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Andersen GT, Ianevski A, Resell M, Pojskic N, Rabben HL, Geithus S, Kodama Y, Hiroyuki T, Kainov D, Grønbech JE, Hayakawa Y, Wang TC, Zhao CM, Chen D. Multi-bioinformatics revealed potential biomarkers and repurposed drugs for gastric adenocarcinoma-related gastric intestinal metaplasia. NPJ Syst Biol Appl 2024; 10:127. [PMID: 39496635 PMCID: PMC11535201 DOI: 10.1038/s41540-024-00455-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 10/13/2024] [Indexed: 11/06/2024] Open
Abstract
Biomarkers associated with the progression from gastric intestinal metaplasia (GIM) to gastric adenocarcinoma (GA), i.e., GA-related GIM, could provide valuable insights into identifying patients with increased risk for GA. The aim of this study was to utilize multi-bioinformatics to reveal potential biomarkers for the GA-related GIM and predict potential drug repurposing for GA prevention in patients. The multi-bioinformatics included gene expression matrix (GEM) by microarray gene expression (MGE), ScType (a fully automated and ultra-fast cell-type identification based solely on a given scRNA-seq data), Ingenuity Pathway Analysis, PageRank centrality, GO and MSigDB enrichments, Cytoscape, Human Protein Atlas and molecular docking analysis in combination with immunohistochemistry. To identify GA-related GIM, paired surgical biopsies were collected from 16 GIM-GA patients who underwent gastrectomy, yielding 64 samples (4 biopsies per stomach x 16 patients) for MGE. Co-analysis was performed by including scRNAseq and immunohistochemistry datasets of endoscopic biopsies of 37 patients. The results of the present study showed potential biomarkers for GA-related GIM, including GEM of individual patients, individual genes (such as RBP2 and CD44), signaling pathways, network of molecules, and network of signaling pathways with key topological nodes. Accordingly, potential treatment targets with repurposed drugs were identified including epidermal growth factor receptor, proto-oncogene tyrosine-protein kinase Src, paxillin, transcription factor Jun, breast cancer type 1 susceptibility protein, cellular tumor antigen p53, mouse double minute 2, and CD44.
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Affiliation(s)
- Gøran Troseth Andersen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Surgery, St. Olav's Hospital, Trondheim, Norway
- Department of Surgery, Namsos Hospital, Namsos, Norway
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Mathilde Resell
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Naris Pojskic
- Laboratory for Bioinformatics and Biostatistics, University of Sarajevo - Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Hanne-Line Rabben
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Synne Geithus
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Yosuke Kodama
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Tomita Hiroyuki
- Department of Tumor Pathology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jon Erik Grønbech
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Surgery, St. Olav's Hospital, Trondheim, Norway
| | - Yoku Hayakawa
- Department of Gastroenterology, Tokyo University Hospital, Tokyo, Japan
| | - Timothy C Wang
- Department of Digestive and Liver Diseases and Herbert Iring Comprehensive Cancer Center, Columbia University Medical Center, New York, USA
| | - Chun-Mei Zhao
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Duan Chen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
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Borogovac A, Siddiqi T. Advancing CAR T-cell therapy for chronic lymphocytic leukemia: exploring resistance mechanisms and the innovative strategies to overcome them. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2024; 7:18. [PMID: 38835348 PMCID: PMC11149098 DOI: 10.20517/cdr.2023.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 04/04/2024] [Accepted: 04/23/2024] [Indexed: 06/06/2024]
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has ushered in substantial advancements in the management of various B-cell malignancies. However, its integration into chronic lymphocytic leukemia (CLL) treatment has been challenging, attributed largely to the development of very effective chemo-free alternatives. Additionally, CAR T-cell responses in CLL have not been as high as in other B-cell lymphomas or leukemias. However, a critical void exists in therapeutic options for patients with high-risk diseases who are resistant to the current CLL therapies, underscoring the urgency for adoptive immunotherapies in these patients. The diminished CAR T-cell efficacy within CLL can be traced to factors such as compromised T-cell fitness due to persistent antigenic stimulation inherent to CLL. Resistance mechanisms encompass tumor-related factors like antigen escape, CAR T-cell-intrinsic factors like T-cell exhaustion, and a suppressive tumor microenvironment (TME). New strategies to combat CAR T-cell resistance include the concurrent administration of therapies that augment CAR T-cell endurance and function, as well as the engineering of novel CAR T-cells targeting different antigens. Moreover, the concept of "armored" CAR T-cells, armed with transgenic modulators to modify both CAR T-cell function and the tumor milieu, is gaining traction. Beyond this, the development of readily available, allogeneic CAR T-cells and natural killer (NK) cells presents a promising countermeasure to innate T-cell defects in CLL patients. In this review, we explore the role of CAR T-cell therapy in CLL, the intricate tapestry of resistance mechanisms, and the pioneering methods studied to overcome resistance.
