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Sim MJW, Hanada KI, Stotz Z, Yu Z, Lu J, Brennan P, Quastel M, Gillespie GM, Long EO, Yang JC, Sun PD. Identification and structural characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3. Eur J Immunol 2024:e2451079. [PMID: 39030753 DOI: 10.1002/eji.202451079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/22/2024]
Abstract
Mutations in KRAS are some of the most common across multiple cancer types and are thus attractive targets for therapy. Recent studies demonstrated that mutant KRAS generates immunogenic neoantigens that are targetable by adoptive T-cell therapy in metastatic diseases. To expand mutant KRAS-specific immunotherapies, it is critical to identify additional HLA-I allotypes that can present KRAS neoantigens and their cognate T-cell receptors (TCR). Here, we identified a murine TCR specific to a KRAS-G12V neoantigen (7VVVGAVGVGK16) using a vaccination approach with transgenic mice expressing HLA-A*03:01 (HLA-A3). This TCR demonstrated exquisite specificity for mutant G12V and not WT KRAS peptides. To investigate the molecular basis for neoantigen recognition by this TCR, we determined its structure in complex with HLA-A3(G12V). G12V-TCR CDR3β and CDR1β formed a hydrophobic pocket to interact with p6 Val of the G12V but not the WT KRAS peptide. To improve the tumor sensitivity of this TCR, we designed rational substitutions to improve TCR:HLA-A3 contacts. Two substitutions exhibited modest improvements in TCR binding avidity to HLA-A3 (G12V) but did not sufficiently improve T-cell sensitivity for further clinical development. Our study provides mechanistic insight into how TCRs detect neoantigens and reveals the challenges in targeting KRAS-G12V mutations.
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Affiliation(s)
- Malcolm J W Sim
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Zachary Stotz
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, NCI, NIH, Bethesda, Maryland, USA
| | - Jinghua Lu
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Paul Brennan
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Max Quastel
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Eric O Long
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - James C Yang
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Peter D Sun
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
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2
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Torres-Jiménez J, Espinar JB, de Cabo HB, Berjaga MZ, Esteban-Villarrubia J, Fraile JZ, Paz-Ares L. Targeting KRAS G12C in Non-Small-Cell Lung Cancer: Current Standards and Developments. Drugs 2024; 84:527-548. [PMID: 38625662 DOI: 10.1007/s40265-024-02030-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2024] [Indexed: 04/17/2024]
Abstract
Among the most common molecular alterations detected in non-small-cell lung cancer (NSCLC) are mutations in Kristen Rat Sarcoma viral oncogene homolog (KRAS). KRAS mutant NSCLC is a heterogenous group of diseases, different from other oncogene-driven tumors in terms of biology and response to therapies. Despite efforts to develop drugs aimed at inhibiting KRAS or its signaling pathways, KRAS had remained undruggable for decades. The discovery of a small pocket in the binding switch II region of KRASG12C has revolutionized the treatment of KRASG12C-mutated NSCLC patients. Sotorasib and adagrasib, direct KRASG12C inhibitors, have been approved by the US Food and Drug Administration (FDA) and other regulatory agencies for patients with previously treated KRASG12C-mutated NSCLC, and these advances have become practice changing. However, first-line treatment in KRASG12C-mutated NSCLC does not differ from NSCLC without actionable driver genomic alterations. Treatment with KRASG12C inhibitors is not curative and patients develop progressive disease, so understanding associated mechanisms of drug resistance is key. New KRASG12C inhibitors and several combination therapy strategies, including with immune checkpoint inhibitors, are being studied in clinical trials. The aim of this review is to explore the clinical impact of KRAS, and outline different treatment approaches, focusing on the novel treatment of KRASG12C-mutated NSCLC.
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Affiliation(s)
- Javier Torres-Jiménez
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain.
| | - Javier Baena Espinar
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
| | - Helena Bote de Cabo
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
| | - María Zurera Berjaga
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
| | - Jorge Esteban-Villarrubia
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
| | - Jon Zugazagoitia Fraile
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Lung Cancer Group, Clinical Research Program, CNIO (Centro Nacional de Investigaciones Oncológicas) and Instituto de Investigación i+12, Madrid, Spain
| | - Luis Paz-Ares
- Medical Oncology Department, Hospital Universitario 12 de Octubre, Avda de Córdoba s/n, 28041, Madrid, Spain
- Lung Cancer Group, Clinical Research Program, CNIO (Centro Nacional de Investigaciones Oncológicas) and Instituto de Investigación i+12, Madrid, Spain
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3
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Zhang M, Xu W, Luo L, Guan F, Wang X, Zhu P, Zhang J, Zhou X, Wang F, Ye S. Identification and affinity enhancement of T-cell receptor targeting a KRAS G12V cancer neoantigen. Commun Biol 2024; 7:512. [PMID: 38684865 PMCID: PMC11058820 DOI: 10.1038/s42003-024-06209-2] [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: 10/31/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Neoantigens derived from somatic mutations in Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS), the most frequently mutated oncogene, represent promising targets for cancer immunotherapy. Recent research highlights the potential role of human leukocyte antigen (HLA) allele A*11:01 in presenting these altered KRAS variants to the immune system. In this study, we successfully generate and identify murine T-cell receptors (TCRs) that specifically recognize KRAS8-16G12V from three predicted high affinity peptides. By determining the structure of the tumor-specific 4TCR2 bound to KRASG12V-HLA-A*11:01, we conduct structure-based design to create and evaluate TCR variants with markedly enhanced affinity, up to 15.8-fold. This high-affinity TCR mutant, which involved only two amino acid substitutions, display minimal conformational alterations while maintaining a high degree of specificity for the KRASG12V peptide. Our research unveils the molecular mechanisms governing TCR recognition towards KRASG12V neoantigen and yields a range of affinity-enhanced TCR mutants with significant potential for immunotherapy strategies targeting tumors harboring the KRASG12V mutation.
