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Wu Y, Han Y, Li Q, Zhang P, Yuan P, Luo Y, Fan Y, Chen S, Cai R, Li Q, Xu H, Wang Y, Ma F, Wang J, Xu B. Predictive value of topoisomerase II alpha protein for clinicopathological characteristics and prognosis in early breast cancer. Breast Cancer Res Treat 2022; 193:381-392. [PMID: 35297009 DOI: 10.1007/s10549-022-06559-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/27/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Topoisomerase II alpha (TOP2A) has been identified as a proliferation marker, of which the most common method for detection is immunohistochemistry (IHC). However, the optimal cut-off of TOP2A expression regarding prognostic value remains controversial. This study was to identify the optimal cut-off value of TOP2A expression and its correlation with clinicopathological variables and prognosis in early stage breast cancer in China. METHODS Between January 2013 and January 2015, a total of 1084 early breast cancer patients were enrolled. The optimal cut-off of TOP2A expression was assessed using the minimum P value approach. Correlations between TOP2A expression and clinicopathological characteristics were explored by the Spearman's correlation analysis, while the impact of TOP2A expression on disease-free survival (DFS) and overall survival (OS) was evaluated by the Kaplan-Meier methods. Univariate and multivariate Cox regression analyses were executed to identify statistically significant prognostic factors. RESULTS The optimal cut-off value of TOP2A was recommended as 15%. Overall, 603 (55.6%) patients were TOP2A over-expression and 481 (44.4%) patients were TOP2A low expression. TOP2A over-expression was in positive associations with a higher Ki67 index (r = 0.83, P < 0.001), HER2 positive (r = 0.26, P < 0.001), a larger tumor size (r = 0.14, P < 0.001), and a higher histologic grade (r = 0.59, P < 0.001), and in a significantly negative correlation with hormone receptor (HR) positive expression (r = - 0.40, P < 0.001) in early breast cancer. TOP2A over-expression significantly associated with worse DFS (P = 0.001) and OS (P < 0.001) and was an independent prognostic factor for both DFS (hazard ratio [HR] = 2.04; 95% confidence interval [95% CI] 1.30-3.18, P = 0.0018) and OS (HR = 3.54; 95%CI 1.53-8.23, P = 0.003) in stage I-II breast cancer patients. CONCLUSION To our knowledge, this is the first study to recommend the optimal cut-off value of TOP2A expression in breast cancer. The TOP2A expression is significantly correlated with HER2 status, Ki67 index, tumor size, histologic grade and HR status, and could be a surrogate indicator for poor prognosis of early breast cancer.
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Affiliation(s)
- Yun Wu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Yiqun Han
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Qing Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Pin Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Peng Yuan
- Department of VIP Medical Services, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Luo
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Ying Fan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Shanshan Chen
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Ruigang Cai
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Qiao Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Hangcheng Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Yan Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
| | - Jiayu Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
| | - Binghe Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17, Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
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152
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Cheng R, Xu Z, Luo M, Wang P, Cao H, Jin X, Zhou W, Xiao L, Jiang Q. Identification of alternative splicing-derived cancer neoantigens for mRNA vaccine development. Brief Bioinform 2022; 23:bbab553. [PMID: 35279714 DOI: 10.1093/bib/bbab553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2023] Open
Abstract
Messenger RNA (mRNA) vaccines have shown great potential for anti-tumor therapy due to the advantages in safety, efficacy and industrial production. However, it remains a challenge to identify suitable cancer neoantigens that can be targeted for mRNA vaccines. Abnormal alternative splicing occurs in a variety of tumors, which may result in the translation of abnormal transcripts into tumor-specific proteins. High-throughput technologies make it possible for systematic characterization of alternative splicing as a source of suitable target neoantigens for mRNA vaccine development. Here, we summarized difficulties and challenges for identifying alternative splicing-derived cancer neoantigens from RNA-seq data and proposed a conceptual framework for designing personalized mRNA vaccines based on alternative splicing-derived cancer neoantigens. In addition, several points were presented to spark further discussion toward improving the identification of alternative splicing-derived cancer neoantigens.
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Affiliation(s)
- Rui Cheng
- Harbin Institute of Technology, China
| | | | - Meng Luo
- Harbin Institute of Technology, China
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153
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McCann K, von Witzleben A, Thomas J, Wang C, Wood O, Singh D, Boukas K, Bendjama K, Silvestre N, Nielsen FC, Thomas G, Sanchez-Elsner T, Greenbaum J, Schoenberger S, Peters B, Vijayanand P, Savelyeva N, Ottensmeier C. Targeting the tumor mutanome for personalized vaccination in a TMB low non-small cell lung cancer. J Immunother Cancer 2022; 10:e003821. [PMID: 35361728 PMCID: PMC8971766 DOI: 10.1136/jitc-2021-003821] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cancer is characterized by an accumulation of somatic mutations, of which a significant subset can generate cancer-specific neoepitopes that are recognized by autologous T cells. Such neoepitopes are emerging as important targets for cancer immunotherapy, including personalized cancer vaccination strategies. METHODS We used whole-exome and RNA sequencing analysis to identify potential neoantigens for a patient with non-small cell lung cancer. Thereafter, we assessed the autologous T-cell reactivity to the candidate neoantigens using a long peptide approach in a cultured interferon gamma ELISpot and tracked the neoantigen-specific T-cells in the tumor by T-cell receptor (TCR) sequencing. In parallel, identified gene variants were incorporated into a Modified Vaccinia Ankara-based vaccine, which was evaluated in the human leucocyte antigen A*0201 transgenic mouse model (HHD). RESULTS Sequencing revealed a tumor with a low mutational burden: 2219 sequence variants were identified from the primary tumor, of which 23 were expressed in the transcriptome, involving 18 gene products. We could demonstrate spontaneous T-cell responses to 5/18 (28%) mutated gene variants, and further analysis of the TCR repertoire of neoantigen-specific CD4+ and CD8+ T cells revealed TCR clonotypes that were expanded in both blood and tumor tissue. Following vaccination of HHD mice, de novo T-cell responses were generated to 4/18 (22%) mutated gene variants; T cells reactive against two variants were also evident in the autologous setting. Subsequently, we determined the major histocompatibility complex restriction of the T-cell responses and used in silico prediction tools to determine the likely neoepitopes. CONCLUSIONS Our study demonstrates the feasibility of efficiently identifying tumor-specific neoantigens that can be targeted by vaccination in tumors with a low mutational burden, promising successful clinical exploitation, with trials currently underway.
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Affiliation(s)
- Katy McCann
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Adrian von Witzleben
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Ulm, Ulm, Germany
| | - Jaya Thomas
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Chuan Wang
- Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Oliver Wood
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Divya Singh
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Konstantinos Boukas
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
| | - Kaidre Bendjama
- Research and Development Department, Transgene, Illkirch-Graffenstaden, France
| | - Nathalie Silvestre
- Research and Development Department, Transgene, Illkirch-Graffenstaden, France
| | | | - Gareth Thomas
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Tilman Sanchez-Elsner
- Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Jason Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Stephen Schoenberger
- Laboratory of Cellular Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Natalia Savelyeva
- Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Christian Ottensmeier
- Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton, UK
- Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- La Jolla Institute for Immunology, La Jolla, California, USA
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154
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Zhao Q, Zhang Z, Wu Y. PRAME Is a Potential Carcinogenic Biomarker that Correlates with Patient Prognosis and Tumor Immunity Based on Pan-Cancer Analysis. Ann Clin Lab Sci 2022; 52:185-195. [PMID: 35414497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE This study was designed to visualize the pan-cancer prognostic significance of PReferentially expressed Antigen in Melanoma (PRAME) and investigate the relationship between PRAME expression and tumor immunity. MATERIAL AND METHODS We explored the expression patterns and prognostic value of PRAME across multiple cancers using data from the Cancer Genome Atlas, Genotype-Tissue Expression, and Cancer Cell Line Encyclopedia databases. Spearman's correlation test was used to evaluate correlations between PRAME expression and the tumor immune microenvironment, mutation indicators, and DNA methylation. Finally, the functions of PRAME and potential signaling pathway mechanisms were explored through Gene Set Enrichment Analysis (GSEA). RESULTS Pan-cancer survival analysis indicated that PRAME was widely up-regulated in most tumors, and its high expression was indicative of poor overall survival in different cancer types. In addition, PRAME expression levels were strongly linked to immune infiltration, immune score, immune checkpoint, immune neoantigens, tumor mutation burden, microsatellite instability, mismatch repair, and DNA methyltransferase in a variety of cancers. GSEA analysis revealed that PRAME was related to the regulation of numerous signaling pathways implicated in tumor immunity and tumorigenicity. CONCLUSIONS PRAME has the potential to serve as a prognostic pan-cancer biomarker and is correlated with tumor immunity. Its use may help shed light on optimum cancer therapies.
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Affiliation(s)
- Qi Zhao
- Department of Minimally Invasive Surgery, Shaoxing Second Hospital, Shaoxing, Zhejiang, China
| | - Zhongwei Zhang
- Department of Gastrointestinal Surgery, Shaoxing Second Hospital, Shaoxing, Zhejiang, China
| | - Yinfang Wu
- Department of Gastrointestinal Surgery, Shaoxing Second Hospital, Shaoxing, Zhejiang, China
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155
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Lim SA, Zhou J, Martinko AJ, Wang YH, Filippova EV, Steri V, Wang D, Remesh SG, Liu J, Hann B, Kossiakoff AA, Evans MJ, Leung KK, Wells JA. Targeting a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) for RAS-driven cancers. J Clin Invest 2022; 132:e154604. [PMID: 35166238 PMCID: PMC8843743 DOI: 10.1172/jci154604] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Extracellular proteolysis is frequently dysregulated in disease and can generate proteoforms with unique neoepitopes not found in healthy tissue. Here, we demonstrate that Abs that selectively recognize a proteolytic neoepitope on CUB domain containing protein 1 (CDCP1) could enable more effective and safer treatments for solid tumors. CDCP1 is highly overexpressed in RAS-driven cancers, and its ectodomain is cleaved by extracellular proteases. Biochemical, biophysical, and structural characterization revealed that the 2 cleaved fragments of CDCP1 remain tightly associated with minimal proteolysis-induced conformational change. Using differential phage display, we generated recombinant Abs that are exquisitely selective to cleaved CDCP1 with no detectable binding to the uncleaved form. These Abs potently targeted cleaved CDCP1-expressing cancer cells as an Ab-drug conjugate, an Ab-radionuclide conjugate, and a bispecific T cell engager. In a syngeneic pancreatic tumor model, these cleaved-specific Abs showed tumor-specific localization and antitumor activity with superior safety profiles compared with a pan-CDCP1 approach. Targeting proteolytic neoepitopes could provide an orthogonal "AND" gate for improving the therapeutic index.
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Affiliation(s)
| | - Jie Zhou
- Department of Pharmaceutical Chemistry
| | | | - Yung-Hua Wang
- Department of Radiology and Biomedical Imaging, and
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | - Ekaterina V. Filippova
- Department of Biochemistry and Molecular Biology, and
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Preclinical Therapeutics Core, UCSF, San Francisco, California, USA
| | - Donghui Wang
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
- Preclinical Therapeutics Core, UCSF, San Francisco, California, USA
| | | | - Jia Liu
- Department of Pharmaceutical Chemistry
| | - Byron Hann
- Preclinical Therapeutics Core, UCSF, San Francisco, California, USA
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, and
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA
| | - Michael J. Evans
- Department of Radiology and Biomedical Imaging, and
- Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | | | - James A. Wells
- Department of Pharmaceutical Chemistry
- Chan Zuckerberg Biohub, San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
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156
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Donahue KL, Pasca di Magliano M. Cleaved CDCP1 marks the spot: a neoepitope for RAS-driven cancers. J Clin Invest 2022; 132:e157168. [PMID: 35166242 PMCID: PMC8843638 DOI: 10.1172/jci157168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A challenge in cancer treatment is targeting cancer cells while sparing normal cells. Thus, identifying cancer-specific neoepitopes is an active research area. Neoepitopes are generated by the accumulation of mutations; however, deadly cancer types, including pancreatic cancer, have a low mutational burden and, consequently, a paucity of neoantigens. In this issue of the JCI, Lim, Zhou, and colleagues describe a neoepitope generated upon proteolytic cleavage of the transmembrane CUB domain containing protein 1 (CDCP1). CDCP1 is overexpressed in cancer and portends a worse prognosis; previous attempts to target CDCP1 reduced cancer growth, but adversely affected the host. Here, the authors generated an antibody that specifically targeted cleaved CDCP1 (c-CDCP1) and developed a drug conjugate, a vector for radioactive ions, and a mediator of T cell activation. The therapeutics inhibited pancreatic cancer cell growth in vitro and in vivo. Exploiting proteolytic cleavage-derived neoantigens opens an attractive way for specifically targeting cancer cells.
