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Ghaffari S, Saleh M, Akbari B, Ramezani F, Mirzaei HR. Applications of single-cell omics for chimeric antigen receptor T cell therapy. Immunology 2024; 171:339-364. [PMID: 38009707 DOI: 10.1111/imm.13720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy is a promising cancer treatment modality. The breakthroughs in CAR T cell therapy were, in part, possible with the help of cell analysis methods, such as single-cell analysis. Bulk analyses have provided invaluable information regarding the complex molecular dynamics of CAR T cells, but their results are an average of thousands of signals in CAR T or tumour cells. Since cancer is a heterogeneous disease where each minute detail of a subclone could change the outcome of the treatment, single-cell analysis could prove to be a powerful instrument in deciphering the secrets of tumour microenvironment for cancer immunotherapy. With the recent studies in all aspects of adoptive cell therapy making use of single-cell analysis, a comprehensive review of the recent preclinical and clinical findings in CAR T cell therapy was needed. Here, we categorized and summarized the key points of the studies in which single-cell analysis provided insights into the genomics, epigenomics, transcriptomics and proteomics as well as their respective multi-omics of CAR T cell therapy.
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Affiliation(s)
- Sasan Ghaffari
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Mahshid Saleh
- Wisconsin National Primate Research Center, University of Wisconsin Graduate School, Madison, Wisconsin, USA
| | - Behnia Akbari
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Faezeh Ramezani
- Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Laboratory Sciences, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Reza Mirzaei
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Molecular Imaging and Therapy Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Jalota A, Hershberger CE, Patel MS, Mian A, Faruqi A, Khademi G, Rotroff DM, Hill BT, Gupta N. Host metabolome predicts the severity and onset of acute toxicities induced by CAR T-cell therapy. Blood Adv 2023; 7:4690-4700. [PMID: 36399526 PMCID: PMC10468366 DOI: 10.1182/bloodadvances.2022007456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 08/04/2022] [Accepted: 08/20/2022] [Indexed: 11/19/2022] Open
Abstract
Anti-CD19 chimeric antigen receptor (CAR) T-cell therapy is a highly effective treatment option for patients with relapsed/refractory large B-cell lymphoma. However, widespread use is deterred by the development of clinically significant acute inflammatory toxicities, including cytokine release syndrome (CRS) and immune effector cell-associated neurotoxicity syndrome (ICANS), that induce significant morbidity and require close monitoring. Identification of host biochemical signatures that predict the severity and time-to-onset of CRS and ICANS may assist patient stratification to enable timely mitigation strategies. Here, we report pretreatment host metabolites that are associated with CRS and ICANS induced by axicabtagene ciloleucel or tisagenlecleucel therapy. Both untargeted metabolomics analysis and validation using targeted assays revealed a significant association between the abundance of specific pretreatment biochemical entities and an increased risk and/or onset of clinically significant CRS (q < .1) and ICANS (q < .25). Higher pretreatment levels of plasma glucose and lower levels of cholesterol and glutamate were associated with a faster onset of CRS. In contrast, low baseline levels of the amino acids proline and glycine and the secondary bile acid isoursodeoxycholate were significantly correlated with clinically significant CRS. Lower concentration of the amino acid hydroxyproline was associated with higher grade and faster onset of ICANS, whereas low glutamine was negatively correlated with faster development of ICANS. Overall, our data indicate that the pretreatment host metabolome has biomarker potential in determining the risk of clinically significant CRS and ICANS, and may be useful in risk stratification of patients before anti-CD19 CAR T-cell therapy.
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Affiliation(s)
- Akansha Jalota
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH
| | | | - Manishkumar S. Patel
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH
| | - Agrima Mian
- Department of Internal Medicine, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Aiman Faruqi
- Cleveland Clinic Lerner College of Medicine, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Gholamreza Khademi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland, OH
| | - Daniel M. Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland, OH
- Cleveland Clinic Lerner College of Medicine, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Brian T. Hill
- Cleveland Clinic Lerner College of Medicine, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
| | - Neetu Gupta
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH
- Cleveland Clinic Lerner College of Medicine, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH
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Dias J, Cadiñanos-Garai A, Roddie C. Release Assays and Potency Assays for CAR T-Cell Interventions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1420:117-137. [PMID: 37258787 DOI: 10.1007/978-3-031-30040-0_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chimeric antigen receptor (CAR) T-cells are considered "living drugs" and offer a compelling alternative to conventional anticancer therapies. Briefly, T-cells are redirected, using gene engineering technology, toward a specific cancer cell surface target antigen via a synthetic chimeric antigen receptor (CAR) protein. CARs have a modular design comprising four main structures: an antigen-binding domain, a hinge region, a transmembrane domain, and one or more intracellular signaling domains for T-cell activation. A major challenge in the CAR T-cell manufacturing field is balancing product quality with scalability and cost-effectiveness, especially when transitioning from an academic clinical trial into a marketed product, to be implemented across many collection, manufacturing, and treatment sites. Achieving product consistency while circumnavigating the intrinsic variability associated with autologous products is an additional barrier. To overcome these limitations, a robust understanding of the product and its biological actions is crucial to establish a target product profile with a defined list of critical quality attributes to be assessed for each batch prior to product certification. Additional challenges arise as the field progresses, such as new safety considerations associated with the use of allogenic T-cells and genome editing tools. In this chapter, we will discuss the release and potency assays required for CAR T-cell manufacturing, covering their relevance, current challenges, and future perspectives.