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Affiliation(s)
- Azra Borogovac
- City of Hope, Department of Hematology and Hematopoietic Cell Transplantation, Lennar Foundation Cancer Center, Irvine, CA 92618, USA
| | - Tanya Siddiqi
- City of Hope, Department of Hematology and Hematopoietic Cell Transplantation, Lennar Foundation Cancer Center, Irvine, CA 92618, USA
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Sun B, Yang H, Li Y, Scheerstra JF, van Stevendaal MHME, Li S, van Hest JCM. Targeted pH-Activated Peptide-Based Nanomaterials for Combined Photodynamic Therapy with Immunotherapy. Biomacromolecules 2024; 25:3044-3054. [PMID: 38662992 PMCID: PMC11094723 DOI: 10.1021/acs.biomac.4c00141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/14/2024]
Abstract
Photodynamic therapy (PDT) has demonstrated efficacy in eliminating local tumors, yet its effectiveness against metastasis is constrained. While immunotherapy has exhibited promise in a clinical context, its capacity to elicit significant systemic antitumor responses across diverse cancers is often limited by the insufficient activation of the host immune system. Consequently, the combination of PDT and immunotherapy has garnered considerable attention. In this study, we developed pH-responsive porphyrin-peptide nanosheets with tumor-targeting capabilities (PRGD) that were loaded with the IDO inhibitor NLG919 for a dual application involving PDT and immunotherapy (PRGD/NLG919). In vitro experiments revealed the heightened cellular uptake of PRGD/NLG919 nanosheets in tumor cells overexpressing αvβ3 integrins. The pH-responsive PRGD/NLG919 nanosheets demonstrated remarkable singlet oxygen generation and photocytotoxicity in HeLa cells in an acidic tumor microenvironment. When treating HeLa cells with PRGD/NLG919 nanosheets followed by laser irradiation, a more robust adaptive immune response occurred, leading to a substantial proliferation of CD3+CD8+ T cells and CD3+CD4+ T cells compared to control groups. Our pH-responsive targeted PRGD/NLG919 nanosheets therefore represent a promising nanosystem for combination therapy, offering effective PDT and an enhanced host immune response.
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Affiliation(s)
- Bingbing Sun
- Bio-Organic
Chemistry, Department of Chemical Engineering and Chemistry, Institute
for Complex Molecular Systems, Eindhoven
University of Technology Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Haowen Yang
- Laboratory
of Immunoengineering, Department of Biomedical Engineering, Institute
for Complex Molecular Systems, Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Yudong Li
- Bio-Organic
Chemistry, Department of Chemical Engineering and Chemistry, Institute
for Complex Molecular Systems, Eindhoven
University of Technology Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jari F. Scheerstra
- Bio-Organic
Chemistry, Department of Chemical Engineering and Chemistry, Institute
for Complex Molecular Systems, Eindhoven
University of Technology Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Marleen H. M. E. van Stevendaal
- Bio-Organic
Chemistry, Department of Chemical Engineering and Chemistry, Institute
for Complex Molecular Systems, Eindhoven
University of Technology Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Shukun Li
- Bio-Organic
Chemistry, Department of Chemical Engineering and Chemistry, Institute
for Complex Molecular Systems, Eindhoven
University of Technology Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jan C. M. van Hest
- Bio-Organic
Chemistry, Department of Chemical Engineering and Chemistry, Institute
for Complex Molecular Systems, Eindhoven
University of Technology Helix, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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Borogovac A, Siddiqi T. Transforming CLL management with immunotherapy: Investigating the potential of CAR T-cells and bispecific antibodies. Semin Hematol 2024; 61:119-130. [PMID: 38290860 DOI: 10.1053/j.seminhematol.2024.01.001] [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: 11/14/2023] [Revised: 12/02/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
Immunotherapies, such as chimeric antigen receptor (CAR) T-cell therapy and bispecific antibodies or T-cell engagers, have revolutionized the treatment landscape for various B-cell malignancies, including B-acute lymphoblastic leukemia and many non-Hodgkin lymphomas. Despite their significant impact on these malignancies, their application in chronic lymphocytic leukemia (CLL) management is still largely under investigation. Although the initial success of CD19-directed CAR T-cell therapy was observed in 3 multiply relapsed CLL patients, with 2 of them surviving over 10 years without relapse, recent CAR T-cell therapy trials in CLL have shown reduced response rates compared to their efficacy in other B-cell malignancies. One of the challenges with using immunotherapy in CLL is the compromised T-cell fitness from persistent CLL-related antigenic stimulation, and an immunosuppressive tumor microenvironment (TME). These challenges underscore a critical gap in therapeutic options for CLL patients intolerant or resistant to current therapies, emphasizing the imperative role of effective immunotherapy. Encouragingly, innovative strategies are emerging to overcome these challenges. These include integrating synergistic agents like ibrutinib to enhance CAR T-cell function and persistence and engineering newer CAR T-cell constructs targeting diverse antigens or employing dual-targeting approaches. Bispecific antibodies are an exciting "off-the-shelf" prospect for these patients, with their investigation in CLL currently entering the realm of clinical trials. Additionally, the development of allogeneic CAR T-cells and natural killer (NK) cells from healthy donors presents a promising solution to address the diminished T-cell fitness observed in CLL patients. This comprehensive review delves into the latest insights regarding the role of immunotherapy in CLL, the complex landscape of resistance mechanisms, and a spectrum of innovative approaches to surmount therapeutic challenges.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Antibodies, Bispecific/therapeutic use
- Antibodies, Bispecific/immunology
- Immunotherapy, Adoptive/methods
- Receptors, Chimeric Antigen/immunology
- Immunotherapy/methods
- T-Lymphocytes/immunology
- Tumor Microenvironment/immunology
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Affiliation(s)
- Azra Borogovac
- City of Hope, Lennar Foundation Cancer Center, Irvine, CA.
| | - Tanya Siddiqi
- City of Hope, Lennar Foundation Cancer Center, Irvine, CA
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