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Affiliation(s)
| | - Marina Pasca di Magliano
- Department of Surgery, Department of Cell and Developmental Biology, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
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157
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Abstract
TOPIIA topoisomerases are required for the regulation of DNA topology by DNA cleavage and re-ligation and are important targets of antibiotic and anticancer agents. Humans possess two TOPIIA paralogue genes (TOP2A and TOP2B) with high sequence and structural similarity but distinct cellular functions. Despite their functional and clinical relevance, the evolutionary history of TOPIIA is still poorly understood. Here we show that TOPIIA is highly conserved in Metazoa. We also found that TOPIIA paralogues from jawed and jawless vertebrates had different origins related with tetraploidization events. After duplication, TOP2B evolved under a stronger purifying selection than TOP2A, perhaps promoted by the more specialized role of TOP2B in postmitotic cells. We also detected genetic signatures of positive selection in the highly variable C-terminal domain (CTD), possibly associated with adaptation to cellular interactions. By comparing TOPIIA from modern and archaic humans, we found two amino acid substitutions in the TOP2A CTD, suggesting that TOP2A may have contributed to the evolution of present-day humans, as proposed for other cell cycle-related genes. Finally, we identified six residues conferring resistance to chemotherapy differing between TOP2A and TOP2B. These six residues could be targets for the development of TOP2A-specific inhibitors that would avoid the side effects caused by inhibiting TOP2B. Altogether, our findings clarify the origin, diversification and selection pressures governing the evolution of animal TOPIIA.
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Affiliation(s)
- Filipa Moreira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
- CINBIO, Universidade de Vigo, 36310, Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310, Vigo, Spain
| | - Arnaldo Videira
- ICBAS - Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Filipe Pereira
- IDENTIFICA Genetic Testing, Rua Simão Bolívar 259 3º Dir Tras, 4470-214, Maia, Portugal.
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal.
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158
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Lin H, Wang K, Xiong Y, Zhou L, Yang Y, Chen S, Xu P, Zhou Y, Mao R, Lv G, Wang P, Zhou D. Identification of Tumor Antigens and Immune Subtypes of Glioblastoma for mRNA Vaccine Development. Front Immunol 2022; 13:773264. [PMID: 35185876 PMCID: PMC8847306 DOI: 10.3389/fimmu.2022.773264] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/14/2022] [Indexed: 02/05/2023] Open
Abstract
The use of vaccines for cancer therapy is a promising immunotherapeutic strategy that has been shown to be effective against various cancers. Vaccines directly target tumors but their efficacy against glioblastoma multiforme (GBM) remains unclear. Immunotyping that classifies tumor samples is considered to be a biomarker for immunotherapy. This study aimed to identify potential GBM antigens suitable for vaccine development and develop a tool to predict the response of GBM patients to vaccination based on the immunotype. Gene Expression Profiling Interactive Analysis (GEPIA) was applied to evaluate the expression profile of GBM antigens and their influence on clinical prognosis, while the cBioPortal program was utilized to integrate and analyze genetic alterations. The correlation between antigens and antigen processing cells was assessed using TIMER. RNA-seq data of GBM samples and their corresponding clinical data were downloaded from the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) for further clustering analysis. Six overexpressed and mutated tumor antigens (ARHGAP9, ARHGAP30, CLEC7A, MAN2B1, ARPC1B and PLB1) were highly correlated with the survival rate of GBM patients and the infiltration of antigen presenting cells in GBMs. With distinct cellular and molecular characteristics, three immune subtypes (IS1-IS3) of GBMs were identified and GBMs from IS3 subtype were more likely to benefit from vaccination. Through graph learning-based dimensional reduction, immune landscape was depicted and revealed the existence of heterogeneity among individual GBM patients. Finally, WGCNA can identify potential vaccination biomarkers by clustering immune related genes. In summary, the six tumor antigens are potential targets for developing anti-GBMs mRNA vaccine, and the immunotypes can be used for evaluating vaccination response.
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Affiliation(s)
- Han Lin
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Head and Neck Surgery, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Kun Wang
- Department of Neurosurgery, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Yuxin Xiong
- Division of Vascular Intervention Radiology, The Third Affiliated Hospital of Sun Yet-Sen University, Guangzhou, China
| | - Liting Zhou
- International Department, Affiliated High School of South China Normal University, Guangzhou, China
| | - Yong Yang
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shanwei Chen
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Peihong Xu
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Yujun Zhou
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Southern Medical University, Guangzhou, China
| | - Rui Mao
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Guangzhao Lv
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Peng Wang
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Dong Zhou
- Department of Neurosurgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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159
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Abstract
Neoantigens are tumor-specific proteins and peptides that can be highly immunogenic. Immune-mediated tumor rejection is strongly associated with cytotoxic responses to neoantigen-derived peptides in noncovalent association with self-HLA molecules. Neoantigen-based therapies, such as adoptive T cell transfer, have shown the potential to induce remission of treatment-resistant metastatic disease in select patients. Cancer vaccines are similarly designed to elicit or amplify antigen-specific T cell populations and stimulate directed antitumor immunity, but the selection and prioritization of the neoantigens remains a challenge. Bioinformatic algorithms can predict tumor neoantigens from somatic mutations, insertion-deletions, and other aberrant peptide products, but this often leads to hundreds of potential neoepitopes, all unique for that tumor. Selecting neoantigens for cancer vaccines is complicated by the technical challenges of neoepitope discovery, the diversity of HLA molecules, and intratumoral heterogeneity of passenger mutations leading to immune escape. Despite strong preclinical evidence, few neoantigen cancer vaccines tested in vivo have generated epitope-specific T cell populations, suggesting suboptimal immune system activation. In this chapter, we review factors affecting the prioritization and delivery of candidate neoantigens in the design of therapeutic and preventive cancer vaccines and consider synergism with standard chemotherapies.
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Affiliation(s)
- Alexander S Roesler
- School of Medicine, Duke University, Durham, NC, USA
- Mayo Clinic, Scottsdale, AZ, USA
| | - Karen S Anderson
- Mayo Clinic, Scottsdale, AZ, USA.
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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160
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Michel T, Ollert M, Zimmer J. A Hot Topic: Cancer Immunotherapy and Natural Killer Cells. Int J Mol Sci 2022; 23:ijms23020797. [PMID: 35054985 PMCID: PMC8776043 DOI: 10.3390/ijms23020797] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 12/24/2022] Open
Abstract
Despite significant progress in recent years, the therapeutic approach of the multiple different forms of human cancer often remains a challenge. Besides the well-established cancer surgery, radiotherapy and chemotherapy, immunotherapeutic strategies gain more and more attention, and some of them have already been successfully introduced into the clinic. Among these, immunotherapy based on natural killer (NK) cells is considered as one of the most promising options. In the present review, we will expose the different possibilities NK cells offer in this context, compare data about the theoretical background and mechanism(s) of action, report some results of clinical trials and identify several very recent trends. The pharmaceutical industry is quite interested in NK cell immunotherapy, which will benefit the speed of progress in the field.
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Affiliation(s)
- Tatiana Michel
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (T.M.); (M.O.)
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (T.M.); (M.O.)
- Odense Research Center for Anaphylaxis (ORCA), Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, DK-5000 Odense, Denmark
| | - Jacques Zimmer
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 Rue Henri Koch, L-4354 Esch-sur-Alzette, Luxembourg; (T.M.); (M.O.)
- Correspondence:
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Abrantes R, Duarte HO, Gomes C, Wälchli S, Reis CA. CAR-Ts: new perspectives in cancer therapy. FEBS Lett 2022; 596:403-416. [PMID: 34978080 DOI: 10.1002/1873-3468.14270] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022]
Abstract
Chimeric antigen receptor (CAR)-T-cell therapy is a promising anticancer treatment that exploits the host's immune system to fight cancer. CAR-T cell therapy relies on immune cells being modified to express an artificial receptor targeting cancer-specific markers, and infused into the patients where they will recognize and eliminate the tumour. Although CAR-T cell therapy has produced encouraging outcomes in patients with haematologic malignancies, solid tumours remain challenging to treat, mainly due to the lack of cancer-specific molecular targets and the hostile, often immunosuppressive, tumour microenvironment. CAR-T cell therapy also depends on the quality of the injected product, which is closely connected to CAR design. Here, we explain the technology of CAR-Ts, focusing on the composition of CARs, their application, and limitations in cancer therapy, as well as on the current strategies to overcome the challenges encountered. We also address potential future targets to overcome the flaws of CAR-T cell technology in the treatment of cancer, emphasizing glycan antigens, the aberrant forms of which attain high tumour-specific expression, as promising targets for CAR-T cell therapy.
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Affiliation(s)
- Rafaela Abrantes
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
- ICBAS, Abel Salazar Biomedical Sciences Institute, University of Porto, Portugal
| | - Henrique O Duarte
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Catarina Gomes
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
| | - Sébastien Wälchli
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, Norway
| | - Celso A Reis
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Portugal
- ICBAS, Abel Salazar Biomedical Sciences Institute, University of Porto, Portugal
- FMUP, Faculty of Medicine, University of Porto, Portugal
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Alburquerque-González B, López-Abellán MD, Luengo-Gil G, Montoro-García S, Conesa-Zamora P. Design of Personalized Neoantigen RNA Vaccines Against Cancer Based on Next-Generation Sequencing Data. Methods Mol Biol 2022; 2547:165-185. [PMID: 36068464 DOI: 10.1007/978-1-0716-2573-6_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The good clinical results of immune checkpoint inhibitors (ICIs) in recent cancer therapy and the success of RNA vaccines against SARS-nCoV2 have provided important lessons to the scientific community. On the one hand, the efficacy of ICI depends on the number and immunogenicity of tumor neoantigens (TNAs) which unfortunately are not abundantly expressed in many cancer subtypes. On the other hand, novel RNA vaccines have significantly improved both the stability and immunogenicity of mRNA and its efficient delivery, this way overcoming past technique limitations and also allowing a quick vaccine development at the same time. These two facts together have triggered a resurgence of therapeutic cancer vaccines which can be designed to include individual TNAs and be synthesized in a timeframe short enough to be suitable for the tailored treatment of a given cancer patient.In this chapter, we explain the pipeline for the synthesis of TNA-carrying RNA vaccines which encompasses several steps such as individual tumor next-generation sequencing (NGS), selection of immunogenic TNAs, nucleic acid synthesis, drug delivery systems, and immunogenicity assessment, all of each step comprising different alternatives and variations which will be discussed.
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Affiliation(s)
- Begoña Alburquerque-González
- Pathology and Histology Department Facultad de Ciencias de la Salud, UCAM Universidad Católica San Antonio de Murcia, Murcia, Spain
| | - María Dolores López-Abellán
- Laboratory Medicine Department, Group of Molecular Pathology and Pharmacogenetics, Biomedical Research Institute from Murcia (IMIB), Hospital Universitario Santa Lucía, Cartagena, Spain
| | - Ginés Luengo-Gil
- Laboratory Medicine Department, Group of Molecular Pathology and Pharmacogenetics, Biomedical Research Institute from Murcia (IMIB), Hospital Universitario Santa Lucía, Cartagena, Spain
| | - Silvia Montoro-García
- Cell Culture Lab, Facultad de Ciencias de la Salud, UCAM Universidad Católica San Antonio de Murcia, Murcia, Spain
| | - Pablo Conesa-Zamora
- Pathology and Histology Department Facultad de Ciencias de la Salud, UCAM Universidad Católica San Antonio de Murcia, Murcia, Spain.