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Affiliation(s)
- Juliana Dias
- UCL Cancer Institute, University College London, London, UK.
- Royal Free Hospital London, NHS Foundation Trust, London, UK.
| | - Amaia Cadiñanos-Garai
- USC/CHLA Cell Therapy Program, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA, USA
| | - Claire Roddie
- UCL Cancer Institute, University College London, London, UK
- Department of Haematology, UCL Hospital, London, UK
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Kadasah SF. Establishment and Systematic Evaluation of Gastric Cancer Classification Model Based on Pyroptosis. Diagnostics (Basel) 2022; 12:diagnostics12112858. [PMID: 36428916 PMCID: PMC9689046 DOI: 10.3390/diagnostics12112858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Background: Gastric cancer (GC) is considered the fifth most prevalent type of cancer and the third leading cause of cancer deaths worldwide. This in-depth investigation was performed to generate fresh concepts for the clinical classification, diagnosis, and prognostic evaluation of GC. Methods: The data were retrieved from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Unsupervised cluster analysis was used to divide up the GC patients using pyroptosis-related differentially expressed genes (DEGs), which were discovered to be significantly linked with GC prognosis. The therapeutic importance of pyroptosis in GC patients was discovered using PCA analysis of genes associated with pyroptosis. The models were then carefully scrutinized. Results: Three hub genes, ELANE, IL6, and TIRAP, exhibit significant predictive importance among the 15 pyroptosis-related genes. Unsupervised clustering analysis revealed that the DEGs were enriched in the pathway of cytokine-cytokine receptor interactions, and Clusters 1 and 2 had statistically distinct prognoses. PCA analysis revealed significant differences in the area under the curve, immunological checkpoints, immunogenic cell death, and prognostic value between the high- and low-risk groups. Conclusions: These two GC classification models, based on pyroptosis, have significant clinical value for patients with GC.
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Affiliation(s)
- Sultan F Kadasah
- Department of Biology, Faculty of Sciences, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
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Single-cell polyfunctional proteomics of CD4 cells from patients with AML predicts responses to anti-PD-1-based therapy. Blood Adv 2021; 5:4569-4574. [PMID: 34555853 PMCID: PMC8759127 DOI: 10.1182/bloodadvances.2021004583] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/05/2021] [Indexed: 12/24/2022] Open
Abstract
Acute myeloid leukemia (AML) remains a difficult disease to treat disease. In a phase 2 clinical trial in patients with relapsed/refractory AML, combining the hypomethylating agent, azacitidine, with the PD-1 checkpoint inhibitor, nivolumab, demonstrated encouraging response rates (33%), median event-free, and overall survival, compared with a historical cohort of contemporary patients treated with azacitidine-based therapies, with an acceptable safety profile. Biomarkers of response are yet to be determined. In this study, we leveraged a multiplexed immune assay to assess the functional states of CD4+ and CD8+ cells at a single-cell level in pretherapy bone marrows in 16 patients with relapsed/refractory AML treated with azacitidine/nivolumab. Effector CD4+ but not CD8+ cells had distinct polyfunctional groups and were associated with responses and better outcomes. Further evaluation of the polyfunctional strength index composition across cell types revealed that interferon-gamma (IFN-γ) and tumor necrosis factor-alpha (TNF-α) were the major drivers of enhanced polyfunctionality index of pretherapy CD4+ subset, whereas Granzyme B, IFN-γ, MIP-1b, and TNF-α drove the nonsignificantly enhanced pretreatment Polyfunctional Strength Index of CD8+ subset in the responders. Single-cell polyfunctional assays were predictive of response in AML and may have a potential role as a biomarker in the wider sphere of immunotherapy.
