in vitro tumor models could enhance drug manufactures in developing effective drugs for cancer diseases. The 3D in vitro cancer models can improve the predictability of toxicity and drug sensitivity in cancer. Despite the demonstrated advantages of 3D in vitro disease systems when compared to 2D culture and animal models, they still do not reach the standardization required for preclinical trials. This review highlights in vitro models that may be used as preclinical models, accelerating the drug development process towards more precise and personalized standard of care for cancer patients. We describe the state-of-the art of 3D in vitro culture systems, with a focus on how these different approaches could be coupled in order to achieve a compromise between standardization and reliability in recapitulating tumor microenvironment and drug response.
Collapse
Affiliation(s)
- Virginia Brancato
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal.
| | - Joaquim Miguel Oliveira
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal; The Discoveries Centre for Regenerative and Precision Medicine, Headquarters at University of Minho, Avepark, 4805-017, Barco, Guimarães, Portugal
| | - Vitor Manuel Correlo
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal; The Discoveries Centre for Regenerative and Precision Medicine, Headquarters at University of Minho, Avepark, 4805-017, Barco, Guimarães, Portugal
| | - Rui Luis Reis
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal; The Discoveries Centre for Regenerative and Precision Medicine, Headquarters at University of Minho, Avepark, 4805-017, Barco, Guimarães, Portugal
| | - Subhas C Kundu
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal.
| |
Collapse
|
37
|
Szabo PA, Levitin HM, Miron M, Snyder ME, Senda T, Yuan J, Cheng YL, Bush EC, Dogra P, Thapa P, Farber DL, Sims PA. Single-cell transcriptomics of human T cells reveals tissue and activation signatures in health and disease. Nat Commun 2019; 10:4706. [PMID: 31624246 PMCID: PMC6797728 DOI: 10.1038/s41467-019-12464-3] [Citation(s) in RCA: 324] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/11/2019] [Indexed: 01/04/2023] Open
Abstract
Human T cells coordinate adaptive immunity in diverse anatomic compartments through production of cytokines and effector molecules, but it is unclear how tissue site influences T cell persistence and function. Here, we use single cell RNA-sequencing (scRNA-seq) to define the heterogeneity of human T cells isolated from lungs, lymph nodes, bone marrow and blood, and their functional responses following stimulation. Through analysis of >50,000 resting and activated T cells, we reveal tissue T cell signatures in mucosal and lymphoid sites, and lineage-specific activation states across all sites including distinct effector states for CD8+ T cells and an interferon-response state for CD4+ T cells. Comparing scRNA-seq profiles of tumor-associated T cells to our dataset reveals predominant activated CD8+ compared to CD4+ T cell states within multiple tumor types. Our results therefore establish a high dimensional reference map of human T cell activation in health for analyzing T cells in disease.
Collapse
Affiliation(s)
- Peter A Szabo
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hanna Mendes Levitin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michelle Miron
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Mark E Snyder
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Takashi Senda
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA
| | - Jinzhou Yuan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yim Ling Cheng
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Erin C Bush
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Pranay Dogra
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Puspa Thapa
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Donna L Farber
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Surgery, Columbia University Irving Medical Center, New York, NY, USA.
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
38
|
IJsselsteijn ME, Sanz-Pamplona R, Hermitte F, de Miranda NF. Colorectal cancer: A paradigmatic model for cancer immunology and immunotherapy. Mol Aspects Med 2019; 69:123-129. [DOI: 10.1016/j.mam.2019.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 12/28/2022]
|
39
|
Finotello F, Rieder D, Hackl H, Trajanoski Z. Next-generation computational tools for interrogating cancer immunity. Nat Rev Genet 2019; 20:724-746. [PMID: 31515541 DOI: 10.1038/s41576-019-0166-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2019] [Indexed: 12/17/2022]
Abstract
The remarkable success of cancer therapies with immune checkpoint blockers is revolutionizing oncology and has sparked intensive basic and translational research into the mechanisms of cancer-immune cell interactions. In parallel, numerous novel cutting-edge technologies for comprehensive molecular and cellular characterization of cancer immunity have been developed, including single-cell sequencing, mass cytometry and multiplexed spatial cellular phenotyping. In order to process, analyse and visualize multidimensional data sets generated by these technologies, computational methods and software tools are required. Here, we review computational tools for interrogating cancer immunity, discuss advantages and limitations of the various methods and provide guidelines to assist in method selection.