- Laboratory Medicine Department, Group of Molecular Pathology and Pharmacogenetics, Biomedical Research Institute from Murcia (IMIB), Hospital Universitario Santa Lucía, Cartagena, Spain.
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Abstract
Growing bodies of evidence have demonstrated that the identification of prostate cancer (PCa) biomarkers in the patients' blood and urine may remarkably improve PCa diagnosis and progression monitoring. Among diverse cancer-derived circulating materials, extracellular RNA molecules (exRNAs) represent a compelling component to investigate cancer-related alterations. Once outside the intracellular environment, exRNAs circulate in biofluids either in association with protein complexes or encapsulated inside extracellular vesicles (EVs). Notably, EV-associated RNAs (EV-RNAs) were used for the development of several assays (such as the FDA-approved Progensa Prostate Cancer Antigen 3 (PCA3 test) aiming at improving early PCa detection. EV-RNAs encompass a mixture of species, including small non-coding RNAs (e.g. miRNA and circRNA), lncRNAs and mRNAs. Several methods have been proposed to isolate EVs and relevant RNAs, and to perform RNA-Seq studies to identify potential cancer biomarkers. However, EVs in the circulation of a cancer patient include a multitude of diverse populations that are released by both cancer and normal cells from different tissues, thereby leading to a heterogeneous EV-RNA-associated transcriptional signal. Decrypting the complexity of such a composite signal is nowadays the major challenge faced in the identification of specific tumor-associated RNAs. Multiple deconvolution algorithms have been proposed so far to infer the enrichment of cancer-specific signals from gene expression data. However, novel strategies for EVs sorting and sequencing of RNA associated to single EVs populations will remarkably facilitate the identification of cancer-related molecules. Altogether, the studies summarized here demonstrate the high potential of using EV-RNA biomarkers in PCa and highlight the urgent need of improving technologies and computational approaches to characterize specific EVs populations and their relevant RNA cargo.
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Affiliation(s)
- Vera Mugoni
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Caterina Nardella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.
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Zuo Z, Yu Y, Ren B, Liu S, Nelson J, Wang Z, Tao J, Pradhan‐Sundd T, Bhargava R, Michalopoulos G, Chen Q, Zhang J, Ma D, Pennathur A, Luketich J, Satdarshan Monga P, Nalesnik M, Luo J. Oncogenic Activity of Solute Carrier Family 45 Member 2 and Alpha-Methylacyl-Coenzyme A Racemase Gene Fusion Is Mediated by Mitogen-Activated Protein Kinase. Hepatol Commun 2022; 6:209-222. [PMID: 34505419 PMCID: PMC8710797 DOI: 10.1002/hep4.1724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/23/2021] [Accepted: 02/28/2021] [Indexed: 11/09/2022] Open
Abstract
Chromosome rearrangement is one of the hallmarks of human malignancies. Gene fusion is one of the consequences of chromosome rearrangements. In this report, we show that gene fusion between solute carrier family 45 member 2 (SLC45A2) and alpha-methylacyl-coenzyme A racemase (AMACR) occurs in eight different types of human malignancies, with frequencies ranging from 45% to 97%. The chimeric protein is translocated to the lysosomal membrane and activates the extracellular signal-regulated kinase signaling cascade. The fusion protein promotes cell growth, accelerates migration, resists serum starvation-induced cell death, and is essential for cancer growth in mouse xenograft cancer models. Introduction of SLC45A2-AMACR into the mouse liver using a sleeping beauty transposon system and somatic knockout of phosphatase and TENsin homolog (Pten) generated spontaneous liver cancers within a short period. Conclusion: The gene fusion between SLC45A2 and AMACR may be a driving event for human liver cancer development.
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Affiliation(s)
- Ze‐Hua Zuo
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Yan‐Ping Yu
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
| | - Bao‐Guo Ren
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Silvia Liu
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
| | - Joel Nelson
- Department of UrologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Zhou Wang
- Department of UrologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Junyan Tao
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | | | - Rohit Bhargava
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - George Michalopoulos
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
| | - Qi Chen
- Department of PharmacologyToxicology, and TherapeuticsUniversity of KansasKansas CityKSUSA
| | - Jun Zhang
- Department of MedicineUniversity of IowaIowa CityIAUSA
- Present address:
Department of MedicineUniversity of Kansas Medical CenterKansas CityKSUSA
| | - Deqin Ma
- Department of PathologyUniversity of IowaIowa CityIAUSA
| | - Arjun Pennathur
- Thoracic SurgeryUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - James Luketich
- Thoracic SurgeryUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Paul Satdarshan Monga
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
| | - Michael Nalesnik
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Jian‐Hua Luo
- Department of PathologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
- Pittsburgh Liver Research Center of University of Pittsburgh Medical CenterPittsburghPAUSA
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Abstract
The remarkable specificity of antibodies has enabled precision cancer immunotherapies, including chimeric antigen receptor T cells and antibody-drug conjugates. In parallel, single-cell genomics technologies present the possibility of a comprehensive annotation of antigen expression throughout tissues of the human body and on cancer cells. We reflect on the rationale for antigen targets currently used in immunotherapies, their adverse effects revealed in the clinic, and the opportunity to utilize large genomics datasets to de-risk potential targets and nominate optimal antigens for therapy.
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Affiliation(s)
- Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | | | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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Li H, Fang H, Chang L, Qiu S, Ren X, Cao L, Bian J, Wang Z, Guo Y, Lv J, Sun Z, Wang T, Li B. TC2N: A Novel Vital Oncogene or Tumor Suppressor Gene In Cancers. Front Immunol 2021; 12:764749. [PMID: 34925334 PMCID: PMC8674203 DOI: 10.3389/fimmu.2021.764749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
Several C2 domain-containing proteins play key roles in tumorigenesis, signal transduction, and mediating protein–protein interactions. Tandem C2 domains nuclear protein (TC2N) is a tandem C2 domain-containing protein that is differentially expressed in several types of cancers and is closely associated with tumorigenesis and tumor progression. Notably, TC2N has been identified as an oncogene in lung and gastric cancer but as a tumor suppressor gene in breast cancer. Recently, a large number of tumor-associated antigens (TAAs), such as heat shock proteins, alpha-fetoprotein, and carcinoembryonic antigen, have been identified in a variety of malignant tumors. Differences in the expression levels of TAAs between cancer cells and normal cells have led to these antigens being investigated as diagnostic and prognostic biomarkers and as novel targets in cancer treatment. In this review, we summarize the clinical characteristics of TC2N-positive cancers and potential mechanisms of action of TC2N in the occurrence and development of specific cancers. This article provides an exploration of TC2N as a potential target for the diagnosis and treatment of different types of cancers.
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Affiliation(s)
- Hanyang Li
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun, China
- Department of Thyroid Surgery, The Second Hospital of Jilin University, Changchun, China
| | - He Fang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Li Chang
- Department of Pathology, The Second Hospital of Jilin University, Changchun, China
| | - Shuang Qiu
- Department of Biobank, The China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xiaojun Ren
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun, China
| | - Lidong Cao
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Jinda Bian
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Zhenxiao Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Yi Guo
- Department of Breast Surgery, The Affiliated Hospital Changchun University of Chinese Medicine, Changchun, China
| | - Jiayin Lv
- Department of Orthopedics, The China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhihui Sun
- Department of Pharmacy, The Second Hospital of Jilin University, Changchun, China
| | - Tiejun Wang
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun, China
- *Correspondence: Tiejun Wang, ; Bingjin Li,
| | - Bingjin Li
- Jilin Provincial Key Laboratory on Molecular and Chemical Genetic, The Second Hospital of Jilin University, Changchun, China
- *Correspondence: Tiejun Wang, ; Bingjin Li,
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Smith V, Mukherjee D, Lunj S, Choudhury A, Hoskin P, West C, Illidge T. The effect of hypoxia on PD-L1 expression in bladder cancer. BMC Cancer 2021; 21:1271. [PMID: 34819027 PMCID: PMC8613983 DOI: 10.1186/s12885-021-09009-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/09/2021] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Recent data has demonstrated that hypoxia drives an immunosuppressive tumour microenvironment (TME) via various mechanisms including hypoxia inducible factor (HIF)-dependent upregulation of programmed death ligand 1 (PD-L1). Both hypoxia and an immunosuppressive TME are targetable independent negative prognostic factors for bladder cancer. Therefore we sought to investigate whether hypoxia is associated with upregulation of PD-L1 in the disease. MATERIALS AND METHODS Three human muscle-invasive bladder cancer cell lines (T24, J82, UMUC3) were cultured in normoxia (20% oxygen) or hypoxia (1 and 0.1% oxygen) for 24 h. Differences in PD-L1 expression were measured using Western blotting, quantitative polymerase chain reaction (qPCR) and flow cytometry (≥3 independent experiments). Statistical tests performed were unpaired t tests and ANOVA. For in silico work an hypoxia signature was used to apply hypoxia scores to muscle-invasive bladder cancers from a clinical trial (BCON; n = 142) and TCGA (n = 404). Analyses were carried out using R and RStudio and statistical tests performed were linear models and one-way ANOVA. RESULTS When T24 cells were seeded at < 70% confluence, there was decreased PD-L1 protein (p = 0.009) and mRNA (p < 0.001) expression after culture in 0.1% oxygen. PD-L1 protein expression decreased in both 0.1% oxygen and 1% oxygen in a panel of muscle-invasive bladder cancer cells: T24 (p = 0.009 and 0.001), J82 (p = 0.008 and 0.013) and UMUC3 (p = 0.003 and 0.289). Increasing seeding density decreased PD-L1 protein (p < 0.001) and mRNA (p = 0.001) expression in T24 cells grown in both 20 and 1% oxygen. Only when cells were 100% confluent, were PD-L1 protein and mRNA levels higher in 1% versus 20% oxygen (p = 0.056 and p = 0.037). In silico analyses showed a positive correlation between hypoxia signature scores and PD-L1 expression in both BCON (p = 0.003) and TCGA (p < 0.001) cohorts, and between hypoxia and IFNγ signature scores (p < 0.001 for both). CONCLUSION Tumour hypoxia correlates with increased PD-L1 expression in patient derived bladder cancer tumours. In vitro PD-L1 expression was affected by cell density and decreased PD-L1 expression was observed after culture in hypoxia in muscle-invasive bladder cancer cell lines. As cell density has such an important effect on PD-L1 expression, it should be considered when investigating PD-L1 expression in vitro.
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Affiliation(s)
- Vicky Smith
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK.
| | - Debayan Mukherjee
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK
| | - Sapna Lunj
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK
| | - Ananya Choudhury
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Peter Hoskin
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
- Manchester Academic Health Science Centre, Manchester, UK
| | - Catharine West
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK
| | - Tim Illidge
- Division of Cancer Sciences, University of Manchester, M20 4BX, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
- Manchester Academic Health Science Centre, Manchester, UK
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168
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Sun J, Zhang J, Hu H, Qin H, Liao X, Wang F, Zhang W, Yin Q, Su X, He Y, Li W, Wang K, Li Q. Anti-tumour effect of neo-antigen-reactive T cells induced by RNA mutanome vaccine in mouse lung cancer. J Cancer Res Clin Oncol 2021; 147:3255-3268. [PMID: 34291357 PMCID: PMC8484245 DOI: 10.1007/s00432-021-03735-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 12/25/2022]
Abstract
PURPOSE Mutation-specific T-cell response to epithelial cancers and T-cell-based immunotherapy has been successfully used to treat several human solid cancers. We aimed to investigate the anti-tumour effect of neo-antigen-reactive T(NRT) cells induced by RNA mutanome vaccine, which may serve as a feasible and effective therapeutic approach for lung cancer. METHODS We predicted candidate neo-antigens according to the mutant gene analysis by sequencing the mouse Lewis cells and C57BL/6 mouse tail tissue. RNA vaccine was prepared with the neo-antigens as the template. We assessed antitumor efficacy, cytokine secretion and pathological changes after adoptive transfer of NRT cells in vitro and vivo experiments. RESULTS We identified 10 non-synonymous somatic mutations and successfully generated NRT cells. The percentage of T-cell activation proportion was increased from 0.072% in conventional T cells to 9.96% in NRT cells. Interferon-γ secretion augmented from 17.8 to 24.2% as well. As an in vivo model, adoptive NRT cell infusion could promote active T-cell infiltration into the tumour tissue and could delay tumour progression. CONCLUSION NRT cells induced by RNA mutanome vaccine exert a significant anti-tumour effect in mouse lung cancer, and adoptive NRT cell therapy might be considered a feasible, effective therapeutic approach for lung cancer.
