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Li Z, Ma L, Gao Z, Wang X, Che X, Zhang P, Li Y, Zhang Q, Liu T, Sun Y, Bai Y, Deng H. Identification and validation of tumor-specific T cell receptors from tumor infiltrating lymphocytes using tumor organoid co-cultures. Cancer Immunol Immunother 2024; 73:164. [PMID: 38954022 PMCID: PMC11219989 DOI: 10.1007/s00262-024-03749-8] [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: 03/20/2024] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
T cell receptor-engineered T cells (TCR-Ts) therapy is promising for cancer immunotherapy. Most studies have focused on identifying tumor-specific T cell receptors (TCRs) through predicted tumor neoantigens. However, current algorithms for predicting tumor neoantigens are unreliable and many neoantigens are derived from non-coding regions. Thus, the technological platform for identifying tumor-specific TCRs using natural antigens expressed on tumor cells is urgently needed. In this study, tumor organoids-enriched tumor infiltrating lymphocytes (oeT) were obtained by repeatedly stimulation of autologous patient-derived organoids (PDO) in vitro. The oeT cells specifically responded to autologous tumor PDO by detecting CD137 expression and the secretion of IFN-γ using enzyme-linked immunospot assay. The measurement of oeT cell-mediated killing of three-dimensional organoids was conducted using a caspase3/7 flow cytometry assay kit. Subsequently, tumor-specific T cells were isolated based on CD137 expression and their TCRs were identified through single-cell RT-PCR analysis. The specificity cytotoxicity of TCRs were confirmed by transferring to primary peripheral blood T cells. The co-culture system proved highly effective in generating CD8+ tumor-specific oeT cells. These oeT cells effectively induced IFN-γ secretion and exhibited specificity in killing autologous tumor organoids, while not eliciting a cytotoxic response against normal organoids. The analysis conducted by TCRs revealed a significant expansion of T cells within a specific subset of TCRs. Subsequently, the TCRs were cloned and transferred to peripheral blood T cells generation engineered TCR-Ts, which adequately recognized and killed tumor cell in a patient-specific manner. The co-culture system provided an approach to generate tumor-specific TCRs from tumor-infiltrating lymphocytes of patients with colorectal cancer, and tumor-specific TCRs can potentially be used for personalized TCR-T therapy.
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Affiliation(s)
- Zhilang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Lisha Ma
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zhaoya Gao
- Department of Gastrointestinal Surgery, Peking University Shougang Hospital, Beijing, 100041, China
| | - Xiya Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xuan Che
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Pengchong Zhang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yixian Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qianjing Zhang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Tianxing Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100091, China
| | - Yuan Sun
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yun Bai
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Hongkui Deng
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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2
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Kalli M, Stylianopoulos T. Toward innovative approaches for exploring the mechanically regulated tumor-immune microenvironment. APL Bioeng 2024; 8:011501. [PMID: 38390314 PMCID: PMC10883717 DOI: 10.1063/5.0183302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Within the complex tumor microenvironment, cells experience mechanical cues-such as extracellular matrix stiffening and elevation of solid stress, interstitial fluid pressure, and fluid shear stress-that significantly impact cancer cell behavior and immune responses. Recognizing the significance of these mechanical cues not only sheds light on cancer progression but also holds promise for identifying potential biomarkers that would predict therapeutic outcomes. However, standardizing methods for studying how mechanical cues affect tumor progression is challenging. This challenge stems from the limitations of traditional in vitro cell culture systems, which fail to encompass the critical contextual cues present in vivo. To address this, 3D tumor spheroids have been established as a preferred model, more closely mimicking cancer progression, but they usually lack reproduction of the mechanical microenvironment encountered in actual solid tumors. Here, we review the role of mechanical forces in modulating tumor- and immune-cell responses and discuss how grasping the importance of these mechanical cues could revolutionize in vitro tumor tissue engineering. The creation of more physiologically relevant environments that better replicate in vivo conditions will eventually increase the efficacy of currently available treatments, including immunotherapies.
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Affiliation(s)
- Maria Kalli
- Cancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus
| | - Triantafyllos Stylianopoulos
- Cancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus
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3
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Katsikis PD, Ishii KJ, Schliehe C. Challenges in developing personalized neoantigen cancer vaccines. Nat Rev Immunol 2024; 24:213-227. [PMID: 37783860 DOI: 10.1038/s41577-023-00937-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have been championed as a tool to direct and amplify immune responses against tumours while sparing healthy tissue. In recent years, extensive preclinical research and more than one hundred clinical trials have tested different strategies of neoantigen discovery and vaccine formulations. However, despite the enthusiasm for neoantigen vaccines, proof of unequivocal efficacy has remained beyond reach for the majority of clinical trials. In this Review, we focus on the key obstacles pertaining to vaccine design and tumour environment that remain to be overcome in order to unleash the true potential of neoantigen vaccines in cancer therapy.
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Affiliation(s)
- Peter D Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
- International Vaccine Design Center (vDesC), The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Christopher Schliehe
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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4
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Tan T, Mouradov D, Lee M, Gard G, Hirokawa Y, Li S, Lin C, Li F, Luo H, Wu K, Palmieri M, Leong E, Clarke J, Sakthianandeswaren A, Brasier H, Tie J, Tebbutt NC, Jalali A, Wong R, Burgess AW, Gibbs P, Sieber OM. Unified framework for patient-derived, tumor-organoid-based predictive testing of standard-of-care therapies in metastatic colorectal cancer. Cell Rep Med 2023; 4:101335. [PMID: 38118423 PMCID: PMC10783557 DOI: 10.1016/j.xcrm.2023.101335] [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: 05/17/2023] [Revised: 09/11/2023] [Accepted: 11/18/2023] [Indexed: 12/22/2023]
Abstract
Predictive drug testing of patient-derived tumor organoids (PDTOs) holds promise for personalizing treatment of metastatic colorectal cancer (mCRC), but prospective data are limited to chemotherapy regimens with conflicting results. We describe a unified framework for PDTO-based predictive testing across standard-of-care chemotherapy and biologic and targeted therapy options. In an Australian community cohort, PDTO predictions based on treatment-naive patients (n = 56) and response rates from first-line mCRC clinical trials achieve 83% accuracy for forecasting responses in patients receiving palliative treatments (18 patients, 29 treatments). Similar assay accuracy is achieved in a prospective study of third-line or later mCRC treatment, AGITG FORECAST-1 (n = 30 patients). "Resistant" predictions are associated with inferior progression-free survival; misclassification rates are similar by regimen. Liver metastases are the optimal site for sampling, with testing achievable within 7 weeks for 68.8% cases. Our findings indicate that PDTO drug panel testing can provide predictive information for multifarious standard-of-care therapies for mCRC.
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Affiliation(s)
- Tao Tan
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Dmitri Mouradov
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Margaret Lee
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia; Department of Medical Oncology, Eastern Health, Box Hill, VIC 3128, Australia; Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University, Box Hill, VIC 3128, Australia
| | - Grace Gard
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia
| | - Yumiko Hirokawa
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Shan Li
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Cong Lin
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, BGI Research, Hangzhou 310000, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Fuqiang Li
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, BGI Research, Hangzhou 310000, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Huijuan Luo
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, BGI Research, Hangzhou 310000, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Kui Wu
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, BGI Research, Hangzhou 310000, China; Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen 518083, China
| | - Michelle Palmieri
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Evelyn Leong
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Jordan Clarke
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Anuratha Sakthianandeswaren
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Helen Brasier
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Jeanne Tie
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia
| | - Niall C Tebbutt
- Department of Medical Oncology, Olivia Newton-John Cancer Wellness & Research Centre, Austin Health, Heidelberg, VIC 3084, Australia
| | - Azim Jalali
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia; Department of Cancer Services, Latrobe Regional Hospital, Traralogon, VIC 3844, Australia; Department of Medical Oncology, The Northern Hospital, Epping, VIC 3076, Australia
| | - Rachel Wong
- Department of Medical Oncology, Eastern Health, Box Hill, VIC 3128, Australia; Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University, Box Hill, VIC 3128, Australia
| | - Antony W Burgess
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Peter Gibbs
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Medical Oncology, Western Health, Footscray, VIC 3011, Australia
| | - Oliver M Sieber
- Personalised Oncology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Surgery, The University of Melbourne, Parkville, VIC 3050, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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5
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Klebanoff CA, Chandran SS, Baker BM, Quezada SA, Ribas A. T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome. Nat Rev Drug Discov 2023; 22:996-1017. [PMID: 37891435 PMCID: PMC10947610 DOI: 10.1038/s41573-023-00809-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 10/29/2023]
Abstract
The T cell receptor (TCR) complex is a naturally occurring antigen sensor that detects, amplifies and coordinates cellular immune responses to epitopes derived from cell surface and intracellular proteins. Thus, TCRs enable the targeting of proteins selectively expressed by cancer cells, including neoantigens, cancer germline antigens and viral oncoproteins. As such, TCRs have provided the basis for an emerging class of oncology therapeutics. Herein, we review the current cancer treatment landscape using TCRs and TCR-like molecules. This includes adoptive cell transfer of T cells expressing endogenous or engineered TCRs, TCR bispecific engagers and antibodies specific for human leukocyte antigen (HLA)-bound peptides (TCR mimics). We discuss the unique complexities associated with the clinical development of these therapeutics, such as HLA restriction, TCR retrieval, potency assessment and the potential for cross-reactivity. In addition, we highlight emerging clinical data that establish the antitumour potential of TCR-based therapies, including tumour-infiltrating lymphocytes, for the treatment of diverse human malignancies. Finally, we explore the future of TCR therapeutics, including emerging genome editing methods to safely enhance potency and strategies to streamline patient identification.
