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Boretti A. Improving chimeric antigen receptor T-cell therapies by using artificial intelligence and internet of things technologies: A narrative review. Eur J Pharmacol 2024; 974:176618. [PMID: 38679117 DOI: 10.1016/j.ejphar.2024.176618] [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: 01/20/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Cancer poses a formidable challenge in the field of medical science, prompting the exploration of innovative and efficient treatment strategies. One revolutionary breakthrough in cancer therapy is Chimeric Antigen Receptor (CAR) T-cell therapy, an avant-garde method involving the customization of a patient's immune cells to combat cancer. Particularly successful in addressing blood cancers, CAR T-cell therapy introduces an unprecedented level of effectiveness, offering the prospect of sustained disease management. As ongoing research advances to overcome current challenges, CAR T-cell therapy stands poised to become an essential tool in the fight against cancer. Ongoing enhancements aim to improve its effectiveness and reduce time and cost, with the integration of Artificial Intelligence (AI) and Internet of Things (IoT) technologies. The synergy of AI and IoT could enable more precise tailoring of CAR T-cell therapy to individual patients, streamlining the therapeutic process. This holds the potential to elevate treatment efficacy, mitigate adverse effects, and expedite the overall progress of CAR T-cell therapies.
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Affiliation(s)
- Alberto Boretti
- Independent Scientist, Johnsonville, Wellington, New Zealand.
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2
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Zhou K, Xiao Z, Liu Q, Wang X, Huo J, Wu X, Zhao X, Feng X, Fu B, Xu P, Deng Y, Xiao W, Sun T, Da L. Comprehensive application of AI algorithms with TCR NGS data for glioma diagnosis. Sci Rep 2024; 14:15361. [PMID: 38965388 PMCID: PMC11224284 DOI: 10.1038/s41598-024-65305-9] [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: 11/11/2023] [Accepted: 06/19/2024] [Indexed: 07/06/2024] Open
Abstract
T-cell receptor (TCR) detection can examine the extent of T-cell immune responses. Therefore, the article analyzed characteristic data of glioma obtained by DNA-based TCR high-throughput sequencing, to predict the disease with fewer biomarkers and higher accuracy. We downloaded data online and obtained six TCR-related diversity indices to establish a multidimensional classification system. By comparing actual presence of the 602 correlated sequences, we obtained two-dimensional and multidimensional datasets. Multiple classification methods were utilized for both datasets with the classification accuracy of multidimensional data slightly less to two-dimensional datasets. This study reduced the TCR β sequences through feature selection methods like RFECV (Recursive Feature Elimination with Cross-Validation). Consequently, using only the presence of these three sequences, the classification AUC value of 96.67% can be achieved. The combination of the three correlated TCR clones obtained at a source data threshold of 0.1 is: CASSLGGNTEAFF_TRBV12_TRBJ1-1, CASSYSDTGELFF_TRBV6_TRBJ2-2, and CASSLTGNTEAFF_TRBV12_TRBJ1-1. At 0.001, the combination is: CASSLGETQYF_TRBV12_TRBJ2-5, CASSLGGNQPQHF_TRBV12_TRBJ1-5, and CASSLSGNTIYF_TRBV12_TRBJ1-3. This method can serve as a potential diagnostic and therapeutic tool, facilitating diagnosis and treatment of glioma and other cancers.
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Affiliation(s)
- Kaiyue Zhou
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Zhengliang Xiao
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Qi Liu
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Xu Wang
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Jiaxin Huo
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Xiaoqi Wu
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Xiaoxiao Zhao
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Xiaohan Feng
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Baoyi Fu
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China
| | - Pengfei Xu
- Hangzhou ImmuQuad Biotechnologies, LLC, Hangzhou, China
| | - Yunyun Deng
- Hangzhou ImmuQuad Biotechnologies, LLC, Hangzhou, China
| | - Wenwen Xiao
- Hangzhou ImmuQuad Biotechnologies, LLC, Hangzhou, China
| | - Tao Sun
- Hangzhou ImmuQuad Biotechnologies, LLC, Hangzhou, China.
- Institute of Wenzhou, Zhejiang University, Wenzhou, China.
| | - Lin Da
- Department of Mathematics, School of Mathematical Sciences, Inner Mongolia University, Hohhot, China.