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Affiliation(s)
- Mengyu Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Wei Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing, 100049, China
| | - Lingjie Luo
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Fenghui Guan
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xiangyao Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Pei Zhu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Jianhua Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing, 100049, China
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing, 100049, China.
| | - Feng Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China.
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Nussinov R, Jang H. Direct K-Ras Inhibitors to Treat Cancers: Progress, New Insights, and Approaches to Treat Resistance. Annu Rev Pharmacol Toxicol 2024; 64:231-253. [PMID: 37524384 DOI: 10.1146/annurev-pharmtox-022823-113946] [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] [Indexed: 08/02/2023]
Abstract
Here we discuss approaches to K-Ras inhibition and drug resistance scenarios. A breakthrough offered a covalent drug against K-RasG12C. Subsequent innovations harnessed same-allele drug combinations, as well as cotargeting K-RasG12C with a companion drug to upstream regulators or downstream kinases. However, primary, adaptive, and acquired resistance inevitably emerge. The preexisting mutation load can explain how even exceedingly rare mutations with unobservable effects can promote drug resistance, seeding growth of insensitive cell clones, and proliferation. Statistics confirm the expectation that most resistance-related mutations are in cis, pointing to the high probability of cooperative, same-allele effects. In addition to targeted Ras inhibitors and drug combinations, bifunctional molecules and innovative tri-complex inhibitors to target Ras mutants are also under development. Since the identities and potential contributions of preexisting and evolving mutations are unknown, selecting a pharmacologic combination is taxing. Collectively, our broad review outlines considerations and provides new insights into pharmacology and resistance.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA;
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA;
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Zhu Y, Li X, Chen T, Wang J, Zhou Y, Mu X, Du Y, Wang J, Tang J, Liu J. Personalised neoantigen-based therapy in colorectal cancer. Clin Transl Med 2023; 13:e1461. [PMID: 37921274 PMCID: PMC10623652 DOI: 10.1002/ctm2.1461] [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: 03/08/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Colorectal cancer (CRC) has become one of the most common tumours with high morbidity, mortality and distinctive evolution mechanism. The neoantigens arising from the somatic mutations have become considerable treatment targets in the management of CRC. As cancer-specific aberrant peptides, neoantigens can trigger the robust host immune response and exert anti-tumour effects while minimising the emergence of adverse events commonly associated with alternative therapeutic regimens. In this review, we summarised the mechanism, generation, identification and prognostic significance of neoantigens, as well as therapeutic strategies challenges of neoantigen-based therapy in CRC. The evidence suggests that the establishment of personalised neoantigen-based therapy holds great promise as an effective treatment approach for patients with CRC.
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Affiliation(s)
- Ya‐Juan Zhu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiong Li
- Department of GastroenterologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Ting‐Ting Chen
- The Second Clinical Medical College of Lanzhou UniversityLanzhouChina
| | - Jia‐Xiang Wang
- Department of Renal Cancer and MelanomaPeking University Cancer Hospital & InstituteBeijingChina
| | - Yi‐Xin Zhou
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiao‐Li Mu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Du
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jia‐Ling Wang
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jie Tang
- Clinical Trial CenterWest China HospitalSichuan UniversityChengduChina
| | - Ji‐Yan Liu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
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6
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Lam KK, Wong SH, Cheah PY. Targeting the 'Undruggable' Driver Protein, KRAS, in Epithelial Cancers: Current Perspective. Cells 2023; 12:cells12040631. [PMID: 36831298 PMCID: PMC9954350 DOI: 10.3390/cells12040631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
This review summarizes recent development in synthetic drugs and biologics targeting intracellular driver genes in epithelial cancers, focusing on KRAS, and provides a current perspective and potential leads for the field. Compared to biologics, small molecule inhibitors (SMIs) readily penetrate cells, thus being able to target intracellular proteins. However, SMIs frequently suffer from pleiotropic effects, off-target cytotoxicity and invariably elicit resistance. In contrast, biologics are much larger molecules limited by cellular entry, but if this is surmounted, they may have more specific effects and less therapy-induced resistance. Exciting breakthroughs in the past two years include engineering of non-covalent KRAS G12D-specific inhibitor, probody bispecific antibodies, drug-peptide conjugate as MHC-restricted neoantigen to prompt immune response by T-cells, and success in the adoptive cell therapy front in both breast and pancreatic cancers.