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Affiliation(s)
- Christopher A Klebanoff
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA.
| | - Smita S Chandran
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, ID, USA
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, ID, USA
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Achilles Therapeutics, London, UK
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
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6
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Ning J, Ding J, Wang S, Jiang Y, Wang D, Jiang S. GPC3 Promotes Lung Squamous Cell Carcinoma Progression and HLA-A2-Restricted GPC3 Antigenic Peptide-Modified Dendritic Cell-Induced Cytotoxic T Lymphocytes to Kill Lung Squamous Cell Carcinoma Cells. J Immunol Res 2023; 2023:5532617. [PMID: 37965271 PMCID: PMC10643027 DOI: 10.1155/2023/5532617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/29/2023] [Indexed: 11/16/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is associated with poor clinical prognosis and lacks available targeted agents. GPC3 is upregulated in LUSC. Our study aimed to explore the roles of GPC3 in LUSC and the antitumor effects of HLA-A2-restricted GPC3 antigenic peptide-sensitized dendritic cell (DC)-induced cytotoxic T lymphocytes (CTLs) on LUSC. LUSC cells with GPC3 knockdown and overexpression were built using lentivirus packaging, and cell viability, clone formation, apoptosis, cycle, migration, and invasion were determined. Western blotting was used to detect the expression of cell cycle-related proteins and PI3K-AKT pathway-associated proteins. Subsequently, HLA-A2-restricted GPC3 antigenic peptides were predicted and synthesized by bioinformatic databases, and DCs were induced and cultured in vitro. Finally, HLA-A2-restricted GPC3 antigenic peptide-modified DCs were co-cultured with T cells to generate specific CTLs, and the killing effects of different CTLs on LUSC cells were studied. A series of cell function experiments showed that GPC3 overexpression promoted the proliferation, migration, and invasion of LUSC cells, inhibited their apoptosis, increased the number of cells in S phase, and reduced the cells in G2/M phase. GPC3 knockdown downregulated cyclin A, c-Myc, and PI3K, upregulated E2F1, and decreased the pAKT/AKT level. Three HLA-A2-restricted GPC3 antigenic peptides were synthesized, with GPC3522-530 FLAELAYDL and GPC3102-110 FLIIQNAAV antigenic peptide-modified DCs inducing CTL production, and exhibiting strong targeted killing ability in LUSC cells at 80 : 1 multiplicity of infection. GPC3 may advance the onset and progression of LUSC, and GPC3522-530 FLAELAYDL and GPC3102-110 FLIIQNAAV antigenic peptide-loaded DC-induced CTLs have a superior killing ability against LUSC cells.
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Affiliation(s)
- Jing Ning
- Department of General Medicine, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, China
- Molecular Oncology Department of Cancer Research Institution, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Jianqiao Ding
- Department of Thoracic Surgery (2), Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, China
| | - Shu Wang
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun 130000, China
| | - Youhong Jiang
- Molecular Oncology Department of Cancer Research Institution, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Daqing Wang
- Hope Plaza Children's Hospital District of Dalian Municipal Women and Children's Medical Center, Dalian 116000, China
| | - Shenyi Jiang
- Department of General Practice, The First Affiliated Hospital of China Medical University, Shengyang 110001, China
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7
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Aldea M, Friboulet L, Apcher S, Jaulin F, Mosele F, Sourisseau T, Soria JC, Nikolaev S, André F. Precision medicine in the era of multi-omics: can the data tsunami guide rational treatment decision? ESMO Open 2023; 8:101642. [PMID: 37769400 PMCID: PMC10539962 DOI: 10.1016/j.esmoop.2023.101642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/30/2023] Open
Abstract
Precision medicine for cancer is rapidly moving to an approach that integrates multiple dimensions of the biology in order to model mechanisms of cancer progression in each patient. The discovery of multiple drivers per tumor challenges medical decision that faces several treatment options. Drug sensitivity depends on the actionability of the target, its clonal or subclonal origin and coexisting genomic alterations. Sequencing has revealed a large diversity of drivers emerging at treatment failure, which are potential targets for clinical trials or drug repurposing. To effectively prioritize therapies, it is essential to rank genomic alterations based on their proven actionability. Moving beyond primary drivers, the future of precision medicine necessitates acknowledging the intricate spatial and temporal heterogeneity inherent in cancer. The advent of abundant complex biological data will make artificial intelligence algorithms indispensable for thorough analysis. Here, we will discuss the advancements brought by the use of high-throughput genomics, the advantages and limitations of precision medicine studies and future perspectives in this field.
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Affiliation(s)
- M Aldea
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif.
| | | | - S Apcher
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Jaulin
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Mosele
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif
| | | | - J-C Soria
- Paris Saclay University, Orsay; Drug Development Department, Gustave Roussy, Villejuif, France
| | - S Nikolaev
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F André
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif; Paris Saclay University, Orsay
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8
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Zhou B, Feng Z, Xu J, Xie J. Organoids: approaches and utility in cancer research. Chin Med J (Engl) 2023; 136:1783-1793. [PMID: 37365679 PMCID: PMC10406116 DOI: 10.1097/cm9.0000000000002477] [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: 09/27/2022] [Indexed: 06/28/2023] Open
Abstract
ABSTRACT Organoids are three-dimensional cellular structures with self-organizing and self-differentiation capacities. They faithfully recapitulate structures and functions of in vivo organs as represented by functionality and microstructural definitions. Heterogeneity in in vitro disease modeling is one of the main reasons for anti-cancer therapy failures. Establishing a powerful model to represent tumor heterogeneity is crucial for elucidating tumor biology and developing effective therapeutic strategies. Tumor organoids can retain the original tumor heterogeneity and are commonly used to mimic the cancer microenvironment when co-cultured with fibroblasts and immune cells; therefore, considerable effort has been made recently to promote the use of this new technology from basic research to clinical studies in tumors. In combination with gene editing technology and microfluidic chip systems, engineered tumor organoids show promising abilities to recapitulate tumorigenesis and metastasis. In many studies, the responses of tumor organoids to various drugs have shown a positive correlation with patient responses. Owing to these consistent responses and personalized characteristics with patient data, tumor organoids show excellent potential for preclinical research. Here, we summarize the properties of different tumor models and review their current state and progress in tumor organoids. We further discuss the substantial challenges and prospects in the rapidly developing tumor organoid field.
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Affiliation(s)
- Bingrui Zhou
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Zhiwei Feng
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jun Xu
- Department of Hepatobiliary and Pancreatic Surgery and Liver Transplant Center, The First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jun Xie
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, Shanxi Medical University, Taiyuan, Shanxi 030001, China
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9
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Yang C, Xiao W, Wang R, Hu Y, Yi K, Sun X, Wang G, Xu X. Tumor organoid model of colorectal cancer (Review). Oncol Lett 2023; 26:328. [PMID: 37415635 PMCID: PMC10320425 DOI: 10.3892/ol.2023.13914] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
The establishment of self-organizing 'mini-gut' organoid models has brought about a significant breakthrough in biomedical research. Patient-derived tumor organoids have emerged as valuable tools for preclinical studies, offering the retention of genetic and phenotypic characteristics of the original tumor. These organoids have applications in various research areas, including in vitro modelling, drug discovery and personalized medicine. The present review provided an overview of intestinal organoids, focusing on their unique characteristics and current understanding. The progress made in colorectal cancer (CRC) organoid models was then delved into, discussing their role in drug development and personalized medicine. For instance, it has been indicated that patient-derived tumor organoids are able to predict response to irinotecan-based neoadjuvant chemoradiotherapy. Furthermore, the limitations and challenges associated with current CRC organoid models were addressed, along with proposed strategies for enhancing their utility in future basic and translational research.
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Affiliation(s)
- Chi Yang
- Department of Gastroenterology, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Wangwen Xiao
- Central Laboratory, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Rui Wang
- School of Pharmacy, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Yan Hu
- Central Laboratory, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Ke Yi
- Central Laboratory, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Xuan Sun
- Department of Gastroenterology, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
| | - Guanghui Wang
- School of Pharmacy, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215123, P.R. China
| | - Xiaohui Xu
- Department of Gastroenterology, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
- Central Laboratory, The First People's Hospital of Taicang, Taicang Affiliated Hospital of Soochow University, Soochow Medical College of Soochow University, Suzhou, Jiangsu 215400, P.R. China
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10
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Szabó L, Seubert AC, Kretzschmar K. Modelling adult stem cells and their niche in health and disease with epithelial organoids. Semin Cell Dev Biol 2023; 144:20-30. [PMID: 36127261 DOI: 10.1016/j.semcdb.2022.09.006] [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: 05/27/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Adult stem cells are responsible for homoeostasis and regeneration of epithelial tissues. Stem cell function is regulated by both cell autonomous mechanisms as well as the niche. Deregulated stem cell function contributes to diseases such as cancer. Epithelial organoid cultures generated from tissue-resident adult stem cells have allowed unprecedented insights into the biology of epithelial tissues. The subsequent adaptation of organoid technology enabled the modelling of the communication of stem cells with their cellular and non-cellular niche as well as diseases. Starting from its first model described in 2009, the murine small intestinal organoid, we discuss here how epithelial organoid cultures have been become a prime in vitro research tool for cell and developmental biology, bioengineering, and biomedicine in the last decade.