Collapse
Affiliation(s)
- Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
40
|
Liu C, Tong Z, Tan J, Xin Z. Analysis of Treg/Th17 cells in patients with tongue squamous cell carcinoma. Exp Ther Med 2019; 18:2187-2193. [PMID: 31452709 PMCID: PMC6704530 DOI: 10.3892/etm.2019.7814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/27/2019] [Indexed: 12/31/2022] Open
Abstract
The aim of the present study was to analyze the percentage of regulatory T cells (Treg) and T helper cell 17 (Th17) cells in the peripheral blood of patients with tongue squamous cell carcinoma (TSCC) to provide novel insight into the development of immune-targeting therapies for TSCC. Peripheral blood samples were collected from 40 patients with TSCC then the peripheral blood mononuclear cells (PBMCs) and plasma were isolated for flow cytometry, cytometric bead array and reverse transcription-quantitative PCR. Results demonstrated that the percentage of cluster of differentiation (CD)4+ T cells in the peripheral blood of patients with TSCC decreased significantly compared with the control. However, the percentage of Treg and Th17 cells increased significantly compared with the control. The levels of interleukin (IL)-10 and IL-17a increased significantly in patients with TSCC. Expression of IL-10 and IL-17 in the advanced stages of cancer (stage III or IV) were significantly higher compared with the early stages (I and II). The mRNA expression levels of the transcription factors forkhead box protein 3 and RAR-related orphan receptor-γ increased significantly with stage of cancer. The percentage of Treg cells and Th17 cells increased significantly in patients with TSCC suggesting that there was an imbalance between Treg and Th17 cells. In conclusion, altered Treg/Th17 balance in TSCC may promote the disease progression and these results provide a theoretical basis for the development of immunomodulators targeting Treg/Th17.
Collapse
Affiliation(s)
- Changfu Liu
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
| | - Zhou Tong
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
| | - Jingyu Tan
- Department of Stomatology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
| | - Zengxi Xin
- Department of Prosthodontics, The Second Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
| |
Collapse
|
41
|
Abstract
Tumor-infiltrating immune cells comprise various cells of the innate and the adaptive immune system, which influence tumor growth and response to immunotherapy by exerting anti- and protumorigenic functions. Therefore, the quantification of tumor immune infiltrates is of paramount importance for cancer immunology and immunotherapy. We recently developed quanTIseq, a computational pipeline for the quantification of immune-cell fractions from bulk RNA sequencing (RNA-seq) data from blood or tumor samples. In this chapter, we show the capabilities of quanTIseq by analyzing two publicly available data sets. In the first example, we demonstrate how quanTIseq can be used to quantify circulating immune cells from preprocessed RNA-seq data and how to validate the results using matched flow cytometry data. In the second example, we analyze raw RNA-seq data from bulk tumor samples of melanoma patients collected before and on-treatment with kinase inhibitors to show how quanTIseq can be used to reveal the immunological effects of targeted and conventional drugs.
Collapse
Affiliation(s)
- Christina Plattner
- Division for Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Francesca Finotello
- Division for Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Rieder
- Division for Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
| |
Collapse
|
42
|
Duranti C, Arcangeli A. Ion Channel Targeting with Antibodies and Antibody Fragments for Cancer Diagnosis. Antibodies (Basel) 2019; 8:E33. [PMID: 31544839 DOI: 10.3390/antib8020033] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/17/2019] [Accepted: 05/20/2019] [Indexed: 12/12/2022] Open
Abstract
The antibody era has greatly impacted cancer management in recent decades. Indeed, antibodies are currently applied for both cancer diagnosis and therapy. For example, monoclonal antibodies are the main constituents of several in vitro diagnostics, which are applied at many levels of cancer diagnosis. Moreover, the great improvement provided by in vivo imaging, especially for early-stage cancer diagnosis, has traced the path for the development of a complete new class of antibodies, i.e., engineered antibody fragments. The latter embody the optimal characteristics (e.g., low renal retention, rapid clearance, and small size) which make them ideal for in vivo applications. Furthermore, the present review focuses on reviewing the main applications of antibodies and antibody fragments for solid cancer diagnosis, both in vitro and in vivo. Furthermore, we review the scientific evidence showing that ion channels represent an almost unexplored class of ideal targets for both in vitro and in vivo diagnostic purposes. In particular, we review the applications, in solid cancers, of monoclonal antibodies and engineered antibody fragments targeting the voltage-dependent ion channel Kv 11.1, also known as hERG1.
Collapse
|
43
|
Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, de Miranda NFDCC, Trajanoski Z. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med 2019; 11:34. [PMID: 31126321 PMCID: PMC6534875 DOI: 10.1186/s13073-019-0638-6] [Citation(s) in RCA: 615] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/09/2019] [Indexed: 12/26/2022] Open
Abstract
We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry, and immunohistochemistry data.quanTIseq analysis of 8000 tumor samples revealed that cytotoxic T cell infiltration is more strongly associated with the activation of the CXCR3/CXCL9 axis than with mutational load and that deconvolution-based cell scores have prognostic value in several solid cancers. Finally, we used quanTIseq to show how kinase inhibitors modulate the immune contexture and to reveal immune-cell types that underlie differential patients' responses to checkpoint blockers.Availability: quanTIseq is available at http://icbi.at/quantiseq .