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Affiliation(s)
- Kuen Kuen Lam
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169856, Singapore
| | | | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169856, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
- Correspondence:
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7
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Wang J, Song J, Liu Z, Zhang T, Liu Y. High tumor mutation burden indicates better prognosis in colorectal cancer patients with KRAS mutations. Front Oncol 2022; 12:1015308. [PMID: 36452508 PMCID: PMC9702324 DOI: 10.3389/fonc.2022.1015308] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/10/2022] [Indexed: 08/20/2023] Open
Abstract
OBJECTIVE Colorectal cancer (CRC) is a common type of malignant tumor of the digestive tract. Tumor mutation burden (TMB) is a potential prognostic indicator of numerous malignant tumors. This study investigated the prognostic value of TMB in CRC. METHODS This study analyzed the clinical and somatic mutation data of patients with CRC from the Memorial Sloan Kettering Cancer Center (MSKCC) and The Cancer Genome Atlas (TCGA) cohorts. The genetic landscape was visualized using the maftools package in R software. Survival curves were constructed using the Kaplan-Meier method, and Cox regression analysis was performed to confirm that TMB is an independent prognostic indicator. A nomogram was developed to construct the prognostic model, which was evaluated using the C-index, calibration curve, and decision curve analysis. RESULTS In patients with CRC, APC mutations indicated longer overall survival (OS), whereas KRAS mutations indicated shorter OS. For all included patients, there was no significant difference in the OS between the TMB-high and TMB-low groups. For patients with KRAS mutations, the OS in the TMB-high group was longer than that in the TMB-low group. Cox regression analysis showed that TMB was an independent prognostic factor in CRC patients with KRAS mutations. This explains the good accuracy of the nomogram prognostic model using TMB and indicates its good prospect in clinical applications. CONCLUSIONS A high TMB indicates better prognosis in CRC patients with KRAS mutations, thus confirming the value of TMB in clinical applications.
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Affiliation(s)
- Jianlei Wang
- Department of Organ Transplantation, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jianping Song
- Department of General Surgery, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Zeyang Liu
- Department of Organ Transplantation, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Tingxiao Zhang
- Department of Organ Transplantation, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yanfeng Liu
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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[Preclinical study of T cell receptor specifically reactive with KRAS G12V mutation in the treatment of malignant tumors]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2022; 54. [PMID: 36241231 PMCID: PMC9568380 DOI: 10.19723/j.issn.1671-167x.2022.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVE KRAS gene is one of the most common mutations of proto-oncogenes in human tumors, G12V is one of the most common mutation types for KRAS. It's challenging to chemically acquire the targeted drug for this mutation. Recent studies reported that this mutation peptides can form a neoepitope for T cell recognition. Our study aims to clone the T cell receptor (TCR) which specifically recognizes the neoepitope for KRAS G12V mutation and constructs TCR engineered T cells (TCR-T), and to investigate if TCR-Ts have strong antitumor response ability. METHODS In this study, tumor infiltrating lymphocytes were obtained from one colorectal cancer patient carrying KRAS G12V mutation. Tumor-reactive TCR was obtained by single-cell RT-5' rapid-amplification of cDNA ends PCR analysis and introduced into peripheral blood lymphocytes to generate TCR-Ts. RESULTS We obtained a high-affinity TCR sequence that specifically recognized the HLA-A*11:01-restricted KRAS G12V8-16 epitope: KVA11-01. KVA11-01 TCR-T could significantly kill various tumor cells such as PANC-1, SW480 and HeLa (overexpressing HLA-A*11:01 and KRAS G12V), and secreting high levels of interferon-γ (IFN-γ). Non-specific killing experiments suggested KVA11-01 specifically recognized tumor cells expressing both mutant KRAS G12V and HLA-A*11:01. In vivo assay, tumor inhibition experiments demonstrated that infusion of approximately 1E7 KVA11-01 TCR-T could significantly inhibit the growth of subcuta-neously transplanted tumors of PANC-1 and HeLa (overexpressing HLA-A*11:01 and KRAS G12V) cells in nude mice. No destruction of the morphologies of the liver, spleen and brain were observed. We also found that KVA11-01 TCR-T could significantly infiltrate into tumor tissue and had a better homing ability. CONCLUSION KVA11-01 TCR-T cells can effectively target a variety of malignant tumor cells carrying KRAS G12V mutation through in vitro and in vivo assay. KVA11-01 TCR-T cells have excellent biological activity, high specificity of target antigen and homing ability into solid tumor tissue. KVA11-01 TCR-T is expected to be an effective treatment for patients with KRAS G12V mutant solid malignancies.