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Affiliation(s)
- Lili Szabó
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany
| | - Anna C Seubert
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany
| | - Kai Kretzschmar
- Mildred Scheel Early Career Centre (MSNZ) for Cancer Research, University Hospital Würzburg, IZKF/MSNZ, Würzburg, Germany.
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11
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Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler AR, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. CELL REPORTS METHODS 2023; 3:100511. [PMID: 37426761 PMCID: PMC10326451 DOI: 10.1016/j.crmeth.2023.100511] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The identification of tumor-specific antigens (TSAs) is critical for developing effective cancer immunotherapies. Mass spectrometry (MS)-based immunopeptidomics has emerged as a powerful tool for identifying TSAs as physical molecules. However, current immunopeptidomics platforms face challenges in measuring low-abundance TSAs in a precise, sensitive, and reproducible manner from small needle-tissue biopsies (<1 mg). Inspired by recent advances in single-cell proteomics, microfluidics technology offers a promising solution to these limitations by providing improved isolation of human leukocyte antigen (HLA)-associated peptides with higher sensitivity. In this context, we highlight the challenges in sample preparation and the rationale for developing microfluidics technology in immunopeptidomics. Additionally, we provide an overview of promising microfluidic methods, including microchip pillar arrays, valved-based systems, droplet microfluidics, and digital microfluidics, and discuss the latest research on their application in MS-based immunopeptidomics and single-cell proteomics.
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Affiliation(s)
| | - Jiaxi Peng
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Zhaoguan Wu
- CHU Sainte Justine Research Center, Montreal, QC, Canada
| | | | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, Canada
- Department of Chemistry, University of Montreal, Montreal, QC, Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON, Canada
| | - Etienne Caron
- CHU Sainte Justine Research Center, Montreal, QC, Canada
- Department of Pathology and Cellular Biology, University of Montreal, Montreal, QC, Canada
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12
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Li X, Pak HS, Huber F, Michaux J, Taillandier-Coindard M, Altimiras ER, Bassani-Sternberg M. A microfluidics-enabled automated workflow of sample preparation for MS-based immunopeptidomics. CELL REPORTS METHODS 2023; 3:100479. [PMID: 37426762 PMCID: PMC10326370 DOI: 10.1016/j.crmeth.2023.100479] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/22/2023] [Accepted: 04/19/2023] [Indexed: 07/11/2023]
Abstract
Mass spectrometry (MS)-based immunopeptidomics is an attractive antigen discovery method with growing clinical implications. However, the current experimental approach to extract HLA-restricted peptides requires a bulky sample source, which remains a challenge for obtaining clinical specimens. We present an innovative workflow that requires a low sample volume, which streamlines the immunoaffinity purification (IP) and C18 peptide cleanup on a single microfluidics platform with automated liquid handling and minimal sample transfers, resulting in higher assay sensitivity. We also demonstrate how the state-of-the-art data-independent acquisition (DIA) method further enhances the depth of tandem MS spectra-based peptide sequencing. Consequently, over 4,000 and 5,000 HLA-I-restricted peptides were identified from as few as 0.2 million RA957 cells and a melanoma tissue of merely 5 mg, respectively. We also identified multiple immunogenic tumor-associated antigens and hundreds of peptides derived from non-canonical protein sources. This workflow represents a powerful tool for identifying the immunopeptidome of sparse samples.
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Affiliation(s)
- Xiaokang Li
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Hui Song Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Florian Huber
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Marie Taillandier-Coindard
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Emma Ricart Altimiras
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Rue du Bugnon 46, 1005 Lausanne, Switzerland
- Agora Cancer Research Centre, Rue du Bugnon 25A, 1005 Lausanne, Switzerland
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13
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Zhao J, Fong A, Seow SV, Toh HC. Organoids as an Enabler of Precision Immuno-Oncology. Cells 2023; 12:cells12081165. [PMID: 37190074 DOI: 10.3390/cells12081165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Since the dawn of the past century, landmark discoveries in cell-mediated immunity have led to a greater understanding of the innate and adaptive immune systems and revolutionised the treatment of countless diseases, including cancer. Today, precision immuno-oncology (I/O) involves not only targeting immune checkpoints that inhibit T-cell immunity but also harnessing immune cell therapies. The limited efficacy in some cancers results mainly from a complex tumour microenvironment (TME) that, in addition to adaptive immune cells, comprises innate myeloid and lymphoid cells, cancer-associated fibroblasts, and the tumour vasculature that contribute towards immune evasion. As the complexity of TME has called for more sophisticated human-based tumour models, organoids have allowed the dynamic study of spatiotemporal interactions between tumour cells and individual TME cell types. Here, we discuss how organoids can study the TME across cancers and how these features may improve precision I/O. We outline the approaches to preserve or recapitulate the TME in tumour organoids and discuss their potential, advantages, and limitations. We will discuss future directions of organoid research in understanding cancer immunology in-depth and identifying novel I/O targets and treatment strategies.
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Affiliation(s)
- Junzhe Zhao
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore 169857, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583, Singapore
- Doctor of Medicine Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Antoinette Fong
- Doctor of Medicine Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - See Voon Seow
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583, Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583, Singapore
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14
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El Harane S, Zidi B, El Harane N, Krause KH, Matthes T, Preynat-Seauve O. Cancer Spheroids and Organoids as Novel Tools for Research and Therapy: State of the Art and Challenges to Guide Precision Medicine. Cells 2023; 12:cells12071001. [PMID: 37048073 PMCID: PMC10093533 DOI: 10.3390/cells12071001] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023] Open
Abstract
Spheroids and organoids are important novel players in medical and life science research. They are gradually replacing two-dimensional (2D) cell cultures. Indeed, three-dimensional (3D) cultures are closer to the in vivo reality and open promising perspectives for academic research, drug screening, and personalized medicine. A large variety of cells and tissues, including tumor cells, can be the starting material for the generation of 3D cultures, including primary tissues, stem cells, or cell lines. A panoply of methods has been developed to generate 3D structures, including spontaneous or forced cell aggregation, air-liquid interface conditions, low cell attachment supports, magnetic levitation, and scaffold-based technologies. The choice of the most appropriate method depends on (i) the origin of the tissue, (ii) the presence or absence of a disease, and (iii) the intended application. This review summarizes methods and approaches for the generation of cancer spheroids and organoids, including their advantages and limitations. We also highlight some of the challenges and unresolved issues in the field of cancer spheroids and organoids, and discuss possible therapeutic applications.
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Affiliation(s)
- Sanae El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Bochra Zidi
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Nadia El Harane
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Karl-Heinz Krause
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Thomas Matthes
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
| | - Olivier Preynat-Seauve
- Department of Medicine, Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland
- Laboratory of Experimental Cell Therapy, Department of Diagnostics, Geneva University Hospitals, 1206 Geneva, Switzerland
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15
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Zhu J, Ji L, Chen Y, Li H, Huang M, Dai Z, Wang J, Xiang D, Fu G, Lei Z, Chu X. Organoids and organs-on-chips: insights into predicting the efficacy of systemic treatment in colorectal cancer. Cell Death Discov 2023; 9:72. [PMID: 36813783 PMCID: PMC9947255 DOI: 10.1038/s41420-023-01354-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 02/24/2023] Open
Abstract
Cancer heterogeneity has posed a great challenge to traditional cancer treatment, with the reappearance of cancer heterogeneity of inter and intra patients being especially critical. Based on this, personalized therapy has emerged as significant research focus in recent and even future years. Cancer-related therapeutic models are developing, including cell lines, patient-derived xenografts, organoids, etc. Organoids are three-dimensional in vitro models emerged in the past dozen years and are able to reproduce the cellular and molecular composition of the original tumor. These advantages demonstrate the great potential for patient-derived organoids to develop personalized anticancer therapies, including preclinical drug screening and the prediction of patient treatment response. The impact of microenvironment on cancer treatment cannot be underestimated, and the remodeling of microenvironment also allows organoids to interact with other technologies, among which organs-on-chips is a representative one. This review highlights the use of organoids and organs-on-chips as complementary reference tools in treating colorectal cancer from the perspective of clinical efficacy predictability. We also discuss the limitations of both techniques and how they complement each other well.
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Affiliation(s)
- Jialong Zhu
- grid.284723.80000 0000 8877 7471Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000 China
| | - Linlin Ji
- grid.41156.370000 0001 2314 964XDepartment of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000 China
| | - Yitian Chen
- grid.284723.80000 0000 8877 7471Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000 China ,grid.41156.370000 0001 2314 964XDepartment of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000 China ,grid.89957.3a0000 0000 9255 8984Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, 210000 China ,grid.410745.30000 0004 1765 1045Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, 210000 China
| | - Huiyu Li
- grid.41156.370000 0001 2314 964XDepartment of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000 China
| | - Mengxi Huang
- grid.41156.370000 0001 2314 964XDepartment of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000 China
| | - Zhe Dai
- grid.41156.370000 0001 2314 964XDepartment of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000 China
| | - Jing Wang
- grid.41156.370000 0001 2314 964XDepartment of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000 China
| | - Dan Xiang
- grid.41156.370000 0001 2314 964XDepartment of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000 China
| | - Gongbo Fu
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000, China. .,Department of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000, China. .,Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, 210000, China. .,Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, 210000, China.
| | - Zengjie Lei
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000, China. .,Department of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000, China. .,Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, 210000, China. .,Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, 210000, China.
| | - Xiaoyuan Chu
- Department of Medical Oncology, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, 210000, China. .,Department of Medical Oncology, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, 210000, China. .,Department of Medical Oncology, Jinling Hospital, Nanjing Medical University, Nanjing, 210000, China. .,Department of Medical Oncology, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, 210000, China.