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MESH Headings
- Animals
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Cancer Vaccines/immunology
- Cancer Vaccines/pharmacology
- Carcinoma, Lewis Lung/genetics
- Carcinoma, Lewis Lung/immunology
- Carcinoma, Lewis Lung/therapy
- Cell Line, Tumor
- Female
- Immunotherapy, Adoptive/methods
- Interferon-gamma/immunology
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/therapy
- Male
- Mice
- Mice, Inbred C57BL
- Point Mutation
- Random Allocation
- T-Lymphocytes/immunology
- T-Lymphocytes/transplantation
- Tumor Necrosis Factor-alpha/immunology
- Vaccines, Synthetic/immunology
- Vaccines, Synthetic/pharmacology
- mRNA Vaccines
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Affiliation(s)
- Jiaxing Sun
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Haiyan Hu
- Center of Diagnosis and Treatment of Breast Disease, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Huan Qin
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ximing Liao
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Feilong Wang
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Qi Yin
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoping Su
- School of Basic Medicine, Wenzhou Medical University, Wenzhou Tea Mountain Higher Education Park, Wenzhou, China
| | - Yanan He
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenfeng Li
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kun Wang
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Qiang Li
- Department of Pulmonary and Critical Care Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.
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Shaldam M, Nocentini A, Elsayed ZM, Ibrahim TM, Salem R, El-Domany RA, Capasso C, Supuran CT, Eldehna WM. Development of Novel Quinoline-Based Sulfonamides as Selective Cancer-Associated Carbonic Anhydrase Isoform IX Inhibitors. Int J Mol Sci 2021; 22:11119. [PMID: 34681794 PMCID: PMC8541628 DOI: 10.3390/ijms222011119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/01/2023] Open
Abstract
A new series of quinoline-based benzenesulfonamides (QBS) were developed as potential carbonic anhydrase inhibitors (CAIs). The target QBS CAIs is based on the 4-anilinoquinoline scaffold where the primary sulphonamide functionality was grafted at C4 of the anilino moiety as a zinc anchoring group (QBS 13a-c); thereafter, the sulphonamide group was switched to ortho- and meta-positions to afford regioisomers 9a-d and 11a-g. Moreover, a linker elongation approach was adopted where the amino linker was replaced by a hydrazide one to afford QBS 16. All the described QBS have been synthesized and investigated for their CA inhibitory action against hCA I, II, IX and XII. In general, para-sulphonamide derivatives 13a-c displayed the best inhibitory activity against both cancer-related isoforms hCA IX (KIs = 25.8, 5.5 and 18.6 nM, respectively) and hCA XII (KIs = 9.8, 13.2 and 8.7 nM, respectively), beside the excellent hCA IX inhibitory activity exerted by meta-sulphonamide derivative 11c (KI = 8.4 nM). The most promising QBS were further evaluated for their anticancer and pro-apoptotic activities on two cancer cell lines (MDA-MB-231 and MCF-7). In addition, molecular docking simulation studies were applied to justify the acquired CA inhibitory action of the target QBS.
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Affiliation(s)
- Moataz Shaldam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (M.S.); (T.M.I.); (R.S.)
| | - Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, Sesto Fiorentino, 50019 Firenze, Italy;
| | - Zainab M. Elsayed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
| | - Tamer M. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (M.S.); (T.M.I.); (R.S.)
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
| | - Rofaida Salem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (M.S.); (T.M.I.); (R.S.)
| | - Ramadan A. El-Domany
- Department of Microbiology and Immunology, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, Italian National Research Council (CNR)CNR, Via Pietro Castellino 111, 80131 Napoli, Italy;
| | - Claudiu T. Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Polo Scientifico, Via U. Schiff 6, Sesto Fiorentino, 50019 Firenze, Italy;
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt; (M.S.); (T.M.I.); (R.S.)
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt;
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Gebert J, Gelincik O, Oezcan-Wahlbrink M, Marshall JD, Hernandez-Sanchez A, Urban K, Long M, Cortes E, Tosti E, Katzenmaier EM, Song Y, Elsaadi A, Deng N, Vilar E, Fuchs V, Nelius N, Yuan YP, Ahadova A, Sei S, Shoemaker RH, Umar A, Wei L, Liu S, Bork P, Edelmann W, von Knebel Doeberitz M, Lipkin SM, Kloor M. Recurrent Frameshift Neoantigen Vaccine Elicits Protective Immunity With Reduced Tumor Burden and Improved Overall Survival in a Lynch Syndrome Mouse Model. Gastroenterology 2021; 161:1288-1302.e13. [PMID: 34224739 PMCID: PMC10184299 DOI: 10.1053/j.gastro.2021.06.073] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 06/02/2021] [Accepted: 06/28/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS DNA mismatch repair deficiency drives microsatellite instability (MSI). Cells with MSI accumulate numerous frameshift mutations. Frameshift mutations affecting cancer-related genes may promote tumorigenesis and, therefore, are shared among independently arising MSI tumors. Consequently, such recurrent frameshift mutations can give rise to shared immunogenic frameshift peptides (FSPs) that represent ideal candidates for a vaccine against MSI cancer. Pathogenic germline variants of mismatch repair genes cause Lynch syndrome (LS), a hereditary cancer syndrome affecting approximately 20-25 million individuals worldwide. Individuals with LS are at high risk of developing MSI cancer. Previously, we demonstrated safety and immunogenicity of an FSP-based vaccine in a phase I/IIa clinical trial in patients with a history of MSI colorectal cancer. However, the cancer-preventive effect of FSP vaccination in the scenario of LS has not yet been demonstrated. METHODS A genome-wide database of 488,235 mouse coding mononucleotide repeats was established, from which a set of candidates was selected based on repeat length, gene expression, and mutation frequency. In silico prediction, in vivo immunogenicity testing, and epitope mapping was used to identify candidates for FSP vaccination. RESULTS We identified 4 shared FSP neoantigens (Nacad [FSP-1], Maz [FSP-1], Senp6 [FSP-1], Xirp1 [FSP-1]) that induced CD4/CD8 T cell responses in naïve C57BL/6 mice. Using VCMsh2 mice, which have a conditional knockout of Msh2 in the intestinal tract and develop intestinal cancer, we showed vaccination with a combination of only 4 FSPs significantly increased FSP-specific adaptive immunity, reduced intestinal tumor burden, and prolonged overall survival. Combination of FSP vaccination with daily naproxen treatment potentiated immune response, delayed tumor growth, and prolonged survival even more effectively than FSP vaccination alone. CONCLUSIONS Our preclinical findings support a clinical strategy of recurrent FSP neoantigen vaccination for LS cancer immunoprevention.
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MESH Headings
- Adjuvants, Immunologic/pharmacology
- Animals
- Anti-Inflammatory Agents, Non-Steroidal/pharmacology
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/pharmacology
- Cancer Vaccines/genetics
- Cancer Vaccines/immunology
- Cancer Vaccines/pharmacology
- Colorectal Neoplasms, Hereditary Nonpolyposis/drug therapy
- Colorectal Neoplasms, Hereditary Nonpolyposis/genetics
- Colorectal Neoplasms, Hereditary Nonpolyposis/immunology
- Colorectal Neoplasms, Hereditary Nonpolyposis/pathology
- Databases, Genetic
- Disease Models, Animal
- Epitopes
- Frameshift Mutation
- Immunity, Cellular/drug effects
- Immunity, Humoral/drug effects
- Immunogenetic Phenomena
- Mice, Inbred C57BL
- Mice, Knockout
- MutS Homolog 2 Protein/genetics
- Naproxen/pharmacology
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Peptide Fragments/pharmacology
- Tumor Burden/drug effects
- Tumor Microenvironment
- Vaccination
- Vaccine Efficacy
- Mice
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Affiliation(s)
- Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany.
| | | | - Mine Oezcan-Wahlbrink
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Jason D Marshall
- Cancer ImmunoPrevention Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Alejandro Hernandez-Sanchez
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Katharina Urban
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Mark Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Eduardo Cortes
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Elena Tosti
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York
| | - Eva-Maria Katzenmaier
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Yurong Song
- Cancer ImmunoPrevention Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Ali Elsaadi
- Weill Cornell Medical College, New York, New York
| | - Nan Deng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vera Fuchs
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Nina Nelius
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Yan P Yuan
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany
| | - Shizuko Sei
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland
| | - Robert H Shoemaker
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland
| | - Asad Umar
- Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland
| | - Lei Wei
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany; Max Delbrück Centre for Molecular Medicine, Berlin, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany.
| | | | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center, Heidelberg, Germany.
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171
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Westcott PMK, Sacks NJ, Schenkel JM, Ely ZA, Smith O, Hauck H, Jaeger AM, Zhang D, Backlund CM, Beytagh MC, Patten JJ, Elbashir R, Eng G, Irvine DJ, Yilmaz OH, Jacks T. Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer. Nat Cancer 2021; 2:1071-1085. [PMID: 34738089 PMCID: PMC8562866 DOI: 10.1038/s43018-021-00247-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 07/16/2021] [Indexed: 02/08/2023]
Abstract
Immune evasion is a hallmark of cancer, and therapies that restore immune surveillance have proven highly effective in cancers with high tumor mutation burden (TMB) (e.g., those with microsatellite instability (MSI)). Whether low TMB cancers, which are largely refractory to immunotherapy, harbor potentially immunogenic neoantigens remains unclear. Here, we show that tumors from all patients with microsatellite stable (MSS) colorectal cancer (CRC) express clonal predicted neoantigens despite low TMB. Unexpectedly, these neoantigens are broadly expressed at lower levels compared to those in MSI CRC. Using a versatile platform for modulating neoantigen expression in CRC organoids and transplantation into the distal colon of mice, we show that low expression precludes productive cross priming and drives immediate T cell dysfunction. Strikingly, experimental or therapeutic rescue of priming rendered T cells capable of controlling tumors with low neoantigen expression. These findings underscore a critical role of neoantigen expression level in immune evasion and therapy response.
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Affiliation(s)
- Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nathan J Sacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jason M Schenkel
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Zackery A Ely
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Olivia Smith
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haley Hauck
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex M Jaeger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Zhang
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Coralie M Backlund
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mary C Beytagh
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J J Patten
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan Elbashir
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George Eng
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Darrell J Irvine
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Omer H Yilmaz
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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172
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Cao S, Peterson SM, Müller S, Reichelt M, McRoberts Amador C, Martinez-Martin N. A membrane protein display platform for receptor interactome discovery. Proc Natl Acad Sci U S A 2021; 118:e2025451118. [PMID: 34531301 PMCID: PMC8488672 DOI: 10.1073/pnas.2025451118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
Cell surface receptors are critical for cell signaling and constitute a quarter of all human genes. Despite their importance and abundance, receptor interaction networks remain understudied because of difficulties associated with maintaining membrane proteins in their native conformation and their typically weak interactions. To overcome these challenges, we developed an extracellular vesicle-based method for membrane protein display that enables purification-free and high-throughput detection of receptor-ligand interactions in membranes. We demonstrate that this platform is broadly applicable to a variety of membrane proteins, enabling enhanced detection of extracellular interactions over a wide range of binding affinities. We were able to recapitulate and expand the interactome for prominent members of the B7 family of immunoregulatory proteins such as PD-L1/CD274 and B7-H3/CD276. Moreover, when applied to the orphan cancer-associated fibroblast protein, LRRC15, we identified a membrane-dependent interaction with the tumor stroma marker TEM1/CD248. Furthermore, this platform enabled profiling of cellular receptors for target-expressing as well as endogenous extracellular vesicles. Overall, this study presents a sensitive and easy to use screening platform that bypasses membrane protein purification and enables characterization of interactomes for any cell surface-expressed target of interest in its native state.