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Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen. Nat Commun 2022; 13:5333. [PMID: 36088370 PMCID: PMC9464187 DOI: 10.1038/s41467-022-32811-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
Neoantigens derived from somatic mutations are specific to cancer cells and are ideal targets for cancer immunotherapy. KRAS is the most frequently mutated oncogene and drives the pathogenesis of several cancers. Here we show the identification and development of an affinity-enhanced T cell receptor (TCR) that recognizes a peptide derived from the most common KRAS mutant, KRASG12D, presented in the context of HLA-A*11:01. The affinity of the engineered TCR is increased by over one million-fold yet fully able to distinguish KRASG12D over KRASWT. While crystal structures reveal few discernible differences in TCR interactions with KRASWT versus KRASG12D, thermodynamic analysis and molecular dynamics simulations reveal that TCR specificity is driven by differences in indirect electrostatic interactions. The affinity enhanced TCR, fused to a humanized anti-CD3 scFv, enables selective killing of cancer cells expressing KRASG12D. Our work thus reveals a molecular mechanism that drives TCR selectivity and describes a soluble bispecific molecule with therapeutic potential against cancers harboring a common shared neoantigen. Cancers often harbor mutations in genes encoding important regulatory proteins, but therapeutic targeting of these molecules proves difficult due to their high structural similarity to their non-mutated counterpart. Here authors show the engineering of T cell engaging bispecific protein able to selectively target cancer cells with a high-frequency mutation in the KRAS oncogene.
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10
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Mutant RAS and the tumor microenvironment as dual therapeutic targets for advanced colorectal cancer. Cancer Treat Rev 2022; 109:102433. [PMID: 35905558 DOI: 10.1016/j.ctrv.2022.102433] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022]
Abstract
RAS genes are the most frequently mutated oncogenes in cancer. These mutations occur in roughly half of the patients with colorectal cancer (CRC). RAS mutant tumors are resistant to therapy with anti-EGFR monoclonal antibodies. Therefore, patients with RAS mutant CRC currently have few effective therapy options. RAS mutations lead to constitutively active RAS GTPases, involved in multiple downstream signaling pathways. These alterations are associated with a tumor microenvironment (TME) that drives immune evasion and disease progression by mechanisms that remain incompletely understood. In this review, we focus on the available evidence in the literature explaining the potential effects of RAS mutations on the CRC microenvironment. Ongoing efforts to influence the TME by targeting mutant RAS and thereby sensitizing these tumors to immunotherapy will be discussed as well.
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Corral de la Fuente E, Olmedo Garcia ME, Gomez Rueda A, Lage Y, Garrido P. Targeting KRAS in Non-Small Cell Lung Cancer. Front Oncol 2022; 11:792635. [PMID: 35083149 PMCID: PMC8784727 DOI: 10.3389/fonc.2021.792635] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/13/2021] [Indexed: 12/12/2022] Open
Abstract
Kirsten Rat Sarcoma viral oncogene homolog (KRAS) is the most frequently altered oncogene in Non-Small Cell Lung Cancer (NSCLC). KRAS mutant tumors constitute a heterogeneous group of diseases, different from other oncogene-derived tumors in terms of biology and response to treatment, which hinders the development of effective drugs against KRAS. Therefore, for decades, despite enormous efforts invested in the development of drugs aimed at inhibiting KRAS or its signaling pathways, KRAS was considered to be undruggable. Recently, the discovery of a new pocket under the effector binding switch II region of KRAS G12C has allowed the development of direct KRAS inhibitors such as sotorasib, the first FDA-approved drug targeting KRAS G12C, or adagrasib, initiating a new exciting era. However, treatment with targeted KRAS G12C inhibitors also leads to resistance, and understanding the possible mechanisms of resistance and which drugs could be useful to overcome it is key. Among others, KRAS G12C (ON) tricomplex inhibitors and different combination therapy strategies are being analyzed in clinical trials. Another area of interest is the potential role of co-mutations in treatment selection, particularly immunotherapy. The best first-line strategy remains to be determined and, due to the heterogeneity of KRAS, is likely to be based on combination therapies.
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Affiliation(s)
- Elena Corral de la Fuente
- Early Phase Clinical Drug Development in Oncology, South Texas Accelerated Research Therapeutics (START) Madrid-Centro Integral Oncológico Clara Campal (CIOCC), Centro Integral Oncológico Clara Campal, Madrid, Spain
| | | | - Ana Gomez Rueda
- Department of Medical Oncology, Ramón y Cajal University Hospital, Madrid, Spain
| | - Yolanda Lage
- Department of Medical Oncology, Ramón y Cajal University Hospital, Madrid, Spain
| | - Pilar Garrido
- Department of Medical Oncology, Ramón y Cajal University Hospital, Madrid, Spain
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Hofmann MH, Gerlach D, Misale S, Petronczki M, Kraut N. Expanding the Reach of Precision Oncology by Drugging All KRAS Mutants. Cancer Discov 2022; 12:924-937. [DOI: 10.1158/2159-8290.cd-21-1331] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/12/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022]
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13
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Nussinov R, Zhang M, Maloney R, Tsai CJ, Yavuz BR, Tuncbag N, Jang H. Mechanism of activation and the rewired network: New drug design concepts. Med Res Rev 2021; 42:770-799. [PMID: 34693559 PMCID: PMC8837674 DOI: 10.1002/med.21863] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022]
Abstract