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16
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Chai C, Ji P, Xu H, Tang H, Wang Z, Zhang H, Zhou W. Targeting cancer drug resistance utilizing organoid technology. Biomed Pharmacother 2023; 158:114098. [PMID: 36528918 DOI: 10.1016/j.biopha.2022.114098] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer organoids generated from 3D in vitro cell cultures have contributed to the study of drug resistance. Maintenance of genomic and transcriptomic similarity between organoids and parental cancer allows organoids to have the ability of accurate prediction in drug resistance testing. Protocols of establishing therapy-sensitive and therapy-resistant organoids are concluded in two aspects, which are generated directly from respective patients' cancer and by induction of anti-cancer drug. Genomic and transcriptomic analyses and gene editing have been applied to organoid studies to identify key targets in drug resistance and FGFR3, KHDRBS3, lnc-RP11-536 K7.3 and FBN1 were found to be key targets. Furthermore, mechanisms contributing to resistance have been identified, including metabolic adaptation, activation of DNA damage response, defects in apoptosis, reduced cellular senescence, cellular plasticity, subpopulation interactions and gene fusions. Additionally, cancer stem cells (CSCs) have been verified to be involved in drug resistance utilizing organoid technology. Reversal of drug resistance can be achieved by targeting key genes and CSCs in cancer organoids. In this review, we summarize applications of organoids to cancer drug resistance research, indicating prospects and limitations.
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Affiliation(s)
- Changpeng Chai
- The First Hospital of Lanzhou University, Lanzhou University, Lanzhou 730000, Gansu, China; The Forth Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu, China.
| | - Pengfei Ji
- The Second Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu, China.
| | - Hao Xu
- The First Hospital of Lanzhou University, Lanzhou University, Lanzhou 730000, Gansu, China.
| | - Huan Tang
- The Second Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu, China.
| | - Zhengfeng Wang
- The First Hospital of Lanzhou University, Lanzhou University, Lanzhou 730000, Gansu, China.
| | - Hui Zhang
- The Second Hospital of Lanzhou University, Lanzhou University, Lanzhou 730000, Gansu, China.
| | - Wence Zhou
- Department of General Surgery, The Second Hospital of Lanzhou University, Lanzhou 730000, Gansu, China; The Second Hospital of Lanzhou University, Lanzhou University, Lanzhou 730000, Gansu, China.
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17
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Schwarz S, Schmitz J, Löffler MW, Ghosh M, Rammensee HG, Olshvang E, Markel M, Mockel-Tenbrinck N, Dzionek A, Krake S, Arslan B, Kampe KD, Wendt A, Bauer P, Mullins CS, Schlosser A, Linnebacher M. T cells of colorectal cancer patients' stimulated by neoantigenic and cryptic peptides better recognize autologous tumor cells. J Immunother Cancer 2022; 10:jitc-2022-005651. [PMID: 36460334 PMCID: PMC9723954 DOI: 10.1136/jitc-2022-005651] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Patients with cancers that exhibit extraordinarily high somatic mutation numbers are ideal candidates for immunotherapy and enable identifying tumor-specific peptides through stimulation of tumor-reactive T cells (Tc). METHODS Colorectal cancers (CRC) HROC113 and HROC285 were selected based on high TMB, microsatellite instability and HLA class I expression. Their HLA ligandome was characterized using mass spectrometry, compared with the HLA ligand atlas and HLA class I-binding affinity was predicted. Cryptic peptides were identified using Peptide-PRISM. Patients' Tc were isolated from either peripheral blood (pTc) or tumor material (tumor-infiltrating Tc, TiTc) and expanded. In addition, B-lymphoblastoid cells (B-LCL) were generated and used as antigen-presenting cells. pTc and TiTc were stimulated twice for 7 days using peptide pool-loaded B-LCL. Subsequently, interferon gamma (IFNγ) release was quantified by ELISpot. Finally, cytotoxicity against autologous tumor cells was assessed in a degranulation assay. RESULTS 100 tumor-specific candidate peptides-97 cryptic peptides and 3 classically mutated neoantigens-were selected. The neoantigens originated from single nucleotide substitutions in the genes IQGAP1, CTNNB1, and TRIT1. Cryptic and neoantigenic peptides inducing IFNγ secretion of Tc were further investigated. Stimulation of pTc and TiTc with neoantigens and selected cryptic peptides resulted in increased release of cytotoxic granules in the presence of autologous tumor cells, substantiating their improved tumor cell recognition. Tetramer staining showed an enhanced number of pTc and TiTc specific for the IQGAP1 neoantigen. Subpopulation analysis prior to peptide stimulation revealed that pTc mainly consisted of memory Tc, whereas TiTc constituted primarily of effector and effector memory Tc. This allows to infer that TiTc reacting to neoantigens and cryptic peptides must be present within the tumor microenvironment. CONCLUSION These results prove that the analyzed CRC present both mutated neoantigenic and cryptic peptides on their HLA class I molecules. Moreover, stimulation with these peptides significantly strengthened tumor cell recognition by Tc. Since the overall number of neoantigenic peptides identifiable by HLA ligandome analysis hitherto is small, our data emphasize the relevance of increasing the target scope for cancer vaccines by the cryptic peptide category.
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Affiliation(s)
- Sandra Schwarz
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Johanna Schmitz
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Markus W Löffler
- Department of General, Visceral and Transplant Surgery, Universitätsklinikum Tübingen, Tubingen, Germany,Department of Immunology, University of Tübingen, Tubingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, University of Tübingen, Tübingen, Germany,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany
| | - Michael Ghosh
- Department of Immunology, University of Tübingen, Tubingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, University of Tübingen, Tubingen, Germany,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) Partner Site Tübingen, University of Tübingen, Tübingen, Germany
| | | | - Marvin Markel
- Miltenyi Biotec BV & Co KG, Bergisch Gladbach, Germany
| | | | | | | | | | | | | | | | - Christina S Mullins
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
| | - Andreas Schlosser
- Center for Integrative and Translational Bioimaging, Rudolf-Virchow Center, University of Würzburg, Würzburg, Germany
| | - Michael Linnebacher
- Department of General Surgery, Molecular Oncology and Immunotherapy, Rostock University Medical Center, Rostock, Germany
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18
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Neoantigen discovery and applications in glioblastoma: An immunotherapy perspective. Cancer Lett 2022; 550:215945. [DOI: 10.1016/j.canlet.2022.215945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/21/2022]
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19
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Xu BL, Wang XM, Chen GY, Yuan P, Han L, Qin P, Li TP, You HQ, Zhang CJ, Fu XM, Yuan L, Wang ZB, Gao QL. In vivo growth of subclones derived from Lewis lung carcinoma is determined by the tumor microenvironment. Am J Cancer Res 2022; 12:5255-5270. [PMID: 36504888 PMCID: PMC9729899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/02/2022] [Indexed: 12/15/2022] Open
Abstract
Heterogeneity is a fundamental feature of human tumors and plays a major role in drug resistance and disease progression. In the present study, we selected single-cell-derived cell lines (SCDCLs) derived from Lewis lung carcinoma (LLC1) cells to investigate tumorigenesis and heterogeneity. SCDCLs were generated using limiting dilution. Five SCDCLs were subcutaneously injected into wild-type C57BL/6N mice; however, they displayed significant differences in tumor growth. Subclone SCC1 grew the fastest in vivo, whereas it grew slower in vitro. The growth pattern of SCC2 was the opposite to that of SCC1. Genetic differences in these two subclones showed marked differences in cell adhesion and proliferation. Pathway enrichment results indicate that signal transduction and immune system responses were the most significantly altered functional categories in SCC2 cells compared to those in SCC1 cells in vitro. The number and activation of CD3+ and CD8+ T cells and NK cells in the tumor tissue of tumor-bearing mice inoculated with SCC2 were significantly higher, whereas those of myeloid cells were significantly lower, than those in the SCC1 and LLC1 groups. Our results suggest that the in vivo growth of two subclones derived from LLC1 was determined by the tumor microenvironment rather than their intrinsic proliferative cell characteristics.
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Affiliation(s)
- Ben-Ling Xu
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Xiao-Ming Wang
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Guang-Yu Chen
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Peng Yuan
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Lu Han
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Peng Qin
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Tie-Peng Li
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Hong-Qin You
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Cheng-Juan Zhang
- Center of Bio Repository, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Xiao-Min Fu
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Long Yuan
- Department of General Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Zi-Bing Wang
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
| | - Quan-Li Gao
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer HospitalZhengzhou 450008, Henan, P. R. China
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20
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Minegishi Y, Kiyotani K, Nemoto K, Inoue Y, Haga Y, Fujii R, Saichi N, Nagayama S, Ueda K. Differential ion mobility mass spectrometry in immunopeptidomics identifies neoantigens carrying colorectal cancer driver mutations. Commun Biol 2022; 5:831. [PMID: 35982173 PMCID: PMC9388627 DOI: 10.1038/s42003-022-03807-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/05/2022] [Indexed: 11/09/2022] Open
Abstract
Understanding the properties of human leukocyte antigen (HLA) peptides (immunopeptides) is essential for precision cancer medicine, while the direct identification of immunopeptides from small biopsies of clinical tissues by mass spectrometry (MS) is still confronted with technical challenges. Here, to overcome these hindrances, high-field asymmetric waveform ion mobility spectrometry (FAIMS) is introduced to conduct differential ion mobility (DIM)-MS by seamless gas-phase fractionation optimal for scarce samples. By established DIM-MS for immunopeptidomics analysis, on average, 42.9 mg of normal and tumor colorectal tissues from identical patients (n = 17) were analyzed, and on average 4921 immunopeptides were identified. Among these 44,815 unique immunopeptides, two neoantigens, KRAS-G12V and CPPED1-R228Q, were identified. These neoantigens were confirmed by synthetic peptides through targeted MS in parallel reaction monitoring (PRM) mode. Comparison of the tissue-based personal immunopeptidome revealed tumor-specific processing of immunopeptides. Since the direct identification of neoantigens from tumor tissues suggested that more potential neoantigens have yet to be identified, we screened cell lines with known oncogenic KRAS mutations and identified 2 more neoantigens that carry KRAS-G12V. These results indicated that the established FAIMS-assisted DIM-MS is effective in the identification of immunopeptides and potential recurrent neoantigens directly from scarce samples such as clinical tissues.