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Affiliation(s)
- Shengya Cao
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080;
| | - Sean M Peterson
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080
| | - Sören Müller
- Oncology Bioinformatics, Genentech, South San Francisco, CA 94080
| | - Mike Reichelt
- Pathology Labs, Genentech, South San Francisco, CA 94080
| | | | - Nadia Martinez-Martin
- Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080;
- Biologics, Almirall, 08022 Barcelona, Spain
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173
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Barroca-Ferreira J, Cruz-Vicente P, Santos MFA, Rocha SM, Santos-Silva T, Maia CJ, Passarinha LA. Enhanced Stability of Detergent-Free Human Native STEAP1 Protein from Neoplastic Prostate Cancer Cells upon an Innovative Isolation Procedure. Int J Mol Sci 2021; 22:10012. [PMID: 34576175 PMCID: PMC8472055 DOI: 10.3390/ijms221810012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The STEAP1 is a cell-surface antigen over-expressed in prostate cancer, which contributes to tumor progression and aggressiveness. However, the molecular mechanisms underlying STEAP1 and its structural determinants remain elusive. METHODS The fraction capacity of Butyl- and Octyl-Sepharose matrices on LNCaP lysates was evaluated by manipulating the ionic strength of binding and elution phases, followed by a Co-Immunoprecipitation (Co-IP) polishing. Several potential stabilizing additives were assessed, and the melting temperature (Tm) values ranked the best/worst compounds. The secondary structure of STEAP1 was identified by circular dichroism. RESULTS The STEAP1 was not fully captured with 1.375 M (Butyl), in contrast with interfering heterologous proteins, which were strongly retained and mostly eluted with water. This single step demonstrated higher selectivity of Butyl-Sepharose for host impurities removal from injected crude samples. Co-IP allowed recovering a purified fraction of STEAP1 and contributed to unveil potential physiologically interacting counterparts with the target. A Tm of ~55 °C was determined, confirming STEAP1 stability in the purification buffer. A predominant α-helical structure was identified, ensuring the protein's structural stability. CONCLUSIONS A method for successfully isolating human STEAP1 from LNCaP cells was provided, avoiding the use of detergents to achieve stability, even outside a membrane-mimicking environment.
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Affiliation(s)
- Jorge Barroca-Ferreira
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Pedro Cruz-Vicente
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Marino F. A. Santos
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Sandra M. Rocha
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
| | - Teresa Santos-Silva
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Cláudio J. Maia
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
| | - Luís A. Passarinha
- CICS-UBI–Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; (J.B.-F.); (P.C.-V.); (S.M.R.); (C.J.M.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; (M.F.A.S.); (T.S.-S.)
- UCIBIO–Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Laboratório de Fármaco-Toxicologia-UBIMedical, University of Beira Interior, 6201-284 Covilhã, Portugal
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174
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Schmidt J, Oppermann E, Blaheta RA, Schreckenbach T, Lunger I, Rieger MA, Bechstein WO, Holzer K, Malkomes P. Carbonic-anhydrase IX expression is increased in thyroid cancer tissue and represents a potential therapeutic target to eradicate thyroid tumor-initiating cells. Mol Cell Endocrinol 2021; 535:111382. [PMID: 34216643 DOI: 10.1016/j.mce.2021.111382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
The expression of Carbonic-anhydrase IX (CAIX) in thyroid cancer (TC) subtypes was determined and its role in cancer cell growth and tumor-initiating cells (TICs) investigated. Immunohistochemistry in 114 TC patients revealed that CAIX expression was increased in tumor specimens of papillary, follicular and anaplastic TCs compared to normal thyroid tissue. Clinicopathological data indicated that lymph node metastases were more frequent in patients with high CAIX expression. The Cancer Genome Atlas database analysis demonstrated that a strong CAIX-mRNA expression was associated with advanced tumor stages and poor survival in TCs. In TC cell lines, CAIX expression was elevated in tumorspheres compared to monolayer cultures and was associated with an increased expression of stemness markers. Genetic knockdown or pharmacological inhibition of CAIX suppressed cell proliferation and the TIC ability to form tumorspheres by an induction of apoptosis and cell-cycle arrest. These findings suggest CAIX as a potential prognostic marker and a therapeutic target for thyroid cancer.
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Affiliation(s)
- Jennifer Schmidt
- Hospital of the Goethe University Frankfurt, Department of General, Visceral and Transplant Surgery, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Elsie Oppermann
- Hospital of the Goethe University Frankfurt, Department of General, Visceral and Transplant Surgery, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Roman A Blaheta
- Hospital of the Goethe University Frankfurt, Department of Urology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Teresa Schreckenbach
- Hospital of the Goethe University Frankfurt, Department of General, Visceral and Transplant Surgery, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Ilaria Lunger
- Hospital of the Goethe University Frankfurt, Department of General, Visceral and Transplant Surgery, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Hospital of the Goethe University Frankfurt, Department of Inner Medicine, Hematology/Oncology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Michael A Rieger
- Hospital of the Goethe University Frankfurt, Department of Inner Medicine, Hematology/Oncology, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; German Cancer Consortium and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany; Frankfurt Cancer Institute, Paul-Ehrlich-Straße 42-44, 60596, Frankfurt am Main, Germany
| | - Wolf Otto Bechstein
- Hospital of the Goethe University Frankfurt, Department of General, Visceral and Transplant Surgery, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Katharina Holzer
- Hospital of the Goethe University Frankfurt, Department of General, Visceral and Transplant Surgery, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany; Philipps University Hospital of Marburg, Section of Endocrine Surgery, Department of Visceral-, Thoracic- and Vascular Surgery, Baldingerstraße, 35043, Marburg, Germany
| | - Patrizia Malkomes
- Hospital of the Goethe University Frankfurt, Department of General, Visceral and Transplant Surgery, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
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175
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Plavec TV, Mitrović A, Perišić Nanut M, Štrukelj B, Kos J, Berlec A. Targeting of fluorescent Lactococcus lactis to colorectal cancer cells through surface display of tumour-antigen binding proteins. Microb Biotechnol 2021; 14:2227-2240. [PMID: 34347360 PMCID: PMC8449671 DOI: 10.1111/1751-7915.13907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/20/2021] [Accepted: 07/20/2021] [Indexed: 12/11/2022] Open
Abstract
Development of targeted treatment for colorectal cancer is crucial to avoid side effects. To harness the possibilities offered by microbiome engineering, we prepared safe multifunctional cancer cell-targeting bacteria Lactococcus lactis. They displayed, on their surface, binding proteins for cancer-associated transmembrane receptors epithelial cell adhesion molecule (EpCAM) and human epidermal growth factor receptor 2 (HER2) and co-expressed an infrared fluorescent protein for imaging. Binding of engineered L. lactis to tumour antigens EpCAM and HER2 was confirmed and characterised in vitro using soluble receptors. The proof-of-principle of targeting was demonstrated on human cell lines HEK293, HT-29 and Caco-2 with fluorescent microscopy and flow cytometry. The highest L. lactis adhesion was seen for the HEK293 cells with the overexpressed tumour antigens, where colocalisation with their tumour antigens was seen for 39% and 67% of EpCAM-targeting and HER2-targeting bacteria, respectively. On the other hand, no binding was observed to HEK293 cells without tumour antigens, confirming the selectivity of the engineered L. lactis. Apart from cell targeting in static conditions, targeting ability of engineered L. lactis was also shown in conditions of constant flow of bacterial suspension over the HEK293 cells. Successful targeting by engineered L. lactis support the future use of these bacteria in biopharmaceutical delivery for the treatment of colorectal cancer.
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Affiliation(s)
- Tina Vida Plavec
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
- Faculty of PharmacyUniversity of LjubljanaAškerčeva 7LjubljanaSlovenia
| | - Ana Mitrović
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
| | | | - Borut Štrukelj
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
- Faculty of PharmacyUniversity of LjubljanaAškerčeva 7LjubljanaSlovenia
| | - Janko Kos
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
- Faculty of PharmacyUniversity of LjubljanaAškerčeva 7LjubljanaSlovenia
| | - Aleš Berlec
- Department of BiotechnologyJožef Stefan InstituteJamova 39LjubljanaSlovenia
- Faculty of PharmacyUniversity of LjubljanaAškerčeva 7LjubljanaSlovenia
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176
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Nin DS, Wujanto C, Tan TZ, Lim D, Damen JMA, Wu KY, Dai ZM, Lee ZW, Idres SB, Leong YH, Jha S, Ng JSY, Low JJH, Chang SC, Tan DSP, Wu W, Choo BA, Deng LW. GAGE mediates radio resistance in cervical cancers via the regulation of chromatin accessibility. Cell Rep 2021; 36:109621. [PMID: 34469741 DOI: 10.1016/j.celrep.2021.109621] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Radiotherapy (RT) resistance is a major cause of treatment failure in cancers that use definitive RT as their primary treatment modality. This study identifies the cancer/testis (CT) antigen G antigen (GAGE) as a mediator of radio resistance in cervical cancers. Elevated GAGE expression positively associates with de novo RT resistance in clinical samples. GAGE, specifically the GAGE12 protein variant, confers RT resistance through synemin-dependent chromatin localization, promoting the association of histone deacetylase 1/2 (HDAC1/2) to its inhibitor actin. This cumulates to elevated histone 3 lysine 56 acetylation (H3K56Ac) levels, increased chromatin accessibility, and improved DNA repair efficiency. Molecular or pharmacological disruption of the GAGE-associated complex restores radiosensitivity. Molecularly, this study demonstrates the role of GAGE in the regulation of chromatin dynamics. Clinically, this study puts forward the utility of GAGE as a pre-screening biomarker to identify poor responders at initial diagnosis and the therapeutic potential of agents that target GAGE and its associated complex in combination with radiotherapy to improve outcomes.
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Affiliation(s)
- Dawn Sijin Nin
- Department of Biochemistry, Yong Loo Lin School of Medicine (YLLSOM), National University of Singapore (NUS), Singapore 117596, Singapore; NUS Center for Cancer Research, YLLSOM, NUS, Singapore 117599, Singapore.
| | - Caryn Wujanto
- Department of Radiation Oncology, National University Hospital (NUH), Singapore 119074, Singapore; National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, NUS, Singapore 117599, Singapore
| | - Diana Lim
- Department of Pathology, NUH, Singapore 119074, Singapore; National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore
| | - J Mirjam A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht , the Netherlands
| | - Kuan-Yi Wu
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ziyu Melvin Dai
- Department of Biochemistry, Yong Loo Lin School of Medicine (YLLSOM), National University of Singapore (NUS), Singapore 117596, Singapore
| | - Zheng-Wei Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine (YLLSOM), National University of Singapore (NUS), Singapore 117596, Singapore
| | - Shabana Binte Idres
- Department of Biochemistry, Yong Loo Lin School of Medicine (YLLSOM), National University of Singapore (NUS), Singapore 117596, Singapore
| | - Yiat Horng Leong
- Department of Radiation Oncology, National University Hospital (NUH), Singapore 119074, Singapore; National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore
| | - Sudhakar Jha
- Department of Biochemistry, Yong Loo Lin School of Medicine (YLLSOM), National University of Singapore (NUS), Singapore 117596, Singapore; Cancer Science Institute of Singapore, NUS, Singapore 117599, Singapore; National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore; Department of Physiological Sciences, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK, USA; NUS Center for Cancer Research, YLLSOM, NUS, Singapore 117599, Singapore
| | - Joseph Soon-Yau Ng
- National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore; Department of Obstetrics and Gynecology, YLLSOM, NUS, Singapore 119228, Singapore
| | - Jeffrey J H Low
- National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore; Department of Obstetrics and Gynecology, YLLSOM, NUS, Singapore 119228, Singapore
| | - Shih-Chung Chang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - David Shao Peng Tan
- Cancer Science Institute of Singapore, NUS, Singapore 117599, Singapore; National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore; Department of Hematology-Oncology, NUHS, Singapore 119228, Singapore; NUS Center for Cancer Research, YLLSOM, NUS, Singapore 117599, Singapore
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht , the Netherlands
| | - Bok Ai Choo
- Department of Radiation Oncology, National University Hospital (NUH), Singapore 119074, Singapore; National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore
| | - Lih-Wen Deng
- Department of Biochemistry, Yong Loo Lin School of Medicine (YLLSOM), National University of Singapore (NUS), Singapore 117596, Singapore; National University Cancer Institute, Singapore National University Health System (NUHS), Singapore 119074, Singapore; NUS Center for Cancer Research, YLLSOM, NUS, Singapore 117599, Singapore; NUS Graduate School - Integrative Sciences and Engineering Programme, NUS, Singapore 119077, Singapore.