Precision oncology benefits from effective early phase drug discovery decisions. Recently, drugging inactive protein conformations has shown impressive successes, raising the cardinal questions of which targets can profit and what are the principles of the active/inactive protein pharmacology. Cancer driver mutations have been established to mimic the protein activation mechanism. We suggest that the decision whether to target an inactive (or active) conformation should largely rest on the protein mechanism of activation. We next discuss the recent identification of double (multiple) same-allele driver mutations and their impact on cell proliferation and suggest that like single driver mutations, double drivers also mimic the mechanism of activation. We further suggest that the structural perturbations of double (multiple) in cis mutations may reveal new surfaces/pockets for drug design. Finally, we underscore the preeminent role of the cellular network which is deregulated in cancer. Our structure-based review and outlook updates the traditional Mechanism of Action, informs decisions, and calls attention to the intrinsic activation mechanism of the target protein and the rewired tumor-specific network, ushering innovative considerations in precision medicine.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mingzhen Zhang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Ryan Maloney
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
| | - Bengi Ruken Yavuz
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Nurcan Tuncbag
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey.,Department of Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.,Koc University Research Center for Translational Medicine, School of Medicine, Koc University, Istanbul, Turkey
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, Maryland, USA
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14
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Choi J, Goulding SP, Conn BP, McGann CD, Dietze JL, Kohler J, Lenkala D, Boudot A, Rothenberg DA, Turcott PJ, Srouji JR, Foley KC, Rooney MS, van Buuren MM, Gaynor RB, Abelin JG, Addona TA, Juneja VR. Systematic discovery and validation of T cell targets directed against oncogenic KRAS mutations. CELL REPORTS METHODS 2021; 1:100084. [PMID: 35474673 PMCID: PMC9017224 DOI: 10.1016/j.crmeth.2021.100084] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 08/04/2021] [Accepted: 08/20/2021] [Indexed: 12/27/2022]
Abstract
Oncogenic mutations in KRAS can be recognized by T cells on specific class I human leukocyte antigen (HLA-I) molecules, leading to tumor control. To date, the discovery of T cell targets from KRAS mutations has relied on occasional T cell responses in patient samples or the use of transgenic mice. To overcome these limitations, we have developed a systematic target discovery and validation pipeline. We evaluate the presentation of mutant KRAS peptides on individual HLA-I molecules using targeted mass spectrometry and identify 13 unpublished KRASG12C/D/R/V mutation/HLA-I pairs and nine previously described pairs. We assess immunogenicity, generating T cell responses to nearly all targets. Using cytotoxicity assays, we demonstrate that KRAS-specific T cells and T cell receptors specifically recognize endogenous KRAS mutations. The discovery and validation of T cell targets from KRAS mutations demonstrate the potential for this pipeline to aid the development of immunotherapies for important cancer targets.
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Affiliation(s)
- Jaewon Choi
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - Scott P. Goulding
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - Brandon P. Conn
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | | | - Jared L. Dietze
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - Jessica Kohler
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - Divya Lenkala
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - Antoine Boudot
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | | | - Paul J. Turcott
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - John R. Srouji
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - Kendra C. Foley
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - Michael S. Rooney
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | | | - Richard B. Gaynor
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | | | - Terri A. Addona
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
| | - Vikram R. Juneja
- BioNTech US Inc., 40 Erie Street, Suite 110, Cambridge, MA 02139, USA
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15
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Zhao X, Pan X, Wang Y, Zhang Y. Targeting neoantigens for cancer immunotherapy. Biomark Res 2021; 9:61. [PMID: 34321091 PMCID: PMC8317330 DOI: 10.1186/s40364-021-00315-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
Neoantigens, a type of tumor-specific antigens derived from non-synonymous mutations, have recently been characterized as attractive targets for cancer immunotherapy. Owing to the development of next-generation sequencing and utilization of machine-learning algorithms, it has become feasible to computationally predict neoantigens by depicting genetic alterations, aberrant post-transcriptional mRNA processing and abnormal mRNA translation events within tumor tissues. Consequently, neoantigen-based therapies such as cancer vaccines have been widely tested in clinical trials and have demonstrated promising safety and efficacy, opening a new era for cancer immunotherapy. We systematically summarize recent advances in the identification of both personalized and public neoantigens, neoantigen formulations and neoantigen-based clinical trials in this review. Moreover, we discuss future techniques and strategies for neoantigen-based cancer treatment either as a monotherapy or as a combination therapy with radiotherapy, chemotherapy or immune checkpoint inhibitors.
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Affiliation(s)
- Xuan Zhao
- Biotherapy Center & Cancer Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 450052, Zhengzhou, China
| | - Xiaoxin Pan
- Shenzhen NeoCura Biotechnology Corporation, 518055, Shenzhen, China
| | - Yi Wang
- Shenzhen NeoCura Biotechnology Corporation, 518055, Shenzhen, China
| | - Yi Zhang
- Biotherapy Center & Cancer Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China. .,State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, 450052, Zhengzhou, China. .,School of Life Sciences, Zhengzhou University, 450052, Zhengzhou, China. .,Henan Key Laboratory for Tumor Immunology and Biotherapy, 450052, Zhengzhou, China.