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Affiliation(s)
- Yuriko Minegishi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazuma Kiyotani
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensaku Nemoto
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Yoshimi Haga
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Risa Fujii
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Naomi Saichi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoshi Nagayama
- Development of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
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21
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Jia W, Zhang T, Huang H, Feng H, Wang S, Guo Z, Luo Z, Ji X, Cheng X, Zhao R. Colorectal cancer vaccines: The current scenario and future prospects. Front Immunol 2022; 13:942235. [PMID: 35990683 PMCID: PMC9384853 DOI: 10.3389/fimmu.2022.942235] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. Current therapies such as surgery, chemotherapy, and radiotherapy encounter obstacles in preventing metastasis of CRC even when applied in combination. Immune checkpoint inhibitors depict limited effects due to the limited cases of CRC patients with high microsatellite instability (MSI-H). Cancer vaccines are designed to trigger the elevation of tumor-infiltrated lymphocytes, resulting in the intense response of the immune system to tumor antigens. This review briefly summarizes different categories of CRC vaccines, demonstrates the current outcomes of relevant clinical trials, and provides particular focus on recent advances on nanovaccines and neoantigen vaccines, representing the trend and emphasis of CRC vaccine development.
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Affiliation(s)
- Wenqing Jia
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haiyan Huang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoran Feng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaodong Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zichao Guo
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiping Luo
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaopin Ji
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xiaopin Ji, ; Xi Cheng, ; Ren Zhao,
| | - Xi Cheng
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xiaopin Ji, ; Xi Cheng, ; Ren Zhao,
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Digestive surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Xiaopin Ji, ; Xi Cheng, ; Ren Zhao,
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22
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Song MH, Park JW, Kim MJ, Shin YK, Kim SC, Jeong SY, Ku JL. Colon cancer organoids using monoclonal organoids established in four different lesions of one cancer patient reveal tumor heterogeneity and different real-time responsiveness to anti-cancer drugs. Biomed Pharmacother 2022; 152:113260. [PMID: 35691158 DOI: 10.1016/j.biopha.2022.113260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/02/2022] Open
Abstract
Organoid culture technique has been taking center stage as a next-generation ex-vivo model due to advancement of stem cell research techniques. The importance of the laboratory-based ex vivo model has increasingly been recognized for recapitulating histological, and physioglocal conditions of in vivo microenviorment. Accordingly, the use of this technique has also broadened the understanding of intratumoral heterogeneity which is closely associated with varied drug responses observed in patients. Likewise, studies on heterogeneity within a single tumor tissue have drawn much attention. Here, we isolated 15 single clones from 4 tumor organoid lines from 1 patient at a primary passage from one patient. Each organoid line showed variable alterations in both genotype and phenotype. Furthermore, our methodological approach on drug test employing a high-throughput screening system enabled us to pinpoint the optimal time frame for anti-cancer drugs within a single tumor. We propose that our method can effectively reveal the heterogeneity of time-point in drug response, and the most optimal therapeutic strategies for individual patient.
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Affiliation(s)
- Myoung-Hyun Song
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; Cancer Research Institute, Seoul National University, Seoul 03080, South Korea
| | - Ji Won Park
- Cancer Research Institute, Seoul National University, Seoul 03080, South Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Min Jung Kim
- Cancer Research Institute, Seoul National University, Seoul 03080, South Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Young-Kyoung Shin
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Soon-Chan Kim
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; Cancer Research Institute, Seoul National University, Seoul 03080, South Korea; Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Seung-Yong Jeong
- Cancer Research Institute, Seoul National University, Seoul 03080, South Korea; Department of Surgery, Seoul National University College of Medicine, Seoul 03080, South Korea; Seoul National University Boramae Medical Center, Seoul 07061, South Korea.
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, South Korea; Cancer Research Institute, Seoul National University, Seoul 03080, South Korea; Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, South Korea.
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23
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Wang K, Jiang M, Zhou J, Dong Y, Liu Y, Zong Q, Sandbhor P, Singh NDP, Yuan Y. Spatial specific delivery of combinational chemotherapeutics to combat intratumoral heterogeneity. J Control Release 2022; 348:1004-1015. [PMID: 35779654 DOI: 10.1016/j.jconrel.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/16/2022] [Accepted: 06/25/2022] [Indexed: 10/17/2022]
Abstract
Hypoxia-induced intratumoral heterogeneity poses a major challenge in tumor therapy due to the varying susceptibility to chemotherapy. Moreover, the spatial distribution patterns of hypoxic and normoxic tissues makes conventional combination therapy less effective. In this study, a tumor-acidity and bioorthogonal chemistry mediated in situ size transformable nanocarrier (NP@DOXDBCO plus iCPPAN3) was developed to spatially deliver two combinational chemotherapeutic drugs (doxorubicin (DOX) and PR104A) to combat hypoxia-induced intratumoral heterogeneity. DOX is highly toxic to tumor cells in normoxia state but less toxic in hypoxia state due to the hypoxia-induced chemoresistance. Meanwhile, PR104A is a hypoxia-activated prodrug has less toxic in normoxia state. Two nanocarriers, NP@DOXDBCO and iCPPAN3, can cross-link near the blood vessel extravasation sites through tumor acidity responsive bioorthogonal click chemistry to enhance the retention of DOX in tumor normoxia. Moreover, PR104A conjugated to the small-sized dendritic polyamidoamine (PAMAM) released under tumor acidity can penetrate deep tumor tissues for hypoxic tumor cell killing. Our study has demonstrated that this site-specific combination chemotherapy is better than the traditional combination chemotherapy. Therefore, spatial specific delivery of combinational therapeutics via in situ size transformable nanocarrier addresses the challenges of hypoxia induced intratumoral heterogeneity and provides insights into the combination therapy.
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Affiliation(s)
- Kewei Wang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, PR China; National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, PR China
| | - Maolin Jiang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, PR China; National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, PR China
| | - Jielian Zhou
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, PR China; Guangdong Provincial Key Laboratory of Biomedical Engineering, South China University of Technology, Guangzhou 510006, PR China
| | - Yansong Dong
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, PR China; Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou 510006, PR China
| | - Ye Liu
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, PR China; Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou 510006, PR China
| | - Qingyu Zong
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, PR China; Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, South China University of Technology, Guangzhou 510006, PR China
| | - Puja Sandbhor
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, 400076, India
| | - N D Pradeep Singh
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Youyong Yuan
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou 511442, PR China; National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou 510006, PR China.
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24
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Sharifi-Azad M, Fathi M, Cho WC, Barzegari A, Dadashi H, Dadashpour M, Jahanban-Esfahlan R. Recent advances in targeted drug delivery systems for resistant colorectal cancer. Cancer Cell Int 2022; 22:196. [PMID: 35590367 PMCID: PMC9117978 DOI: 10.1186/s12935-022-02605-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/02/2022] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer (CRC) is one of the deadliest cancers in the world, the incidences and morality rate are rising and poses an important threat to the public health. It is known that multiple drug resistance (MDR) is one of the major obstacles in CRC treatment. Tumor microenvironment plus genomic instability, tumor derived exosomes (TDE), cancer stem cells (CSCs), circulating tumor cells (CTCs), cell-free DNA (cfDNA), as well as cellular signaling pathways are important issues regarding resistance. Since non-targeted therapy causes toxicity, diverse side effects, and undesired efficacy, targeted therapy with contribution of various carriers has been developed to address the mentioned shortcomings. In this paper the underlying causes of MDR and then various targeting strategies including exosomes, liposomes, hydrogels, cell-based carriers and theranostics which are utilized to overcome therapeutic resistance will be described. We also discuss implication of emerging approaches involving single cell approaches and computer-aided drug delivery with high potential for meeting CRC medical needs.
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Affiliation(s)
- Masoumeh Sharifi-Azad
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marziyeh Fathi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Abolfazl Barzegari
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Dadashi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Dadashpour
- Department of Medical Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran. .,Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran.
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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25
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Wang J, Chen C, Wang L, Xie M, Ge X, Wu S, He Y, Mou X, Ye C, Sun Y. Patient-Derived Tumor Organoids: New Progress and Opportunities to Facilitate Precision Cancer Immunotherapy. Front Oncol 2022; 12:872531. [PMID: 35449581 PMCID: PMC9016336 DOI: 10.3389/fonc.2022.872531] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/14/2022] [Indexed: 12/18/2022] Open
Abstract
Cancer immunotherapy has revolutionized the field of cancer treatment in recent years. However, not all patients receiving cancer immunotherapy exhibit durable responses, and reliable, high-throughput testing platforms are urgently needed to guide personalized cancer immunotherapy. The ability of patient-derived tumor organoids to recapitulate pivotal features of original cancer tissues makes them useful as a preclinical model for cancer research and precision medicine. Nevertheless, many challenges exist in the translation of tumor organoid research to clinical decision making. Herein we discuss the applications of patient-derived tumor organoid models and the advances and potential of using complex immune-organoid systems as testing platforms to facilitate precision cancer immunotherapy. In addition, we highlight intriguing applications of tumor organoids with novel multi-omics in preclinical cancer research, highlighting genetic editing, proteomics, and liquid biopsy.