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177
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Koşaloğlu-Yalçın Z, Blazeska N, Carter H, Nielsen M, Cohen E, Kufe D, Conejo-Garcia J, Robbins P, Schoenberger SP, Peters B, Sette A. The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community. Front Immunol 2021; 12:735609. [PMID: 34504503 PMCID: PMC8421848 DOI: 10.3389/fimmu.2021.735609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/09/2021] [Indexed: 12/17/2022] Open
Abstract
Recent years have witnessed a dramatic rise in interest towards cancer epitopes in general and particularly neoepitopes, antigens that are encoded by somatic mutations that arise as a consequence of tumorigenesis. There is also an interest in the specific T cell and B cell receptors recognizing these epitopes, as they have therapeutic applications. They can also aid in basic studies to infer the specificity of T cells or B cells characterized in bulk and single-cell sequencing data. The resurgence of interest in T cell and B cell epitopes emphasizes the need to catalog all cancer epitope-related data linked to the biological, immunological, and clinical contexts, and most importantly, making this information freely available to the scientific community in a user-friendly format. In parallel, there is also a need to develop resources for epitope prediction and analysis tools that provide researchers access to predictive strategies and provide objective evaluations of their performance. For example, such tools should enable researchers to identify epitopes that can be effectively used for immunotherapy or in defining biomarkers to predict the outcome of checkpoint blockade therapies. We present here a detailed vision, blueprint, and work plan for the development of a new resource, the Cancer Epitope Database and Analysis Resource (CEDAR). CEDAR will provide a freely accessible, comprehensive collection of cancer epitope and receptor data curated from the literature and provide easily accessible epitope and T cell/B cell target prediction and analysis tools. The curated cancer epitope data will provide a transparent benchmark dataset that can be used to assess how well prediction tools perform and to develop new prediction tools relevant to the cancer research community.
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MESH Headings
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Computational Biology
- Databases, Genetic
- Epitopes, B-Lymphocyte
- Epitopes, T-Lymphocyte
- Humans
- Immunotherapy
- Mutation
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/therapy
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Tumor Microenvironment
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Affiliation(s)
- Zeynep Koşaloğlu-Yalçın
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Nina Blazeska
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
- Moore’s Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina
| | - Ezra Cohen
- Moore’s Cancer Center, University of California San Diego, La Jolla, CA, United States
| | - Donald Kufe
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Jose Conejo-Garcia
- Department of Gynecologic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Paul Robbins
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Stephen P. Schoenberger
- Laboratory of Cellular Immunology, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
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178
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Ye L, Wang L, Yang J, Hu P, Zhang C, Tong S, Liu Z, Tian D. Identification of tumor antigens and immune subtypes in lower grade gliomas for mRNA vaccine development. J Transl Med 2021; 19:352. [PMID: 34404444 PMCID: PMC8369324 DOI: 10.1186/s12967-021-03014-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND As an important part of tumor immunotherapy for adjunct, therapeutic tumor vaccines have been effective against multiple solid cancers, while their efficacy against lower grade glioma (LGG) remains undefined. Immunophenotyping of tumors is an essential tool to evaluate the immune function of patients with immunodeficiency or autoimmunity. Therefore, this study aims to find the potential tumor antigen of LGG and identify the suitable population for cancer vaccination based on the immune landscape. METHOD The genomic and clinical data of 529 patients with LGG were obtained from TCGA, the mRNA_seq data of normal brain tissue were downloaded from GTEx. Differential expression gene and mutation analysis were performed to screen out potential antigens, K-M curves were carried out to investigate the correlation between the level of potential antigens and OS and DFS of patients. TIMER dataset was used to explore the correlation between genes and immune infiltrating cells. Immunophenotyping of 529 tumor samples was based on the single-sample gene sets enrichment analysis. Cibersort and Estimate algorithm were used to explore the tumor immune microenvironment characteristics in each immune subtype. Weighted gene co-expression network analysis (WGCNA) clustered immune-related genes and screened the hub genes, and pathway enrichment analyses were performed on the hub modules related to immune subtype in the WGCNA. RESULTS Selecting for the mutated, up-regulated, prognosis- and immune-related genes, four potential tumor antigens were identified in LGG. They were also significantly positively associated with the antigen-presenting immune cells (APCs). Three robust immune subtypes, IS1, IS2 and IS3, represented immune status "desert", "immune inhibition", and "inflamed" respectively, which might serve as a predictive parameter. Subsequently, clinicopathological features, including the codeletion status of 1p19q, IDH mutation status, tumor mutation burden, tumor stemness, etc., were significantly different among subtypes. CONCLUSION FCGBP, FLNC, TLR7, and CSF2RA were potential antigens for developing cancer vaccination, and the patients in IS3 were considered the most suitable for vaccination in LGG.
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Affiliation(s)
- Liguo Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R. China
| | - Long Wang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R. China
| | - Ji'an Yang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R. China
| | - Ping Hu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R. China
| | - Chunyu Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R. China
| | - Shi'ao Tong
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R. China
| | - Zhennan Liu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R. China
| | - Daofeng Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, P.R. China.
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179
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Poojary M, Jishnu PV, Kabekkodu SP. Prognostic Value of Melanoma-Associated Antigen-A (MAGE-A) Gene Expression in Various Human Cancers: A Systematic Review and Meta-analysis of 7428 Patients and 44 Studies. Mol Diagn Ther 2021; 24:537-555. [PMID: 32548799 PMCID: PMC7497308 DOI: 10.1007/s40291-020-00476-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Members of the melanoma-associated antigen-A (MAGE-A) subfamily are overexpressed in many cancers and can drive cancer progression, metastasis, and therapeutic recurrence. Objective This study is the first comprehensive meta-analysis evaluating the prognostic utility of MAGE-A members in different cancers. Methods A systematic literature search was conducted in PubMed, Google Scholar, Science Direct, and Web of Science. The pooled hazard ratios with 95% confidence intervals were estimated to evaluate the prognostic significance of MAGE-A expression in various cancers. Results In total, 44 eligible studies consisting of 7428 patients from 11 countries were analysed. Univariate and multivariate analysis for overall survival, progression-free survival, and disease-free survival showed a significant association between high MAGE-A expression and various cancers (P < 0.00001). Additionally, subgroup analysis demonstrated that high MAGE-A expression was significantly associated with poor prognosis for lung, gastrointestinal, breast, and ovarian cancer in both univariate and multivariate analysis for overall survival. Conclusion Overexpression of MAGE-A subfamily members is linked to poor prognosis in multiple cancers. Therefore, it could serve as a potential prognostic marker of poor prognosis in cancers. Electronic supplementary material The online version of this article (10.1007/s40291-020-00476-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manish Poojary
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Padacherri Vethil Jishnu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
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180
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Jiao B, Gulati R, Hendrix N, Gore JL, Rais-Bahrami S, Morgan TM, Etzioni R. Economic Evaluation of Urine-Based or Magnetic Resonance Imaging Reflex Tests in Men With Intermediate Prostate-Specific Antigen Levels in the United States. Value Health 2021; 24:1111-1117. [PMID: 34372976 PMCID: PMC8358184 DOI: 10.1016/j.jval.2021.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/03/2021] [Accepted: 02/28/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVES For men with intermediate prostate-specific antigen (PSA) levels (4-10 ng/mL), urine-based biomarkers and multiparametric magnetic resonance imaging (MRI) are increasingly used as reflex tests before prostate biopsy. We assessed the cost effectiveness of these reflex tests in the United States. METHODS We used an existing microsimulation model of prostate cancer (PCa) progression and survival to predict lifetime outcomes for a hypothetical cohort of 55-year-old men with intermediate PSA levels. Urine-based biomarkers-PCa antigen (PCA3), TMPRSS2:ERG gene fusion (T2:ERG), and the MyProstateScore (MPS) for any PCa and for high-grade (Gleason score ≥7) PCa (MPShg)-were generated using biomarker data from 1112 men presenting for biopsy at 10 United States institutions. MRI results were based on published sensitivity and specificity for high-grade PCa. Costs and utilities were sourced from literature and Medicare reimbursement schedules. Outcome measures included life years, quality-adjusted life years (QALYs), and lifetime medical costs per patient. Incremental cost-effectiveness ratios were empirically calculated on the basis of simulated life histories under different reflex testing strategies. RESULTS Biopsying all men provided the most life years and QALYs, followed by reflex testing using MPShg, MPS, MRI, T2:ERG, PCA3, and biopsying no men (QALY range across strategies 15.98-16.09). Accounting for costs, MRI and MPShg were dominated by other strategies. PCA3, T2:ERG, and MPS were likely to be the most cost-effective strategy at willingness-to-pay thresholds of $100 000/QALY, $125 000/QALY, and $150 000/QALY, respectively. CONCLUSIONS Using PCA3, T2:ERG, or MPS as reflex tests has greater economic value than MRI, biopsying all men, or biopsying no men with intermediate PSA levels.
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Affiliation(s)
- Boshen Jiao
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, University of Washington, Seattle, WA
| | - Roman Gulati
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Nathaniel Hendrix
- The Comparative Health Outcomes, Policy, and Economics (CHOICE) Institute, University of Washington, Seattle, WA
| | - John L Gore
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Soroush Rais-Bahrami
- Department of Urology, Department of Radiology, and O'Neal Comprehensive Cancer Center at UAB, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Todd M Morgan
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Ruth Etzioni
- Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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181
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Kim SK, Nguyen C, Avins AL, Abrams GD. Identification of Three Loci Associated with Achilles Tendon Injury Risk from a Genome-wide Association Study. Med Sci Sports Exerc 2021; 53:1748-1755. [PMID: 33606446 PMCID: PMC8282631 DOI: 10.1249/mss.0000000000002622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
PURPOSE This study aimed to screen the entire genome for genetic markers associated with risk for Achilles tendon injury. METHODS A genome-wide association analysis was performed using data from the Kaiser Permanente Research Board and the UK Biobank. Achilles tendon injury cases were identified based on electronic health records from the Kaiser Permanente Research Board databank and the UK Biobank from individuals of European ancestry. Genome-wide association analyses from both cohorts were tested for Achilles tendon injury using a logistic regression model adjusting for sex, height, weight, and race/ethnicity using allele counts for single nucleotide polymorphisms (SNP). Previously identified genes within the literature were also tested for association with Achilles tendon injury. RESULTS There were a total of 12,354 cases of Achilles tendon injury and 483,080 controls within the two combined cohorts, with 67 SNP in three chromosomal loci demonstrating a genome-wide significant association with Achilles tendon injury. The first locus contains a single SNP (rs183364169) near the CDCP1 and TMEM158 genes on chromosome 3. The second locus contains 65 SNP in three independently segregating sets near the MPP7 gene on chromosome 10. The last locus contains a single SNP (rs4454832) near the SOX21 and GPR180 genes on chromosome 13. The current data were used to test 14 candidate genes previously reported to show an association with Achilles tendon injury, but none showed a significant association (all P > 0.05). CONCLUSION Three loci were identified as potential risk factors for Achilles tendon injury and deserve further validation and investigation of molecular mechanisms.