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16
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Aldahlawi AM, Abdullah ST. Dendritic Cell-Based Immunotherapies and their Potential use in Colorectal Cancer Immunotherapy. J Microsc Ultrastruct 2021; 10:107-113. [PMID: 36504589 PMCID: PMC9728090 DOI: 10.4103/jmau.jmau_20_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022] Open
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells, which are resident or proliferating in organs. Major histocompatibility complex (MHC) Class I and II on DCs in normal steady conditions process and present antigens including cancer antigens. Many approaches are used to enhance antigen presentation process of DCs and capture cancer cells. DCs are harvested from cancer patients and manipulated ex vivo in DC-based cancer immunotherapy. In addition, DCs' vaccines and other anticancer therapy combinations were discussed to optimize DCs' efficiency for cancer immunotherapy. This review addressed the use of the human conventional type-1 DCs, OX40+ plasmacytoid DCs, and DCs-derived exosomes. In addition, different combinations with DCs therapy such as combination with the monoclonal antibody, cytokine-induced killer cells, adjuvants, chemotherapy (DCs-based chemoimmunotherapy), and nanoparticles were listed and explored for their effectiveness against cancer, and mainly against colorectal cancer.
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Affiliation(s)
- Alia M. Aldahlawi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia,Immunology Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Samaa Taha Abdullah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia,Address for correspondence: Dr. Samaa Taha Abdullah, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia. E-mail:
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17
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Dillard P, Casey N, Pollmann S, Vernhoff P, Gaudernack G, Kvalheim G, Wälchli S, Inderberg EM. Targeting KRAS mutations with HLA class II-restricted TCRs for the treatment of solid tumors. Oncoimmunology 2021; 10:1936757. [PMID: 34235003 PMCID: PMC8216182 DOI: 10.1080/2162402x.2021.1936757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
T-cell receptor (TCR) redirected T cells are considered as the next generation of care for the treatment of numerous solid tumors. KRAS mutations are driver neoantigens that are expressed in over 25% of all cancers and are thus regarded as ideal targets for Adoptive Cell Therapy (ACT). We have isolated four KRAS-specific TCRs from a long-term surviving pancreatic cancer patient vaccinated with a mix of mutated KRAS peptides. The sequence of these TCRs could be identified and expressed in primary cells. We demonstrated stable expression of all TCRs as well as target-specific functionality when expressing T cells were co-incubated with target cells presenting KRAS peptides. In addition, these TCRs were all partially co-receptor independent since they were functional in both CD4 and CD8 T cells, thus indicating high affinity. Interestingly, we observed that certain TCRs were able to recognize several KRAS mutations in complex with their cognate Human leukocyte antigen (HLA), suggesting that, here, the point mutations were less important for the HLA binding and TCR recognition, whereas others were single-mutation restricted. Finally, we demonstrated that these peptides were indeed processed and presented, since HLA-matched antigen presenting cells exogenously loaded with KRAS proteins were recognized by TCR-transduced T cells. Taken together, our data demonstrate that KRAS mutations are immunogenic for CD4 T cells and are interesting targets for TCR-based cancer immunotherapy.
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Affiliation(s)
- Pierre Dillard
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, Oslo, Norway
| | - Nicholas Casey
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, Oslo, Norway
| | - Sylvie Pollmann
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, Oslo, Norway
| | - Patrik Vernhoff
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, Oslo, Norway
| | - Gustav Gaudernack
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Gunnar Kvalheim
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, Oslo, Norway
| | - Sébastien Wälchli
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, Oslo, Norway
| | - Else Marit Inderberg
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, Oslo, Norway
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18
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Ito T, Kawai Y, Yasui Y, Iriguchi S, Minagawa A, Ishii T, Miyoshi H, Taketo MM, Kawada K, Obama K, Sakai Y, Kaneko S. The therapeutic potential of multiclonal tumoricidal T cells derived from tumor infiltrating lymphocyte-1derived iPS cells. Commun Biol 2021; 4:694. [PMID: 34099861 PMCID: PMC8184746 DOI: 10.1038/s42003-021-02195-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 05/07/2021] [Indexed: 12/14/2022] Open
Abstract
Tumor-infiltrating lymphocytes (TIL), which include tumor-specific T lymphocytes with frequency, are used for adoptive cell transfer therapy (ACT) in clinical practice. The optimization of TIL preparation has been investigated to reduce the senescence and increase the abundance of TIL, as both the quality and quantity of the transferred cells have great influence on the outcome of TIL-based ACT (TIL-ACT). Considering the effects of cell reprogramming on senescence, we expected that the anti-tumor effect could be enhanced by TIL regeneration. To confirm this hypothesis, we established tumor-specific TIL-derived iPS cells (TIL-iPSC) with human colorectal cancer specimens. T cells differentiated from TIL-iPSC (TIL-iPS-T) retained not only intrinsic T cell functions and tumor specificity, but also exhibited improved proliferation capacity and additional killing activity. Moreover, less differentiated profiles and prolonged persistency were seen in TIL-iPS-T compared with primary cells. Our findings imply that iPSC technology has great potential for TIL-ACT.