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Affiliation(s)
- Ji Wang
- Center for Plastic & Reconstructive Surgery, Department of Plastic & Reconstructive Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Chao Chen
- Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Lu Wang
- Center for Plastic & Reconstructive Surgery, Department of Plastic & Reconstructive Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Mingjun Xie
- State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Materials Processing and Mold, Zhengzhou University, Zhengzhou, China
| | - Xinyang Ge
- College of Letters and Science, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sufan Wu
- Center for Plastic & Reconstructive Surgery, Department of Plastic & Reconstructive Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Yong He
- Cancer Center, Zhejiang University, Hangzhou, China.,State Key Laboratory of Fluid Power and Mechatronic Systems, School of Mechanical Engineering, Zhejiang University, Hangzhou, China.,Key Laboratory of Materials Processing and Mold, Zhengzhou University, Zhengzhou, China.,Key Laboratory of 3D Printing Process and Equipment of Zhejiang Province, College of Mechanical Engineering, Zhejiang University, Hangzhou, China
| | - Xiaozhou Mou
- Center for Plastic & Reconstructive Surgery, Department of Plastic & Reconstructive Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Chenyang Ye
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China.,Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Sun
- Center for Plastic & Reconstructive Surgery, Department of Plastic & Reconstructive Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
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26
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Nielsen M, Ternette N, Barra C. The interdependence of machine learning and LC-MS approaches for an unbiased understanding of the cellular immunopeptidome. Expert Rev Proteomics 2022; 19:77-88. [PMID: 35390265 DOI: 10.1080/14789450.2022.2064278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The comprehensive collection of peptides presented by Major Histocompatibility Complex (MHC) molecules on the cell surface is collectively known as the immunopeptidome. The analysis and interpretation of such data sets holds great promise for furthering our understanding of basic immunology and adaptive immune activation and regulation, and for direct rational discovery of T cell antigens and the design of T-cell based therapeutics and vaccines. These applications are however challenged by the complex nature of immunopeptidome data. AREAS COVERED Here, we describe the benefits and shortcomings of applying liquid chromatography-tandem mass spectrometry (MS) to obtain large scale immunopeptidome data sets and illustrate how the accurate analysis and optimal interpretation of such data is reliant on the availability of refined and highly optimized machine learning approaches. EXPERT OPINION Further we demonstrate how the accuracy of immunoinformatics prediction methods within the field of MHC antigen presentation has benefited greatly from the availability of MS-immunopeptidomics data, and exemplify how optimal antigen discovery is best performed in a synergistic combination of MS experiments and such in silico models trained on large scale immunopeptidomics data.
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Affiliation(s)
- Morten Nielsen
- Department of Health technology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Nicola Ternette
- Centre for Cellular and Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Carolina Barra
- Department of Health technology, Technical University of Denmark, DK-2800 Lyngby, Denmark
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27
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Wang Z, Zhao S, Lin X, Chen G, Kang J, Ma Z, Wang Y, Li Z, Xiao X, He A, Xiang D. Application of Organoids in Carcinogenesis Modeling and Tumor Vaccination. Front Oncol 2022; 12:855996. [PMID: 35371988 PMCID: PMC8968694 DOI: 10.3389/fonc.2022.855996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
Organoids well recapitulate organ-specific functions from their tissue of origin and remain fundamental aspects of organogenesis. Organoids are widely applied in biomedical research, drug discovery, and regenerative medicine. There are various cultivated organoid systems induced by adult stem cells and pluripotent stem cells, or directly derived from primary tissues. Researchers have drawn inspiration by combination of organoid technology and tissue engineering to produce organoids with more physiological relevance and suitable for translational medicine. This review describes the value of applying organoids for tumorigenesis modeling and tumor vaccination. We summarize the application of organoids in tumor precision medicine. Extant challenges that need to be conquered to make this technology be more feasible and precise are discussed.
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Affiliation(s)
- Zeyu Wang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shasha Zhao
- State Key Laboratory of Oncogenes and Related Genes, the Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaolin Lin
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guanglong Chen
- Department of General Surgery, Zhengzhou University, Affiliated Cancer Hospital (Henan Cancer Hospital), Zhengzhou, China
| | - Jiawei Kang
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | | | - Yiming Wang
- Shanghai OneTar Biomedicine, Shanghai, China
| | - Zhi Li
- Department of General Surgery, Zhengzhou University, Affiliated Cancer Hospital (Henan Cancer Hospital), Zhengzhou, China
| | - Xiuying Xiao
- Department of Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aina He
- Department of Oncology, The Sixth People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dongxi Xiang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biliary-Pancreatic Surgery, The Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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28
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Kim S, Park JW, Seo H, Kim M, Park J, Kim G, Lee JO, Shin Y, Bae JM, Koo B, Jeong S, Ku J. Multifocal Organoid Capturing of Colon Cancer Reveals Pervasive Intratumoral Heterogenous Drug Responses. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103360. [PMID: 34918496 PMCID: PMC8844556 DOI: 10.1002/advs.202103360] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Intratumor heterogeneity (ITH) stands as one of the main difficulties in the treatment of colorectal cancer (CRC) as it causes the development of resistant clones and leads to heterogeneous drug responses. Here, 12 sets of patient-derived organoids (PDOs) and cell lines (PDCs) isolated from multiple regions of single tumors from 12 patients, capturing ITH by multiregion sampling of individual tumors, are presented. Whole-exome sequencing and RNA sequencing of the 12 sets are performed. The PDOs and PDCs of the 12 sets are also analyzed with a clinically relevant 24-compound library to assess their drug responses. The results reveal unexpectedly widespread subregional heterogeneity among PDOs and PDCs isolated from a single tumor, which is manifested by genetic and transcriptional heterogeneity and strong variance in drug responses, while each PDO still recapitulates the major histologic, genomic, and transcriptomic characteristics of the primary tumor. The data suggest an imminent drawback of single biopsy-originated PDO-based clinical diagnosis in evaluating CRC patient responses. Instead, the results indicate the importance of targeting common somatic driver mutations positioned in the trunk of all tumor subregional clones in parallel with a comprehensive understanding of the molecular ITH of each tumor.
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Affiliation(s)
- Soon‐Chan Kim
- Korean Cell Line BankLaboratory of Cell BiologyCancer Research InstituteSeoul National University College of MedicineSeoul03080South Korea
- Department of Biomedical SciencesSeoul National University College of MedicineSeoul03080South Korea
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
- Ischemic/Hypoxic Disease InstituteSeoul National University College of MedicineSeoul03080South Korea
| | - Ji Won Park
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
- Department of SurgerySeoul National University College of MedicineSeoul03080South Korea
- Division of Colorectal SurgeryDepartment of SurgerySeoul National University HospitalSeoul03080South Korea
| | - Ha‐Young Seo
- Korean Cell Line BankLaboratory of Cell BiologyCancer Research InstituteSeoul National University College of MedicineSeoul03080South Korea
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
| | - Minjung Kim
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
- Department of SurgerySeoul National University College of MedicineSeoul03080South Korea
- Division of Colorectal SurgeryDepartment of SurgerySeoul National University HospitalSeoul03080South Korea
| | - Jae‐Hyeon Park
- Korean Cell Line BankLaboratory of Cell BiologyCancer Research InstituteSeoul National University College of MedicineSeoul03080South Korea
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
| | - Ga‐Hye Kim
- Korean Cell Line BankLaboratory of Cell BiologyCancer Research InstituteSeoul National University College of MedicineSeoul03080South Korea
- Department of Biomedical SciencesSeoul National University College of MedicineSeoul03080South Korea
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
| | - Ja Oh Lee
- Korean Cell Line BankLaboratory of Cell BiologyCancer Research InstituteSeoul National University College of MedicineSeoul03080South Korea
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
| | - Young‐Kyoung Shin
- Korean Cell Line BankLaboratory of Cell BiologyCancer Research InstituteSeoul National University College of MedicineSeoul03080South Korea
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
- Ischemic/Hypoxic Disease InstituteSeoul National University College of MedicineSeoul03080South Korea
| | - Jeong Mo Bae
- Department of PathologySeoul National University College of MedicineSeoul03080South Korea
| | - Bon‐Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
| | - Seung‐Yong Jeong
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
- Department of SurgerySeoul National University College of MedicineSeoul03080South Korea
- Division of Colorectal SurgeryDepartment of SurgerySeoul National University HospitalSeoul03080South Korea
| | - Ja‐Lok Ku
- Korean Cell Line BankLaboratory of Cell BiologyCancer Research InstituteSeoul National University College of MedicineSeoul03080South Korea
- Department of Biomedical SciencesSeoul National University College of MedicineSeoul03080South Korea
- Cancer Research InstituteSeoul National UniversitySeoul03080South Korea
- Ischemic/Hypoxic Disease InstituteSeoul National University College of MedicineSeoul03080South Korea
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29
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Wang J, Feng X, Li Z, Chen Y, Huang W. Patient-derived organoids as a model for tumor research. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 189:259-326. [PMID: 35595351 DOI: 10.1016/bs.pmbts.2022.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cancer represents a leading cause of death, despite the rapid progress of cancer research, leading to urgent need for accurate preclinical model to further study of tumor mechanism and accelerate translational applications. Cancer cell lines cannot fully recapitulate tumors of different patients due to the lack of tumor complexity and specification, while the high technical difficulty, long time, and substantial cost of patient-derived xenograft model makes it unable to be used extensively for all types of tumors and large-scale drug screening. Patient-derived organoids can be established rapidly with a high success rate from many tumors, and precisely replicate the key histopathological, genetic, and phenotypic features, as well as therapeutic response of patient tumor. Therefore, they are extensively used in cancer basic research, biobanking, disease modeling and precision medicine. The combinations of cancer organoids with other advanced technologies, such as 3D bio-printing, organ-on-a-chip, and CRISPR-Cas9, contributes to the more complete replication of complex tumor microenvironment and tumorigenesis. In this review, we discuss the various methods of the establishment and the application of patient-derived organoids in diverse tumors as well as the limitations and future prospects of these models. Further advances of tumor organoids are expected to bridge the huge gap between bench and bedside and provide the unprecedented opportunities to advance cancer research.