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Affiliation(s)
- Stuart K. Kim
- Department of Developmental Biology, Stanford University Medical School, Stanford, CA
| | - Condor Nguyen
- Department of Developmental Biology, Stanford University Medical School, Stanford, CA
| | - Andy L. Avins
- Kaiser Permanente Northern California, Division of Research, Oakland, CA
| | - Geoffrey D. Abrams
- Department of Orthopaedic Surgery, Stanford University Medical Center, Stanford, CA
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182
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Shi C, Weng M, Zhu H, Guo Y, Xu D, Jin H, Wei B, Cao Z. NUDCD1 knockdown inhibits the proliferation, migration, and invasion of pancreatic cancer via the EMT process. Aging (Albany NY) 2021; 13:18298-18309. [PMID: 34325402 PMCID: PMC8351729 DOI: 10.18632/aging.203276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 04/29/2021] [Indexed: 12/13/2022]
Abstract
NudC domain containing 1 (NUDCD1) is an oncoprotein frequently activated or upregulated in various human cancers, but its role in pancreatic cancer (PC) remains unknown. Thus, we aimed to determine the function and mechanism of NUDCD1 in PC. We employed Western blot and quantitative real-time polymerase chain reaction to assess NUDCD1 expression in cells and PC tissues. NUDCD1 was knocked down in Patu8988 and PANC-1 cells. We conducted real-time cell analysis, wound healing assay, transwell assay and colony formation assay to evaluate the metastatic and proliferative abilities of PC cells. Western blot was conducted to assess the expression of markers associated with apoptosis and epithelial-mesenchymal transition (EMT). Also, we established a tumor xenograft model to determine the role of NUDCD1 in vivo. NUDCD1 was overexpressed in PC tissues and cells. NUDCD1 knockdown suppressed the invasion, migration, and proliferative abilities of the cells and induced PC cell apoptosis. The specific mechanism of NUDCD1 was related to the modulation of the EMT process. Data obtained from in vivo experiments revealed that NUDCD1 knockdown inhibited the tumor growth, proliferation, and metastasis by modulating the EMT and inducing the apoptosis of PC cells.
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Affiliation(s)
- Chunling Shi
- School of Stomatology, Wenzhou Medical University, Wenzhou 110013, China
| | - Min Weng
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Hengyue Zhu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Yangyang Guo
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Dongdong Xu
- School of Stomatology, Wenzhou Medical University, Wenzhou 110013, China
| | - Hairu Jin
- School of Stomatology, Wenzhou Medical University, Wenzhou 110013, China
| | - Binshuang Wei
- School of Stomatology, Wenzhou Medical University, Wenzhou 110013, China
| | - Zhensheng Cao
- School of Stomatology, Wenzhou Medical University, Wenzhou 110013, China
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183
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Abstract
Next-generation sequencing technologies have revolutionized our ability to catalog the landscape of somatic mutations in tumor genomes. These mutations can sometimes create so-called neoantigens, which allow the immune system to detect and eliminate tumor cells. However, efforts that stimulate the immune system to eliminate tumors based on their molecular differences have had less success than has been hoped for, and there are conflicting reports about the role of neoantigens in the success of this approach. Here we review some of the conflicting evidence in the literature and highlight key aspects of the tumor-immune interface that are emerging as major determinants of whether mutation-derived neoantigens will contribute to an immunotherapy response. Accounting for these factors is expected to improve success rates of future immunotherapy approaches.
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Affiliation(s)
- Andrea Castro
- Biomedical Informatics Program, University of California San Diego, La Jolla, California 92093, USA
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA;
| | - Maurizio Zanetti
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
- The Laboratory of Immunology, Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA;
- The Laboratory of Immunology, Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
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184
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Ito T, Tanegashima K, Tanaka Y, Hashimoto H, Murata M, Oda Y, Kaku-Ito Y. Trop2 Expression in Extramammary Paget's Disease and Normal Skin. Int J Mol Sci 2021; 22:ijms22147706. [PMID: 34299325 PMCID: PMC8304908 DOI: 10.3390/ijms22147706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/11/2021] [Accepted: 07/17/2021] [Indexed: 12/18/2022] Open
Abstract
Extramammary Paget's disease (EMPD) is a rare skin cancer arising in the apocrine gland-rich areas. Most EMPD tumors are dormant, but metastatic lesions are associated with poor outcomes owing to the lack of effective systemic therapies. Trophoblast cell surface antigen 2 (Trop2), a surface glycoprotein, has drawn attention as a potential therapeutic target for solid tumors. Sacituzumab govitecan, an antibody-drug conjugate of Trop2, has recently entered clinical use for the treatment of various solid cancers. However, little is known about the role of Trop2 in EMPD. In this study, we immunohistochemically examined Trop2 expression in 116 EMPD tissue samples and 10 normal skin tissues. In normal skin, Trop2 was expressed in the epidermal keratinocytes, inner root sheaths, and infundibulum/isthmus epithelium of hair follicles, eccrine/apocrine glands, and sebaceous glands. Most EMPD tissues exhibited homogeneous and strong Trop2 expression, and high Trop2 expression was significantly associated with worse disease-free survival (p = 0.0343). These results suggest the potential use of Trop2-targeted therapy for EMPD and improve our understanding of the skin-related adverse effects of current Trop2-targeted therapies such as sacituzumab govitecan.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/pharmacology
- Antigens, Neoplasm/biosynthesis
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Apocrine Glands/metabolism
- Biomarkers, Tumor
- Camptothecin/analogs & derivatives
- Camptothecin/pharmacology
- Cell Adhesion Molecules/biosynthesis
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/metabolism
- Female
- Gene Expression/genetics
- Gene Expression Regulation/genetics
- Hair Follicle/metabolism
- Humans
- Immunoconjugates/pharmacology
- Keratinocytes/metabolism
- Male
- Membrane Glycoproteins/metabolism
- Middle Aged
- Paget Disease, Extramammary/drug therapy
- Paget Disease, Extramammary/genetics
- Paget Disease, Extramammary/metabolism
- Paget Disease, Extramammary/pathology
- Sebaceous Glands/metabolism
- Skin/metabolism
- Skin Neoplasms/drug therapy
- Skin Neoplasms/genetics
- Skin Neoplasms/metabolism
- Skin Neoplasms/pathology
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Affiliation(s)
- Takamichi Ito
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.T.); (Y.T.); (H.H.); (M.M.); (Y.K.-I.)
- Correspondence: ; Tel.: +81-92-642-5585
| | - Keiko Tanegashima
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.T.); (Y.T.); (H.H.); (M.M.); (Y.K.-I.)
| | - Yuka Tanaka
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.T.); (Y.T.); (H.H.); (M.M.); (Y.K.-I.)
| | - Hiroki Hashimoto
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.T.); (Y.T.); (H.H.); (M.M.); (Y.K.-I.)
| | - Maho Murata
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.T.); (Y.T.); (H.H.); (M.M.); (Y.K.-I.)
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan;
| | - Yumiko Kaku-Ito
- Department of Dermatology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan; (K.T.); (Y.T.); (H.H.); (M.M.); (Y.K.-I.)
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185
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Cardenas-Rodriguez M, Austin-Tse C, Bergboer JGM, Molinari E, Sugano Y, Bachmann-Gagescu R, Sayer JA, Drummond IA. Genetic compensation for cilia defects in cep290 mutants by upregulation of cilia-associated small GTPases. J Cell Sci 2021; 134:jcs258568. [PMID: 34155518 PMCID: PMC8325957 DOI: 10.1242/jcs.258568] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
Mutations in CEP290 (also known as NPHP6), a large multidomain coiled coil protein, are associated with multiple cilia-associated syndromes. Over 130 CEP290 mutations have been linked to a wide spectrum of human ciliopathies, raising the question of how mutations in a single gene cause different disease syndromes. In zebrafish, the expressivity of cep290 deficiencies were linked to the type of genetic ablation: acute cep290 morpholino knockdown caused severe cilia-related phenotypes, whereas deficiencies in a CRISPR/Cas9 genetic mutant were restricted to photoreceptor defects. Here, we show that milder phenotypes in genetic mutants were associated with the upregulation of genes encoding the cilia-associated small GTPases arl3, arl13b and unc119b. Upregulation of UNC119b was also observed in urine-derived renal epithelial cells from human Joubert syndrome CEP290 patients. Ectopic expression of arl3, arl13b and unc119b in cep290 morphant zebrafish embryos rescued Kupffer's vesicle cilia and partially rescued photoreceptor outer segment defects. The results suggest that genetic compensation by upregulation of genes involved in a common subcellular process, lipidated protein trafficking to cilia, may be a conserved mechanism contributing to genotype-phenotype variations observed in CEP290 deficiencies. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Magdalena Cardenas-Rodriguez
- Department of Medicine, Nephrology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Christina Austin-Tse
- Department of Pathology, Massachusetts General Hospital, 185 Cambridge St, Boston, MA 02114, USA
| | | | - Elisa Molinari
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE1 3BZ, UK
| | - Yuya Sugano
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | | | - John A. Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE1 3BZ, UK
- Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Freeman Road, Newcastle NE7 7DN, UK
| | - Iain A. Drummond
- Department of Medicine, Nephrology Division, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA
- Davis Center for Regenerative Biology and Aging, Mount Desert Island Biological Laboratory, Salisbury Cove, Bar Harbor, ME 04609, USA
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186
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Knupp D, Cooper DA, Saito Y, Darnell RB, Miura P. NOVA2 regulates neural circRNA biogenesis. Nucleic Acids Res 2021; 49:6849-6862. [PMID: 34157123 PMCID: PMC8266653 DOI: 10.1093/nar/gkab523] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 05/03/2021] [Accepted: 06/09/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are highly expressed in the brain and their expression increases during neuronal differentiation. The factors regulating circRNAs in the developing mouse brain are unknown. NOVA1 and NOVA2 are neural-enriched RNA-binding proteins with well-characterized roles in alternative splicing. Profiling of circRNAs from RNA-seq data revealed that global circRNA levels were reduced in embryonic cortex of Nova2 but not Nova1 knockout mice. Analysis of isolated inhibitory and excitatory cortical neurons lacking NOVA2 revealed an even more dramatic reduction of circRNAs and establishes a widespread role for NOVA2 in enhancing circRNA biogenesis. To investigate the cis-elements controlling NOVA2-regulation of circRNA biogenesis, we generated a backsplicing reporter based on the Efnb2 gene. We found that NOVA2-mediated backsplicing of circEfnb2 was impaired when YCAY clusters located in flanking introns were mutagenized. CLIP (cross-linking and immunoprecipitation) and additional reporter analyses demonstrated the importance of NOVA2 binding sites located in both flanking introns of circRNA loci. NOVA2 is the first RNA-binding protein identified to globally promote circRNA biogenesis in the developing brain.
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Affiliation(s)
- David Knupp
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Daphne A Cooper
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | - Yuhki Saito
- Laboratory of Molecular Neuro-oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Pedro Miura
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
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187
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Nadaf J, de Kock L, Chong AS, Korbonits M, Thorner P, Benlimame N, Fu L, Peet A, Warner J, Ploner O, Shuangshoti S, Albrecht S, Hamel N, Priest JR, Rivera B, Ragoussis J, Foulkes WD. Molecular characterization of DICER1-mutated pituitary blastoma. Acta Neuropathol 2021; 141:929-944. [PMID: 33644822 DOI: 10.1007/s00401-021-02283-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022]
Abstract
Pituitary blastoma (PitB) has recently been identified as a rare and potentially lethal pediatric intracranial tumor. All cases that have been studied molecularly possess at least one DICER1 pathogenic variant. Here, we characterized nine pituitary samples, including three fresh frozen PitBs, three normal fetal pituitary glands and three normal postnatal pituitary glands using small-RNA-Seq, RNA-Seq, methylation profiling, whole genome sequencing and Nanostring® miRNA analyses; an extended series of 21 pituitary samples was used for validation purposes. These analyses demonstrated that DICER1 RNase IIIb hotspot mutations in PitBs induced improper processing of miRNA precursors, resulting in aberrant 5p-derived miRNA products and a skewed distribution of miRNAs favoring mature 3p over 5p miRNAs. This led to dysregulation of hundreds of 5p and 3p miRNAs and concomitant dysregulation of numerous mRNA targets. Gene expression analysis revealed PRAME as the most significantly upregulated gene (500-fold increase). PRAME is a member of the Retinoic Acid Receptor (RAR) signaling pathway and in PitBs, the RAR, WNT and NOTCH pathways are dysregulated. Cancer Hallmarks analysis showed that PI3K pathway is activated in the tumors. Whole genome sequencing demonstrated a quiet genome with very few somatic alterations. The comparison of methylation profiles to publicly available data from ~ 3000 other central nervous system tumors revealed that PitBs have a distinct methylation profile compared to all other tumors, including pituitary adenomas. In conclusion, this comprehensive characterization of DICER1-related PitB revealed key molecular underpinnings of PitB and identified pathways that could potentially be exploited in the treatment of this tumor.