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Affiliation(s)
- Takeshi Ito
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Yohei Kawai
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Yutaka Yasui
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
- Thyas Co. Ltd., Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto, Japan
| | - Shoichi Iriguchi
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Atsutaka Minagawa
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Tomoko Ishii
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Hiroyuki Miyoshi
- Institute for Advancement of Clinical and Translational Science (iACT), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan
| | - M Mark Taketo
- Institute for Advancement of Clinical and Translational Science (iACT), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan
| | - Kenji Kawada
- Department of Surgery, Graduate School of Medicine, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Kazutaka Obama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan
| | - Yoshiharu Sakai
- Osaka Red Cross Hospital, Fudegasaki-cho, Tennoji-ku, Osaka, Japan
| | - Shin Kaneko
- Shin Kaneko Laboratory, Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Shogoin-Kawahara-cho, Sakyo-ku, Kyoto, Japan.
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19
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Pearlman AH, Hwang MS, Konig MF, Hsiue EHC, Douglass J, DiNapoli SR, Mog BJ, Bettegowda C, Pardoll DM, Gabelli SB, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S. Targeting public neoantigens for cancer immunotherapy. NATURE CANCER 2021; 2:487-497. [PMID: 34676374 PMCID: PMC8525885 DOI: 10.1038/s43018-021-00210-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023]
Abstract
Several current immunotherapy approaches target private neoantigens derived from mutations that are unique to individual patients' tumors. However, immunotherapeutic agents can also be developed against public neoantigens derived from recurrent mutations in cancer driver genes. The latter approaches target proteins that are indispensable for tumor growth, and each therapeutic agent can be applied to numerous patients. Here we review the opportunities and challenges involved in the identification of suitable public neoantigen targets and the development of therapeutic agents targeting them.
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Affiliation(s)
- Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Genentech, Inc., South San Francisco, CA, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Sandra B Gabelli
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
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20
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Nussinov R, Jang H, Gursoy A, Keskin O, Gaponenko V. Inhibition of Nonfunctional Ras. Cell Chem Biol 2021; 28:121-133. [PMID: 33440168 PMCID: PMC7897307 DOI: 10.1016/j.chembiol.2020.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/28/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Intuitively, functional states should be targeted; not nonfunctional ones. So why could drugging the inactive K-Ras4BG12Cwork-but drugging the inactive kinase will likely not? The reason is the distinct oncogenic mechanisms. Kinase driver mutations work by stabilizing the active state and/or destabilizing the inactive state. Either way, oncogenic kinases are mostly in the active state. Ras driver mutations work by quelling its deactivation mechanisms, GTP hydrolysis, and nucleotide exchange. Covalent inhibitors that bind to the inactive GDP-bound K-Ras4BG12C conformation can thus work. By contrast, in kinases, allosteric inhibitors work by altering the active-site conformation to favor orthosteric drugs. From the translational standpoint this distinction is vital: it expedites effective pharmaceutical development and extends the drug classification based on the mechanism of action. Collectively, here we postulate that drug action relates to blocking the mechanism of activation, not to whether the protein is in the active or inactive state.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Attila Gursoy
- Department of Computer Engineering, Koc University, Istanbul 34450, Turkey
| | - Ozlem Keskin
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Vadim Gaponenko
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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21
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Liu J, Huang X, Liu H, Wei C, Ru H, Qin H, Lai H, Meng Y, Wu G, Xie W, Mo X, Johnson CH, Zhang Y, Tang W. Immune landscape and prognostic immune-related genes in KRAS-mutant colorectal cancer patients. J Transl Med 2021; 19:27. [PMID: 33413474 PMCID: PMC7789428 DOI: 10.1186/s12967-020-02638-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
Background KRAS gene is the most common type of mutation reported in colorectal cancer (CRC). KRAS mutation-mediated regulation of immunophenotype and immune pathways in CRC remains to be elucidated. Methods 535 CRC patients were used to compare the expression of immune-related genes (IRGs) and the abundance of tumor-infiltrating immune cells (TIICs) in the tumor microenvironment between KRAS-mutant and KRAS wild-type CRC patients. An independent dataset included 566 cases of CRC and an in-house RNA sequencing dataset were served as validation sets. An in-house dataset consisting of 335 CRC patients were used to analyze systemic immune and inflammatory state in the presence of KRAS mutation. An immue risk (Imm-R) model consist of IRG and TIICs for prognostic prediction in KRAS-mutant CRC patients was established and validated. Results NF-κB and T-cell receptor signaling pathways were significantly inhibited in KRAS-mutant CRC patients. Regulatory T cells (Tregs) was increased while macrophage M1 and activated CD4 memory T cell was decreased in KRAS-mutant CRC. Prognosis correlated with enhanced Tregs, macrophage M1 and activated CD4 memory T cell and was validated. Serum levels of hypersensitive C-reactive protein (hs-CRP), CRP, and IgM were significantly decreased in KRAS-mutant compared to KRAS wild-type CRC patients. An immune risk model composed of VGF, RLN3, CT45A1 and TIICs signature classified CRC patients with distinct clinical outcomes. Conclusions KRAS mutation in CRC was associated with suppressed immune pathways and immune infiltration. The aberrant immune pathways and immune cells help to understand the tumor immune microenvironments in KRAS-mutant CRC patients.