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Dhar P, Basher F, Ji Z, Huang L, Qin S, Wainwright DA, Robinson J, Hagler S, Zhou J, MacKay S, Wu JD. Tumor-derived NKG2D ligand sMIC reprograms NK cells to an inflammatory phenotype through CBM signalosome activation. Commun Biol 2021; 4:905. [PMID: 34294876 PMCID: PMC8298432 DOI: 10.1038/s42003-021-02440-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 07/05/2021] [Indexed: 12/31/2022] Open
Abstract
Natural Killer (NK) cell dysfunction is associated with poorer clinical outcome in cancer patients. What regulates NK cell dysfunction in tumor microenvironment is not well understood. Here, we demonstrate that the human tumor-derived NKG2D ligand soluble MIC (sMIC) reprograms NK cell to secrete pro-tumorigenic cytokines with diminished cytotoxicity and polyfunctional potential. Antibody clearing sMIC restores NK cell to a normal cytotoxic effector functional state. We discovered that sMIC selectively activates the CBM-signalosome inflammatory pathways in NK cells. Conversely, tumor cell membrane-bound MIC (mMIC) stimulates NK cell cytotoxicity through activating PLC2γ2/SLP-76/Vav1 pathway. Ultimately, antibody targeting sMIC effectuated the in vivo anti-tumor effect of adoptively transferred NK cells. Our findings uncover an unrecognized mechanism that could instruct NK cell to a dysfunctional state in response to cues in the tumor microenvironment. Our findings provide a rationale for co-targeting sMIC to enhance the efficacy of the ongoing NK cell-based cancer immunotherapy.
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Affiliation(s)
- Payal Dhar
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fahmin Basher
- Division of General Internal Medicine, Department of Medicine, University of Miami, Miami, FL, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lei Huang
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Si Qin
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Derek A Wainwright
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | | | - Jing Zhou
- Isoplexis Corporation, Branford, CT, USA
| | | | - Jennifer D Wu
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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Systematic Identification of Key Functional Modules and Genes in Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8853348. [PMID: 33282955 PMCID: PMC7685902 DOI: 10.1155/2020/8853348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022]
Abstract
Gastric cancer (GC) is associated with high incidence and mortality rates worldwide. Differentially expressed gene (DEG) analysis and weighted gene coexpression network analysis (WGCNA) are important bioinformatic methods for screening core genes. In our study, DEG analysis and WGCNA were combined to screen the hub genes, and pathway enrichment analyses were performed on the DEGs. SBNO2 was identified as the hub gene based on the intersection between the DEGs and the purple module in WGCNA. The expression and prognostic value of SBNO2 were verified in UALCAN, GEPIA2, Human Cancer Metastasis Database, Kaplan–Meier plotter, and TIMER. We identified 1974 DEGs, and 28 modules were uncovered via WGCNA. The purple module was identified as the hub module in WGCNA. SBNO2 was identified as the hub gene, which was upregulated in tumour tissues. Moreover, patients with GC and higher SBNO2 expression had worse prognoses. In addition, SBNO2 was suggested to play an important role in immune cell infiltration. In summary, based on DEGs and key modules related to GC, we identified SBNO2 as a hub gene, thereby offering novel insights into the development and treatment of GC.
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Cheng H, Fan R, Wei W. Cancer Systems Biology in the Era of Single-Cell Multi-Omics. Proteomics 2020; 20:e1900106. [PMID: 32957162 DOI: 10.1002/pmic.201900106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Indexed: 01/25/2023]
Affiliation(s)
- Hanjun Cheng
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Wei Wei
- Institute for Systems Biology, Seattle, WA, 98109, USA
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Parra-Hernández RM, Posada-Quintero JI, Acevedo-Charry O, Posada-Quintero HF. Uniform Manifold Approximation and Projection for Clustering Taxa through Vocalizations in a Neotropical Passerine (Rough-Legged Tyrannulet, Phyllomyias burmeisteri). Animals (Basel) 2020; 10:E1406. [PMID: 32806680 PMCID: PMC7460062 DOI: 10.3390/ani10081406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/06/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022] Open
Abstract
Vocalizations from birds are a fruitful source of information for the classification of species. However, currently used analyses are ineffective to determine the taxonomic status of some groups. To provide a clearer grouping of taxa for such bird species from the analysis of vocalizations, more sensitive techniques are required. In this study, we have evaluated the sensitivity of the Uniform Manifold Approximation and Projection (UMAP) technique for grouping the vocalizations of individuals of the Rough-legged Tyrannulet Phyllomyias burmeisteri complex. Although the existence of two taxonomic groups has been suggested by some studies, the species has presented taxonomic difficulties in classification in previous studies. UMAP exhibited a clearer separation of groups than previously used dimensionality-reduction techniques (i.e., principal component analysis), as it was able to effectively identify the two taxa groups. The results achieved with UMAP in this study suggest that the technique can be useful in the analysis of species with complex in taxonomy through vocalizations data as a complementary tool including behavioral traits such as acoustic communication.
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Affiliation(s)
- Ronald M. Parra-Hernández
- Institución Educativa Normal Superior Fabio Lozano Torrijos, Falan, Tolima 732001, Colombia
- Asociación Tolimense de Ornitología, Ibagué, Tolima 730005, Colombia
| | - Jorge I. Posada-Quintero
- Institución Educativa Técnica María Auxiliadora, Fresno, Tolima 731560, Colombia;
- Facultad de Ciencias de la Educación y la Comunicación, Universidad Autónoma de Asunción, Asunción 001013, Paraguay
| | - Orlando Acevedo-Charry
- Colección de Sonidos Ambientales, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá 154001, Colombia;
- Asociación Colombiana de Ornitología, Bogotá, DC 111311, Colombia
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