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Affiliation(s)
- Jia Wang
- The First Affiliated Hospital of Shantou University, Shantou University Medical College, Shantou, China
| | - Xiaoying Feng
- The First Affiliated Hospital of Shantou University, Shantou University Medical College, Shantou, China
| | - Zhichao Li
- Department of Urology, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China; Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, China; International Cancer Center of Shenzhen University, Shenzhen, China
| | - Yongsong Chen
- The First Affiliated Hospital of Shantou University, Shantou University Medical College, Shantou, China
| | - Weiren Huang
- The First Affiliated Hospital of Shantou University, Shantou University Medical College, Shantou, China; Department of Urology, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China; Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, China; International Cancer Center of Shenzhen University, Shenzhen, China; Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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30
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Yeoh Y, Low TY, Abu N, Lee PY. Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance. PeerJ 2021; 9:e12338. [PMID: 34733591 PMCID: PMC8544255 DOI: 10.7717/peerj.12338] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Resistance to anti-cancer treatments is a critical and widespread health issue that has brought serious impacts on lives, the economy and public policies. Mounting research has suggested that a selected spectrum of patients with advanced colorectal cancer (CRC) tend to respond poorly to both chemotherapeutic and targeted therapeutic regimens. Drug resistance in tumours can occur in an intrinsic or acquired manner, rendering cancer cells insensitive to the treatment of anti-cancer therapies. Multiple factors have been associated with drug resistance. The most well-established factors are the emergence of cancer stem cell-like properties and overexpression of ABC transporters that mediate drug efflux. Besides, there is emerging evidence that signalling pathways that modulate cell survival and drug metabolism play major roles in the maintenance of multidrug resistance in CRC. This article reviews drug resistance in CRC as a result of alterations in the MAPK, PI3K/PKB, Wnt/β-catenin and Notch pathways.
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Affiliation(s)
- Yeelon Yeoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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31
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Omenn GS, Lane L, Overall CM, Paik YK, Cristea IM, Corrales FJ, Lindskog C, Weintraub S, Roehrl MHA, Liu S, Bandeira N, Srivastava S, Chen YJ, Aebersold R, Moritz RL, Deutsch EW. Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. J Proteome Res 2021; 20:5227-5240. [PMID: 34670092 DOI: 10.1021/acs.jproteome.1c00590] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The 2021 Metrics of the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 357 (92.8%) of the 19 778 predicted proteins coded in the human genome, a gain of 483 since 2020 from reports throughout the world reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 478 to 1421. This represents remarkable progress on the proteome parts list. The utilization of proteomics in a broad array of biological and clinical studies likewise continues to expand with many important findings and effective integration with other omics platforms. We present highlights from the Immunopeptidomics, Glycoproteomics, Infectious Disease, Cardiovascular, Musculo-Skeletal, Liver, and Cancers B/D-HPP teams and from the Knowledgebase, Mass Spectrometry, Antibody Profiling, and Pathology resource pillars, as well as ethical considerations important to the clinical utilization of proteomics and protein biomarkers.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Young-Ki Paik
- Yonsei Proteome Research Center and Yonsei University, Seoul 03722, Korea
| | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | - Susan Weintraub
- University of Texas Health, San Antonio, San Antonio, Texas 78229-3900, United States
| | - Michael H A Roehrl
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | | | - Yu-Ju Chen
- National Taiwan University, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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32
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Stopfer L, D'Souza A, White F. 1,2,3, MHC: a review of mass-spectrometry-based immunopeptidomics methods for relative and absolute quantification of pMHCs. IMMUNO-ONCOLOGY TECHNOLOGY 2021; 11:100042. [PMID: 35756972 PMCID: PMC9216433 DOI: 10.1016/j.iotech.2021.100042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Quantitative mass-spectrometry-based methods to perform relative and absolute quantification of peptides in the immunopeptidome are growing in popularity as researchers aim to measure the dynamic nature of the peptide major histocompatibility complex repertoire and make copies-per-cell estimations of target antigens of interest. Multiple methods to carry out these experiments have been reported, each with unique advantages and limitations. This article describes existing methods and recent applications, offering guidance for improving quantitative accuracy and selecting an appropriate experimental set-up to maximize data quality and quantity.
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Affiliation(s)
- L.E. Stopfer
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA,Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, USA
| | - A.D. D'Souza
- Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, USA,Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, USA
| | - F.M. White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA,Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, USA,Correspondence to: Prof. Forest M. White, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Tel: 617-258-8949
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33
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Veninga V, Voest EE. Tumor organoids: Opportunities and challenges to guide precision medicine. Cancer Cell 2021; 39:1190-1201. [PMID: 34416168 DOI: 10.1016/j.ccell.2021.07.020] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 01/20/2023]
Abstract
Tumor organoids have been proposed as a model system for precision medicine. The ability of tumor organoids to retain characteristics of the original tumor makes them unique for cancer research on an individual patient level. Hence, the idea to use tumor organoids for clinical decision making and optimize patient outcome is tempting. In vitro responses of tumor organoids to a wide array of drugs have been positively correlated to patient responses. However, substantial challenges remain and prospective studies with large cohorts are highly needed before implementation in clinical cancer care can be considered. Because of their personalized characteristics and the immediate link with patient data, tumor organoids also have great potential in preclinical research. Here, we provide a critical overview of both clinical and preclinical advances using tumor organoids.
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Affiliation(s)
- Vivien Veninga
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Emile E Voest
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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34
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Hoek M, Demmers LC, Wu W, Heck AJR. Allotype-Specific Glycosylation and Cellular Localization of Human Leukocyte Antigen Class I Proteins. J Proteome Res 2021; 20:4518-4528. [PMID: 34415762 PMCID: PMC8419865 DOI: 10.1021/acs.jproteome.1c00466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Presentation of antigens
by human leukocyte antigen (HLA) complexes
at the cell surface is a key process in the immune response. The α-chain,
containing the peptide-binding groove, is one of the most polymorphic
proteins in the proteome. All HLA class I α-chains carry a conserved
N-glycosylation site, but little is known about its nature and function.
Here, we report an in-depth characterization of N-glycosylation features
of HLA class I molecules. We observe that different HLA-A α-chains
carry similar glycosylation, distinctly different from the HLA-B,
HLA-C, and HLA-F α-chains. Although HLA-A displays the broadest
variety of glycan characteristics, HLA-B α-chains carry mostly
mature glycans, and HLA-C and HLA-F α-chains carry predominantly
high-mannose glycans. We expected these glycosylation features to
be directly linked to cellular localization of the HLA complexes.
Indeed, analyzing HLA class I complexes from crude plasma and inner
membrane-enriched fractions confirmed that most HLA-B complexes can
be found at the plasma membrane, while most HLA-C and HLA-F molecules
reside in the endoplasmic reticulum and Golgi membrane, and HLA-A
molecules are more equally distributed over these cellular compartments.
This allotype-specific cellular distribution of HLA molecules should
be taken into account when analyzing peptide antigen presentation
by immunopeptidomics.
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Affiliation(s)
- Max Hoek
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
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35
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Zitvogel L, Perreault C, Finn OJ, Kroemer G. Beneficial autoimmunity improves cancer prognosis. Nat Rev Clin Oncol 2021; 18:591-602. [PMID: 33976418 DOI: 10.1038/s41571-021-00508-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2021] [Indexed: 02/06/2023]
Abstract
Many tumour antigens that do not arise from cancer cell-specific mutations are targets of humoral and cellular immunity despite their expression on non-malignant cells. Thus, in addition to the expected ability to detect mutations and stress-associated shifts in the immunoproteome and immunopeptidome (the sum of MHC class I-bound peptides) unique to malignant cells, the immune system also recognizes antigens expressed in non-malignant cells, which can result in autoimmune reactions against non-malignant cells from the tissue of origin. These autoimmune manifestations include, among others, vitiligo, thyroiditis and paraneoplastic syndromes, concurrent with melanoma, thyroid cancer and non-small-cell lung cancer, respectively. Importantly, despite the undesirable effects of these symptoms, such events can have prognostic value and correlate with favourable disease outcomes, suggesting 'beneficial autoimmunity'. Similarly, the occurrence of dermal and endocrine autoimmune adverse events in patients receiving immune-checkpoint inhibitors can have a positive predictive value for therapeutic outcomes. Neoplasias derived from stem cells deemed 'not essential' for survival (such as melanocytes, thyroid cells and most cells in sex-specific organs) have a particularly good prognosis, perhaps because the host can tolerate autoimmune reactions that destroy tumour cells at some cost to non-malignant tissues. In this Perspective, we discuss examples of spontaneous as well as therapy-induced autoimmunity that correlate with favourable disease outcomes and make a strong case in favour of this 'beneficial autoimmunity' being important not only in patients with advanced-stage disease but also in cancer immunosurveillance.