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Affiliation(s)
- Jungang Liu
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China.,Department of Environmental Health Sciences, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Xiaoliang Huang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Haizhou Liu
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Chunyin Wei
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Haiming Ru
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Haiquan Qin
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hao Lai
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Yongsheng Meng
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Guo Wu
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Weishun Xie
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xianwei Mo
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Caroline H Johnson
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA.
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA.
| | - Weizhong Tang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China. .,Guangxi Clinical Research Center for Colorectal Cancer, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China.
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Sood AK, Nemeth M, Wang J, Wu Y, Gandhi S. Opportunities for Antigen Discovery in Metastatic Breast Cancer. Front Immunol 2020; 11:570049. [PMID: 33193348 PMCID: PMC7661635 DOI: 10.3389/fimmu.2020.570049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/06/2020] [Indexed: 11/13/2022] Open
Abstract
Immune checkpoint inhibitor-based immunotherapy (ICI) of breast cancer is currently efficacious in a fraction of triple negative breast cancers (TNBC) as these cancers generally carry high tumor mutation burden (TMB) and show increased tumor infiltration by CD8+ T cells. However, most estrogen receptor positive breast cancers (ERBC) have low TMB and/or are infiltrated with immunosuppressive regulatory T cells (Tregs) and thus fail to induce a significant anti-tumor immune response. Our understanding of the immune underpinning of the anti-tumor effects of CDK4/6 inhibitor (CDKi) treatment coupled with new knowledge about the mechanisms of tolerance to self-antigens suggests a way forward, specifically via characterizing and exploiting the repertoire of tumor antigens expressed by metastatic ERBC. These treatment-associated tumor antigens (TATA) may include the conventional tumor neoantigens (TNA) encoded by single nucleotide mutations, TNA encoded by tumor specific aberrant RNA transcription, splicing and DNA replication induced frameshift (FS) events as well as the shared tumor antigens. The latter may include the conventional tumor associated antigens (TAA), cancer-testis antigens (CTA) and antigens encoded by the endogenous retroviral (ERV) like sequences and repetitive DNA sequences induced by ET and CDKi treatment. An approach to identifying these antigens is outlined as this will support the development of a multi-antigen-based immunotherapy strategy for improved targeting of metastatic disease with potential for minimal autoimmune toxicity against normal tissues.
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Affiliation(s)
- Ashwani K. Sood
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Michael Nemeth
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Yun Wu
- Department of Biomedical Engineering, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Shipra Gandhi
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
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Glycogen Synthase Kinase 3β in Cancer Biology and Treatment. Cells 2020; 9:cells9061388. [PMID: 32503133 PMCID: PMC7349761 DOI: 10.3390/cells9061388] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022] Open
Abstract
Glycogen synthase kinase (GSK)3β is a multifunctional serine/threonine protein kinase with more than 100 substrates and interacting molecules. GSK3β is normally active in cells and negative regulation of GSK3β activity via phosphorylation of its serine 9 residue is required for most normal cells to maintain homeostasis. Aberrant expression and activity of GSK3β contributes to the pathogenesis and progression of common recalcitrant diseases such as glucose intolerance, neurodegenerative disorders and cancer. Despite recognized roles against several proto-oncoproteins and mediators of the epithelial–mesenchymal transition, deregulated GSK3β also participates in tumor cell survival, evasion of apoptosis, proliferation and invasion, as well as sustaining cancer stemness and inducing therapy resistance. A therapeutic effect from GSK3β inhibition has been demonstrated in 25 different cancer types. Moreover, there is increasing evidence that GSK3β inhibition protects normal cells and tissues from the harmful effects associated with conventional cancer therapies. Here, we review the evidence supporting aberrant GSK3β as a hallmark property of cancer and highlight the beneficial effects of GSK3β inhibition on normal cells and tissues during cancer therapy. The biological rationale for targeting GSK3β in the treatment of cancer is also discussed at length.
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24
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Immunotherapy, Inflammation and Colorectal Cancer. Cells 2020; 9:cells9030618. [PMID: 32143413 PMCID: PMC7140520 DOI: 10.3390/cells9030618] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer type, and third highest in mortality rates among cancer-related deaths in the United States. Originating from intestinal epithelial cells in the colon and rectum, that are impacted by numerous factors including genetics, environment and chronic, lingering inflammation, CRC can be a problematic malignancy to treat when detected at advanced stages. Chemotherapeutic agents serve as the historical first line of defense in the treatment of metastatic CRC. In recent years, however, combinational treatment with targeted therapies, such as vascular endothelial growth factor, or epidermal growth factor receptor inhibitors, has proven to be quite effective in patients with specific CRC subtypes. While scientific and clinical advances have uncovered promising new treatment options, the five-year survival rate for metastatic CRC is still low at about 14%. Current research into the efficacy of immunotherapy, particularly immune checkpoint inhibitor therapy (ICI) in mismatch repair deficient and microsatellite instability high (dMMR-MSI-H) CRC tumors have shown promising results, but its use in other CRC subtypes has been either unsuccessful, or not extensively explored. This Review will focus on the current status of immunotherapies, including ICI, vaccination and adoptive T cell therapy (ATC) in the treatment of CRC and its potential use, not only in dMMR-MSI-H CRC, but also in mismatch repair proficient and microsatellite instability low (pMMR-MSI-L).
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