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Yuan S, Hu Q. Convergence of nanomedicine and neutrophils for drug delivery. Bioact Mater 2024; 35:150-166. [PMID: 38318228 PMCID: PMC10839777 DOI: 10.1016/j.bioactmat.2024.01.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/20/2024] [Accepted: 01/21/2024] [Indexed: 02/07/2024] Open
Abstract
Neutrophils have recently emerged as promising carriers for drug delivery due to their unique properties including rapid response toward inflammation, chemotaxis, and transmigration. When integrated with nanotechnology that has enormous advantages in improving treatment efficacy and reducing side effects, neutrophil-based nano-drug delivery systems have expanded the repertoire of nanoparticles employed in precise therapeutic interventions by either coating nanoparticles with their membranes, loading nanoparticles inside living cells, or engineering chimeric antigen receptor (CAR)-neutrophils. These neutrophil-inspired therapies have shown superior biocompatibility, targeting ability, and therapeutic robustness. In this review, we summarized the benefits of combining neutrophils and nanotechnologies, the design principles and underlying mechanisms, and various applications in disease treatments. The challenges and prospects for neutrophil-based drug delivery systems were also discussed.
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Affiliation(s)
- Sichen Yuan
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, United States
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
- Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, United States
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, United States
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Capponi S, Wang S. AI in cellular engineering and reprogramming. Biophys J 2024:S0006-3495(24)00245-5. [PMID: 38576162 DOI: 10.1016/j.bpj.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
During the last decade, artificial intelligence (AI) has increasingly been applied in biophysics and related fields, including cellular engineering and reprogramming, offering novel approaches to understand, manipulate, and control cellular function. The potential of AI lies in its ability to analyze complex datasets and generate predictive models. AI algorithms can process large amounts of data from single-cell genomics and multiomic technologies, allowing researchers to gain mechanistic insights into the control of cell identity and function. By integrating and interpreting these complex datasets, AI can help identify key molecular events and regulatory pathways involved in cellular reprogramming. This knowledge can inform the design of precision engineering strategies, such as the development of new transcription factor and signaling molecule cocktails, to manipulate cell identity and drive authentic cell fate across lineage boundaries. Furthermore, when used in combination with computational methods, AI can accelerate and improve the analysis and understanding of the intricate relationships between genes, proteins, and cellular processes. In this review article, we explore the current state of AI applications in biophysics with a specific focus on cellular engineering and reprogramming. Then, we showcase a couple of recent applications where we combined machine learning with experimental and computational techniques. Finally, we briefly discuss the challenges and prospects of AI in cellular engineering and reprogramming, emphasizing the potential of these technologies to revolutionize our ability to engineer cells for a variety of applications, from disease modeling and drug discovery to regenerative medicine and biomanufacturing.
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Affiliation(s)
- Sara Capponi
- IBM Almaden Research Center, San Jose, California; Center for Cellular Construction, San Francisco, California.
| | - Shangying Wang
- Bay Area Institute of Science, Altos Labs, Redwood City, California.
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Chowdhury MA, Zhang JJ, Rizk R, Chen WCW. Stem cell therapy for heart failure in the clinics: new perspectives in the era of precision medicine and artificial intelligence. Front Physiol 2024; 14:1344885. [PMID: 38264333 PMCID: PMC10803627 DOI: 10.3389/fphys.2023.1344885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Stem/progenitor cells have been widely evaluated as a promising therapeutic option for heart failure (HF). Numerous clinical trials with stem/progenitor cell-based therapy (SCT) for HF have demonstrated encouraging results, but not without limitations or discrepancies. Recent technological advancements in multiomics, bioinformatics, precision medicine, artificial intelligence (AI), and machine learning (ML) provide new approaches and insights for stem cell research and therapeutic development. Integration of these new technologies into stem/progenitor cell therapy for HF may help address: 1) the technical challenges to obtain reliable and high-quality therapeutic precursor cells, 2) the discrepancies between preclinical and clinical studies, and 3) the personalized selection of optimal therapeutic cell types/populations for individual patients in the context of precision medicine. This review summarizes the current status of SCT for HF in clinics and provides new perspectives on the development of computation-aided SCT in the era of precision medicine and AI/ML.