Collapse
Affiliation(s)
- Francesca Finotello
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Clemens Mayer
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Christina Plattner
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Gerhard Laschober
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Zuzana Loncova
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sieghart Sopper
- Department of Haematology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Marieke Ijsselsteijn
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas P Brouwer
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Douglas Johnson
- Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melinda E Sanders
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Monica V Estrada
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paula Ericsson-Gonzalez
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pornpimol Charoentong
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Division of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Justin Balko
- Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria.
- Austrian Drug Screening Institute, Innrain 66A, Innsbruck, Austria.
| |
Collapse
|
44
|
Chen J, Liu J, Calhoun VD. The Translational Potential of Neuroimaging Genomic Analyses To Diagnosis And Treatment In The Mental Disorders. Proc IEEE Inst Electr Electron Eng 2019; 107:912-927. [PMID: 32051642 PMCID: PMC7015534 DOI: 10.1109/jproc.2019.2913145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Imaging genomics focuses on characterizing genomic influence on the variation of neurobiological traits, holding promise for illuminating the pathogenesis, reforming the diagnostic system, and precision medicine of mental disorders. This paper aims to provide an overall picture of the current status of neuroimaging-genomic analyses in mental disorders, and how we can increase their translational potential into clinical practice. The review is organized around three perspectives. (a) Towards reliability, generalizability and interpretability, where we summarize the multivariate models and discuss the considerations and trade-offs of using these methods and how reliable findings may be reached, to serve as ground for further delineation. (b) Towards improved diagnosis, where we outline the advantages and challenges of constructing a dimensional transdiagnostic model and how imaging genomic analyses map into this framework to aid in deconstructing heterogeneity and achieving an optimal stratification of patients that better inform treatment planning. (c) Towards improved treatment. Here we highlight recent efforts and progress in elucidating the functional annotations that bridge between genomic risk and neurobiological abnormalities, in detecting genomic predisposition and prodromal neurodevelopmental changes, as well as in identifying imaging genomic biomarkers for predicting treatment response. Providing an overview of the challenges and promises, this review hopefully motivates imaging genomic studies with multivariate, dimensional and transdiagnostic designs for generalizable and interpretable findings that facilitate development of personalized treatment.
Collapse
Affiliation(s)
- Jiayu Chen
- The Mind Research Network, Albuquerque, NM 87106 USA
| | - Jingyu Liu
- The Mind Research Network, Albuquerque, NM 87106 USA, and also with the Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM 87131 USA
| | - Vince D Calhoun
- The Mind Research Network, Albuquerque, NM 87106 USA, and also with the Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM 87131 USA
| |
Collapse
|
45
|
Peskov K, Azarov I, Chu L, Voronova V, Kosinsky Y, Helmlinger G. Quantitative Mechanistic Modeling in Support of Pharmacological Therapeutics Development in Immuno-Oncology. Front Immunol 2019; 10:924. [PMID: 31134058 PMCID: PMC6524731 DOI: 10.3389/fimmu.2019.00924] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/10/2019] [Indexed: 12/15/2022] Open
Abstract
Following the approval, in recent years, of the first immune checkpoint inhibitor, there has been an explosion in the development of immuno-modulating pharmacological modalities for the treatment of various cancers. From the discovery phase to late-stage clinical testing and regulatory approval, challenges in the development of immuno-oncology (IO) drugs are multi-fold and complex. In the preclinical setting, the multiplicity of potential drug targets around immune checkpoints, the growing list of immuno-modulatory molecular and cellular forces in the tumor microenvironment-with additional opportunities for IO drug targets, the emergence of exploratory biomarkers, and the unleashed potential of modality combinations all have necessitated the development of quantitative, mechanistically-oriented systems models which incorporate key biology and patho-physiology aspects of immuno-oncology and the pharmacokinetics of IO-modulating agents. In the clinical setting, the qualification of surrogate biomarkers predictive of IO treatment efficacy or outcome, and the corresponding optimization of IO trial design have become major challenges. This mini-review focuses on the evolution and state-of-the-art of quantitative systems models describing the tumor vs. immune system interplay, and their merging with quantitative pharmacology models of IO-modulating agents, as companion tools to support the addressing of these challenges.