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Affiliation(s)
- Laurence Zitvogel
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France. .,Université Paris Saclay, Faculty of Medicine, Le Kremlin-Bicêtre, France. .,INSERM U1015, Gustave Roussy, Villejuif, France. .,Equipe labellisée par la Ligue contre le cancer, Villejuif, France. .,Center of Clinical Investigations in Biotherapies of Cancer (CICBT) BIOTHERIS, Villejuif, France. .,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Olivera J Finn
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Guido Kroemer
- Gustave Roussy Comprehensive Cancer Institute, Villejuif, France. .,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China. .,Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Institut Universitaire de France, Paris, France. .,Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France. .,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France. .,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.
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36
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Bauzá-Martinez J, Heck AJR, Wu W. HLA-B and cysteinylated ligands distinguish the antigen presentation landscape of extracellular vesicles. Commun Biol 2021; 4:825. [PMID: 34211107 PMCID: PMC8249458 DOI: 10.1038/s42003-021-02364-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles can modulate diverse processes ranging from proliferation and tissue repair, to chemo-resistance and cellular differentiation. With the advent of tissue and immunological targeting, extracellular vesicles are also increasingly viewed as promising vectors to deliver peptide-based cancer antigens to the human immune system. Despite the clinical relevance and therapeutic potential of such 'cell-free' approaches, the natural antigen presentation landscape exported in extracellular vesicles is still largely uncharted, due to the challenging nature of such preparations and analyses. In the context of therapeutic vesicle production, a critical evaluation of the similarity in vesicular antigen presentation is also urgently needed. In this work, we compared the HLA-I peptide ligandomes of extracellular vesicles against that of whole-cells of the same cell line. We found that extracellular vesicles not only over-represent HLA-B complexes and peptide ligands, but also cysteinylated peptides that may modulate immune responses. Collectively, these findings describe the pre-existing provision of vesicular HLA complexes that may be utilized to carry peptide vaccines, as well as the propensity for different peptide and post-translationally modified ligands to be presented, and will outline critical considerations in devising novel EV vaccination strategies.
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Affiliation(s)
- Julia Bauzá-Martinez
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands ,grid.4818.50000 0001 0791 5666Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Albert J. R. Heck
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands ,grid.4818.50000 0001 0791 5666Netherlands Proteomics Centre, Utrecht, The Netherlands
| | - Wei Wu
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands ,grid.4818.50000 0001 0791 5666Netherlands Proteomics Centre, Utrecht, The Netherlands
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37
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Zhou B, Gao Y, Zhang P, Chu Q. Acquired Resistance to Immune Checkpoint Blockades: The Underlying Mechanisms and Potential Strategies. Front Immunol 2021; 12:693609. [PMID: 34194441 PMCID: PMC8236848 DOI: 10.3389/fimmu.2021.693609] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/28/2021] [Indexed: 01/05/2023] Open
Abstract
The immune checkpoint blockade therapy has completely transformed cancer treatment modalities because of its unprecedented and durable clinical responses in various cancers. With the increasing use of immune checkpoint blockades in clinical practice, a large number of patients develop acquired resistance. However, the knowledge about acquired resistance to immune checkpoint blockades is limited and poorly summarized. In this review, we clarify the principal elements of acquired resistance to immune checkpoint blockades. The definition of acquired resistance is heterogeneous among groups or societies, but the expert consensus of The Society for Immunotherapy of Cancer can be referred. Oligo-progression is the main pattern of acquired resistance. Acquired resistance can be derived from the selection of resistant cancer cell clones that exist in the tumor mass before therapeutic intervention or gradual acquisition in the sensitive cancer cells. Specifically, tumor intrinsic mechanisms include neoantigen depletion, defects in antigen presentation machinery, aberrations of interferon signaling, tumor-induced exclusion/immunosuppression, and tumor cell plasticity. Tumor extrinsic mechanisms include upregulation of other immune checkpoints. Presently, a set of treatment modalities is applied to patients with similar clinical characteristics or resistance mechanisms for overcoming acquired resistance, and hence, further research is required.
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Affiliation(s)
- Binghan Zhou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Gao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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38
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Wood LD, Ewald AJ. Organoids in cancer research: a review for pathologist-scientists. J Pathol 2021; 254:395-404. [PMID: 33886125 DOI: 10.1002/path.5684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022]
Abstract
The use of three-dimensional (3D) culture models for cancer research has expanded greatly in recent years, with studies in almost every tumor type addressing a wide variety of research questions. Multiple distinct 3D culture approaches are now available, each with its own advantages and disadvantages, as well as most effective applications. In this review, we focus on one of these 3D culture models, organoids, in which multicellular units are isolated from primary or metastatic tumors and cultured in extracellular matrix gels. Organoids can be studied in acute cultures for short times after isolation, or passaged and biobanked for long-term use. We define this model system and describe some key studies in which organoid culture models were used to investigate cellular strategies and molecular mechanisms driving cancer initiation and progression, highlighting research questions for which this model is particularly well suited. In addition, as interest in implementing organoid systems continues to expand, we discuss key considerations in developing a new organoid research program. Our goal is to demonstrate the power and utility of organoid models and provide guidance for investigators who are considering implementation of these models in their own research programs. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Laura D Wood
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew J Ewald
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
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39
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Ma YS, Yang XL, Xin R, Wu TM, Shi Y, Dan Zhang D, Wang HM, Wang PY, Liu JB, Fu D. The power and the promise of organoid models for cancer precision medicine with next-generation functional diagnostics and pharmaceutical exploitation. Transl Oncol 2021; 14:101126. [PMID: 34020369 PMCID: PMC8144479 DOI: 10.1016/j.tranon.2021.101126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/25/2022] Open
Abstract
As organ-specific three-dimensional cell clusters derived from cancer tissue or cancer-specific stem cells, cancer-derived organoids are organized in the same manner of the cell sorting and spatial lineage restriction in vivo, making them ideal for simulating the characteristics of cancer and the heterogeneity of cancer cells in vivo. Besides the applications as a new in vitro model to study the physiological characteristics of normal tissues and organs, organoids are also used for in vivo cancer cell characterization, anti-cancer drug screening, and precision medicine. However, organoid cultures are not without limitations, i.e., the lack of nerves, blood vessels, and immune cells. As a result, organoids could not fully replicate the characteristics of organs but partially simulate the disease process. This review attempts to provide insights into the organoid models for cancer precision medicine.
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Affiliation(s)
- Yu-Shui Ma
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Cancer Institute, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong 226631, China; International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, National Center for Liver Cancer, the Second Military Medical University, Shanghai 200433, China
| | - Xiao-Li Yang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Rui Xin
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Ting-Miao Wu
- Department of Radiology, The Forth Affiliated Hospital of Anhui Medical University, Hefei 230012, China
| | - Yi Shi
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Dan Dan Zhang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hui-Min Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Pei-Yao Wang
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Ji-Bin Liu
- Cancer Institute, Nantong Tumor Hospital, Affiliated Tumor Hospital of Nantong University, Nantong 226631, China
| | - Da Fu
- National Engineering Laboratory for Deep Process of Rice and Byproducts, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China; Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Department of Radiology, The Forth Affiliated Hospital of Anhui Medical University, Hefei 230012, China.
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40
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Demmers LC, Wu W, Heck AJR. HLA Class II Presentation Is Specifically Altered at Elevated Temperatures in the B-Lymphoblastic Cell Line JY. Mol Cell Proteomics 2021; 20:100089. [PMID: 33933681 PMCID: PMC8724904 DOI: 10.1016/j.mcpro.2021.100089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/25/2021] [Accepted: 04/13/2021] [Indexed: 12/22/2022] Open
Abstract
Human leukocyte antigen (HLA) molecules play critical roles in our adaptive immune system by signaling a cell's health status to the immune system, through presentation of small peptides. Understanding HLA biology is important because of its prominent role in autoimmune diseases and cancer immunotherapy. Although both the HLA class I and class II antigen processing and presentation pathways have been studied extensively, the fundamental rules in HLA class II antigen presentation still remain less understood. To clarify the mechanistic and adaptive differences between the HLA systems, we challenged a B lymphoblastic cell line (JY), widely used as model system in studying antigen presentation, with a high temperature treatment to mimic a "fever-like state", representing one of the most common physiological responses to infection. In the absence of real invading pathogenic peptides to present, we could focus on delineating the intrinsic HLA pathway adaptations in response to high temperature in this particular cell line. Following a three-pronged approach, we performed quantitative analyses of the proteome, the HLA class I ligandome, as well as the HLA class II ligandome. The data reveals that elevated temperature may already prepare these cells for an immune-like response through increased HLA class II presentation capacity and specific release of, from the invariant chain originating, CLIP peptides. Interestingly, at high temperature, prominent changes in the composition of the CLIP repertoire were observed, with enrichment of peptides containing C-terminal extensions beyond the CLIP-core region. Collectively, these illustrate intriguing temperature sensitive adaptations in this B cell line.
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Affiliation(s)
- Laura C Demmers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands; Netherlands Proteomics Centre, Utrecht, Netherlands.
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