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Affiliation(s)
- Mohammed A. Chowdhury
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
- Department of Public Health and Health Sciences, Health Sciences Ph.D. Program, School of Health Sciences, University of South Dakota, Vermillion, SD, United States
- Department of Cardiology, North Central Heart, Avera Heart Hospital, Sioux Falls, SD, United States
| | - Jing J. Zhang
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
| | - Rodrigue Rizk
- Department of Computer Science, University of South Dakota, Vermillion, SD, United States
| | - William C. W. Chen
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, United States
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Dixit S, Kumar A, Srinivasan K, Vincent PMDR, Ramu Krishnan N. Advancing genome editing with artificial intelligence: opportunities, challenges, and future directions. Front Bioeng Biotechnol 2024; 11:1335901. [PMID: 38260726 PMCID: PMC10800897 DOI: 10.3389/fbioe.2023.1335901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-based genome editing (GED) technologies have unlocked exciting possibilities for understanding genes and improving medical treatments. On the other hand, Artificial intelligence (AI) helps genome editing achieve more precision, efficiency, and affordability in tackling various diseases, like Sickle cell anemia or Thalassemia. AI models have been in use for designing guide RNAs (gRNAs) for CRISPR-Cas systems. Tools like DeepCRISPR, CRISTA, and DeepHF have the capability to predict optimal guide RNAs (gRNAs) for a specified target sequence. These predictions take into account multiple factors, including genomic context, Cas protein type, desired mutation type, on-target/off-target scores, potential off-target sites, and the potential impacts of genome editing on gene function and cell phenotype. These models aid in optimizing different genome editing technologies, such as base, prime, and epigenome editing, which are advanced techniques to introduce precise and programmable changes to DNA sequences without relying on the homology-directed repair pathway or donor DNA templates. Furthermore, AI, in collaboration with genome editing and precision medicine, enables personalized treatments based on genetic profiles. AI analyzes patients' genomic data to identify mutations, variations, and biomarkers associated with different diseases like Cancer, Diabetes, Alzheimer's, etc. However, several challenges persist, including high costs, off-target editing, suitable delivery methods for CRISPR cargoes, improving editing efficiency, and ensuring safety in clinical applications. This review explores AI's contribution to improving CRISPR-based genome editing technologies and addresses existing challenges. It also discusses potential areas for future research in AI-driven CRISPR-based genome editing technologies. The integration of AI and genome editing opens up new possibilities for genetics, biomedicine, and healthcare, with significant implications for human health.
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Affiliation(s)
- Shriniket Dixit
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - Anant Kumar
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, India
| | - Kathiravan Srinivasan
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - P. M. Durai Raj Vincent
- School of Computer Science Engineering and Information Systems, Vellore Institute of Technology, Vellore, India
| | - Nadesh Ramu Krishnan
- School of Computer Science Engineering and Information Systems, Vellore Institute of Technology, Vellore, India
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Karsten H, Matrisch L, Cichutek S, Fiedler W, Alsdorf W, Block A. Broadening the horizon: potential applications of CAR-T cells beyond current indications. Front Immunol 2023; 14:1285406. [PMID: 38090582 PMCID: PMC10711079 DOI: 10.3389/fimmu.2023.1285406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Engineering immune cells to treat hematological malignancies has been a major focus of research since the first resounding successes of CAR-T-cell therapies in B-ALL. Several diseases can now be treated in highly therapy-refractory or relapsed conditions. Currently, a number of CD19- or BCMA-specific CAR-T-cell therapies are approved for acute lymphoblastic leukemia (ALL), diffuse large B-cell lymphoma (DLBCL), mantle cell lymphoma (MCL), multiple myeloma (MM), and follicular lymphoma (FL). The implementation of these therapies has significantly improved patient outcome and survival even in cases with previously very poor prognosis. In this comprehensive review, we present the current state of research, recent innovations, and the applications of CAR-T-cell therapy in a selected group of hematologic malignancies. We focus on B- and T-cell malignancies, including the entities of cutaneous and peripheral T-cell lymphoma (T-ALL, PTCL, CTCL), acute myeloid leukemia (AML), chronic myeloid leukemia (CML), chronic lymphocytic leukemia (CLL), classical Hodgkin-Lymphoma (HL), Burkitt-Lymphoma (BL), hairy cell leukemia (HCL), and Waldenström's macroglobulinemia (WM). While these diseases are highly heterogenous, we highlight several similarly used approaches (combination with established therapeutics, target depletion on healthy cells), targets used in multiple diseases (CD30, CD38, TRBC1/2), and unique features that require individualized approaches. Furthermore, we focus on current limitations of CAR-T-cell therapy in individual diseases and entities such as immunocompromising tumor microenvironment (TME), risk of on-target-off-tumor effects, and differences in the occurrence of adverse events. Finally, we present an outlook into novel innovations in CAR-T-cell engineering like the use of artificial intelligence and the future role of CAR-T cells in therapy regimens in everyday clinical practice.
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Affiliation(s)
- Hendrik Karsten
- Faculty of Medicine, University of Hamburg, Hamburg, Germany
| | - Ludwig Matrisch
- Department of Rheumatology and Clinical Immunology, University Medical Center Schleswig-Holstein, Lübeck, Germany
- Faculty of Medicine, University of Lübeck, Lübeck, Germany
| | - Sophia Cichutek
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Eppendorf, Hamburg, Germany
| | - Walter Fiedler
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Eppendorf, Hamburg, Germany
| | - Winfried Alsdorf
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Eppendorf, Hamburg, Germany
| | - Andreas Block
- Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Eppendorf, Hamburg, Germany
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Wong WW, Lim WA. Golden age of immunoengineering. Immunol Rev 2023; 320:4-9. [PMID: 37872646 PMCID: PMC10841587 DOI: 10.1111/imr.13283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Affiliation(s)
- Wilson W. Wong
- Biomedical Engineering and Biological Design Center, Boston University, Boston, MA
| | - Wendell A. Lim
- Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA
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