Collapse
Affiliation(s)
- Kirill Peskov
- M&S Decisions, Moscow, Russia.,Computational Oncology Group, I.M. Sechenov First Moscow State Medical University of the Russian Ministry of Health, Moscow, Russia
| | | | - Lulu Chu
- Quantitative Clinical Pharmacology, Early Clinical Development, IMED Biotech Unit, AstraZeneca Pharmaceuticals, Boston, MA, United States
| | | | | | - Gabriel Helmlinger
- Quantitative Clinical Pharmacology, Early Clinical Development, IMED Biotech Unit, AstraZeneca Pharmaceuticals, Boston, MA, United States
| |
Collapse
|
46
|
Hamada T, Nowak JA, Milner DA, Song M, Ogino S. Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms. J Pathol 2019; 247:615-628. [PMID: 30632609 PMCID: PMC6509405 DOI: 10.1002/path.5236] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/24/2018] [Accepted: 01/06/2019] [Indexed: 02/06/2023]
Abstract
Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed 'exposures'), including microorganisms, on disease occurrence and consequences, utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predominantly in research on cancers including breast, lung, prostate, and colorectal carcinomas. Mounting evidence indicates that the microbiome (inclusive of viruses, bacteria, fungi, and parasites) plays an important role in a variety of human diseases including neoplasms. An alteration of the microbiome may be not only a cause of neoplasia but also an informative biomarker that indicates or mediates the association of an epidemiological exposure with health conditions and outcomes. To adequately educate and train investigators in this emerging area, we herein propose the integration of microbiology into the MPE model (termed 'microbiology-MPE'), which could improve our understanding of the complex interactions of environment, tumour cells, the immune system, and microbes in the tumour microenvironment during the carcinogenic process. Using this approach, we can examine how lifestyle factors, dietary patterns, medications, environmental exposures, and germline genetics influence cancer development and progression through impacting the microbial communities in the human body. Further integration of other disciplines (e.g. pharmacology, immunology, nutrition) into microbiology-MPE would expand this developing research frontier. With the advent of high-throughput next-generation sequencing technologies, researchers now have increasing access to large-scale metagenomics as well as other omics data (e.g. genomics, epigenomics, proteomics, and metabolomics) in population-based research. The integrative field of microbiology-MPE will open new opportunities for personalised medicine and public health. Copyright © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Tsuyoshi Hamada
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jonathan A Nowak
- Department of Pathology Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Danny A Milner
- American Society for Clinical Pathology, Chicago, Illinois, USA
| | - Mingyang Song
- Departments of Epidemiology and Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Shuji Ogino
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology Program in MPE Molecular Pathological Epidemiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
47
|
Dal Monte M, Calvani M, Cammalleri M, Favre C, Filippi L, Bagnoli P. β-Adrenoceptors as drug targets in melanoma: novel preclinical evidence for a role of β 3 -adrenoceptors. Br J Pharmacol 2018; 176:2496-2508. [PMID: 30471093 DOI: 10.1111/bph.14552] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/30/2018] [Accepted: 11/13/2018] [Indexed: 02/06/2023] Open
Abstract
Stress plays a role in tumourigenesis through catecholamines acting at β-adrenoceptors including β1 -, β2 - and β3 -adrenoceptors, and the use of β-adrenoceptor antagonists seems to counteract tumour growth and progression. Preclinical evidence and meta-analysis data demonstrate that melanoma shows a positive response to β-adrenoceptor blockers and in particular to propranolol acting mainly at β1 - and β2 -adrenoceptors. Although evidence suggesting that β3 -adrenoceptors may play a role as a therapeutic target in infantile haemangiomas has been recently reviewed, a comprehensive analysis of the data available from preclinical studies supporting a possible role of β3 -adrenoceptors in melanoma was not available. Here, we review data from the literature demonstrating that propranolol may be effective at counteracting melanoma growth, and we provide preclinical evidence that β3 -adrenoceptors may also play a role in the pathophysiology of melanoma, thus opening the door for further clinical assays trying to explore β3 -adrenoceptor blockers as novel alternatives for its treatment. LINKED ARTICLES: This article is part of a themed section on Adrenoceptors-New Roles for Old Players. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.14/issuetoc.
Collapse
Affiliation(s)
| | - Maura Calvani
- Onco-hematology Unit, Department of Pediatric Oncology, Meyer University Children's Hospital, Florence, Italy
| | | | - Claudio Favre
- Onco-hematology Unit, Department of Pediatric Oncology, Meyer University Children's Hospital, Florence, Italy
| | - Luca Filippi
- Neonatal Intensive Care Unit, Medical Surgical Fetal-Neonatal Department, Meyer University Children's Hospital, Florence, Italy
| | - Paola Bagnoli
- Department of Biology, University of Pisa, Pisa, Italy
| |
Collapse
|