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Affiliation(s)
- Javad Nadaf
- Department of Medical Genetics, The Lady Davis Institute, Jewish General Hospital, 3755 Cote St. Catherine Road, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Leanne de Kock
- Department of Medical Genetics, The Lady Davis Institute, Jewish General Hospital, 3755 Cote St. Catherine Road, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Anne-Sophie Chong
- Department of Medical Genetics, The Lady Davis Institute, Jewish General Hospital, 3755 Cote St. Catherine Road, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
| | - Paul Thorner
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Naciba Benlimame
- Research Pathology Facility, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Lili Fu
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Andrew Peet
- Birmingham Children's NHS Foundation Trust, Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Justin Warner
- Department of Child Health, University Hospital of Wales, Heath Park, Cardiff, UK
| | | | - Shanop Shuangshoti
- Department of Pathology and Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Steffen Albrecht
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Nancy Hamel
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | | | - Barbara Rivera
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - William D Foulkes
- Department of Medical Genetics, The Lady Davis Institute, Jewish General Hospital, 3755 Cote St. Catherine Road, Montreal, QC, H3T 1E2, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada.
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188
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Wang H, Jiang X, Cheng Y, Ren H, Hu Y, Zhang Y, Su H, Zou Z, Wang Q, Liu Z, Zhang J, Qiu X. MZT2A promotes NSCLC viability and invasion by increasing Akt phosphorylation via the MOZART2 domain. Cancer Sci 2021; 112:2210-2222. [PMID: 33754417 PMCID: PMC8177791 DOI: 10.1111/cas.14900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022] Open
Abstract
Mitotic spindle organizing protein 2A (MZT2A) is localized at the centrosome and regulates microtubule nucleation activity in cells. This study assessed the role of MZT2A in non-small-cell lung cancer (NSCLC). Differential MZT2A expression was bioinformatically assessed using TCGA database, the GEPIA database, and Kaplan-Meier survival data to determine the association between MZT2A expression and NSCLC prognosis. Furthermore, NSCLC tissue specimens were evaluated by immunohistochemistry. MZT2A was overexpressed or knocked down in NSCLC cells using cDNA and siRNA, respectively. The cells were subjected to various assays and treated with the selective Akt inhibitor LY294002 or co-transfected with galectin-3-binding protein (LGALS3BP) siRNA. MZT2A mRNA and protein levels were upregulated in NSCLC lesions and MTZ2A expression was associated with poor NSCLC prognosis. MZT2A protein was also highly expressed in NSCLC cells compared with the expression in normal bronchial cells. MZT2A expression promoted NSCLC cell viability and invasion, whereas MTZ2A siRNA had the opposite effect on NSCLC cells in vitro. At the protein level, MZT2A induced Akt phosphorylation, promoting NSCLC proliferation and invasion (but the selective Akt inhibitor blocked these effects) through upregulation of LGALS3BP via the MTZ2A MOZART2 domain, whereas LGALS3BP siRNA suppressed MTZ2A activity in NSCLC cells. The limited in vivo experiments confirmed the in vitro data. In conclusion, MZT2A exhibits oncogenic activity by activating LGALS3BP and Akt in NSCLC. Future studies will assess MTZ2A as a biomarker to predict NSCLC prognosis or as a target in the control of NSCLC progression.
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Affiliation(s)
- Huanxi Wang
- Department of PathologyChina Medical UniversityShenyangChina
| | - Xizi Jiang
- Department of PathologyChina Medical UniversityShenyangChina
| | - Yu Cheng
- Department of PathologyChina Medical UniversityShenyangChina
- Departemt of PathologyCancer Research LaboratoryChengde Medical CollegeChengdeChina
| | - Hongjiu Ren
- Department of PathologyChina Medical UniversityShenyangChina
| | - Yujiao Hu
- Department of PathologyChina Medical UniversityShenyangChina
| | - Yao Zhang
- Department of PathologyChina Medical UniversityShenyangChina
| | - Hongbo Su
- Department of PathologyChina Medical UniversityShenyangChina
| | - Zifang Zou
- Department of Thoracic SurgeryThe First Affiliated Hospital of China Medical UniversityShenyangChina
| | - Qiongzi Wang
- Department of PathologyChina Medical UniversityShenyangChina
| | - Zongang Liu
- Department of Thoracic SurgeryShengjing Hospital of China Medical UniversityShenyangChina
| | - Jiameng Zhang
- Department of PathologyChina Medical UniversityShenyangChina
| | - Xueshan Qiu
- Department of PathologyChina Medical UniversityShenyangChina
- Department of PathologyThe First Affiliated Hospital of China Medical UniversityShenyangChina
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189
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Craig AJ, Garcia-Lezana T, Ruiz de Galarreta M, Villacorta-Martin C, Kozlova EG, Martins-Filho SN, von Felden J, Ahsen ME, Bresnahan E, Hernandez-Meza G, Labgaa I, D’Avola D, Schwartz M, Llovet JM, Sia D, Thung S, Losic B, Lujambio A, Villanueva A. Transcriptomic characterization of cancer-testis antigens identifies MAGEA3 as a driver of tumor progression in hepatocellular carcinoma. PLoS Genet 2021; 17:e1009589. [PMID: 34166362 PMCID: PMC8224860 DOI: 10.1371/journal.pgen.1009589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 05/07/2021] [Indexed: 01/15/2023] Open
Abstract
Cancer testis antigens (CTAs) are an extensive gene family with a unique expression pattern restricted to germ cells, but aberrantly reactivated in cancer tissues. Studies indicate that the expression (or re-expression) of CTAs within the MAGE-A family is common in hepatocellular carcinoma (HCC). However, no systematic characterization has yet been reported. The aim of this study is to perform a comprehensive profile of CTA de-regulation in HCC and experimentally evaluate the role of MAGEA3 as a driver of HCC progression. The transcriptomic analysis of 44 multi-regionally sampled HCCs from 12 patients identified high intra-tumor heterogeneity of CTAs. In addition, a subset of CTAs was significantly overexpressed in histologically poorly differentiated regions. Further analysis of CTAs in larger patient cohorts revealed high CTA expression related to worse overall survival and several other markers of poor prognosis. Functional analysis of MAGEA3 was performed in human HCC cell lines by gene silencing and in a genetic mouse model by overexpression of MAGEA3 in the liver. Knockdown of MAGEA3 decreased cell proliferation, colony formation and increased apoptosis. MAGEA3 overexpression was associated with more aggressive tumors in vivo. In conclusion MAGEA3 enhances tumor progression and should be considered as a novel therapeutic target in HCC.
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Affiliation(s)
- Amanda J. Craig
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Teresa Garcia-Lezana
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Marina Ruiz de Galarreta
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Oncological Sciences, The Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Precision Immunology Institute at Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Carlos Villacorta-Martin
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Edgar G. Kozlova
- Department of Genetics and Genomic Sciences, Cancer Immunology Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Sebastiao N. Martins-Filho
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, Canada
| | - Johann von Felden
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mehmet Eren Ahsen
- Department of Genetics and Genomic Sciences, Cancer Immunology Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Erin Bresnahan
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Oncological Sciences, The Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Precision Immunology Institute at Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Gabriela Hernandez-Meza
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Ismail Labgaa
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Visceral Surgery, Lausanne University Hospital CHUV, Lausanne, Switzerland
| | - Delia D’Avola
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Liver Unit and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Clínica Universidad de Navarra, Pamplona, Spain
| | - Myron Schwartz
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Josep M. Llovet
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Translational Research Laboratory, BCLC Group, IDIBAPS, Hospital Clinic, Universitat de Barcelona, Catalonia and Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Daniela Sia
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Swan Thung
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Bojan Losic
- Department of Genetics and Genomic Sciences, Cancer Immunology Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Diabetes, Obesity and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Amaia Lujambio
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Oncological Sciences, The Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Precision Immunology Institute at Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
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190
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Zhao Y, Li Z, Zhu Y, Fu J, Zhao X, Zhang Y, Wang S, Wu J, Wang K, Wu R, Sui C, Shen S, Wu X, Wang H, Gao D, Chen L. Single-Cell Transcriptome Analysis Uncovers Intratumoral Heterogeneity and Underlying Mechanisms for Drug Resistance in Hepatobiliary Tumor Organoids. Adv Sci (Weinh) 2021; 8:e2003897. [PMID: 34105295 PMCID: PMC8188185 DOI: 10.1002/advs.202003897] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/29/2020] [Indexed: 05/30/2023]
Abstract
Molecular heterogeneity of hepatobiliary tumor including intertumoral and intratumoral disparity always leads to drug resistance. Here, seven hepatobiliary tumor organoids are generated to explore heterogeneity and evolution via single-cell RNA sequencing. HCC272 with high status of epithelia-mesenchymal transition proves broad-spectrum drug resistance. By examining the expression pattern of cancer stem cells markers (e.g., PROM1, CD44, and EPCAM), it is found that CD44 positive population may render drug resistance in HCC272. UMAP and pseudo-time analysis identify the intratumoral heterogeneity and distinct evolutionary trajectories, of which catenin beta-1 (CTNNB1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and nuclear paraspeckle assembly transcript 1 (NEAT1) advantage expression clusters are commonly shared across hepatobiliary organoids. CellphoneDB analysis further implies that metabolism advantage organoids with enrichment of hypoxia signal upregulate NEAT1 expression in CD44 subgroup and mediate drug resistance that relies on Jak-STAT pathway. Moreover, metabolism advantage clusters shared in several organoids have similar characteristic genes (GAPDH, NDRG1 (N-Myc downstream regulated 1), ALDOA, and CA9). The combination of GAPDH and NDRG1 is an independent risk factor and predictor for patient survival. This study delineates heterogeneity of hepatobiliary tumor organoids and proposes that the collaboration of intratumoral heterogenic subpopulations renders malignant phenotypes and drug resistance.
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Affiliation(s)
- Yan Zhao
- School of Life Sciences and Institute of Metabolism and Integrative BiologyFudan UniversityShanghai200438China
| | - Zhi‐Xuan Li
- National Center for Liver CancerShanghai200441China
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
| | - Yan‐Jing Zhu
- National Center for Liver CancerShanghai200441China
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
| | - Jing Fu
- National Center for Liver CancerShanghai200441China
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
| | - Xiao‐Fang Zhao
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Ya‐Ni Zhang
- Institute of Metabolism and Integrative BiologyFudan UniversityShanghai200438China
| | - Shan Wang
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Jian‐Min Wu
- School of Life Sciences and Institute of Metabolism and Integrative BiologyFudan UniversityShanghai200438China
| | - Kai‐Ting Wang
- School of Life Sciences and Institute of Metabolism and Integrative BiologyFudan UniversityShanghai200438China
| | - Rui Wu
- Eastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
| | - Cheng‐Jun Sui
- Eastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
| | - Si‐Yun Shen
- National Center for Liver CancerShanghai200441China
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
| | - Xuan Wu
- Department of Laboratory MedicineThe Tenth People's Hospital of ShanghaiTongji UniversityShanghai200072China
| | - Hong‐Yang Wang
- National Center for Liver CancerShanghai200441China
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Dong Gao
- The State Key Laboratory of Cell BiologyShanghai Key Laboratory of Molecular AndrologyCAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijing100101China
| | - Lei Chen
- National Center for Liver CancerShanghai200441China
- The International Cooperation Laboratory on Signal TransductionEastern Hepatobiliary Surgery HospitalSecond Military Medical UniversityShanghai200438China
- Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
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191
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Leerach N, Munesue S, Harashima A, Kimura K, Oshima Y, Kawano S, Tanaka M, Niimura A, Sakulsak N, Yamamoto H, Hori O, Yamamoto Y. RAGE signaling antagonist suppresses mouse macrophage foam cell formation. Biochem Biophys Res Commun 2021; 555:74-80. [PMID: 33813279 DOI: 10.1016/j.bbrc.2021.03.139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 03/24/2021] [Indexed: 01/23/2023]
Abstract
The engagement of the receptor for advanced glycation end-products (receptor for AGEs, RAGE) with diverse ligands could elicit chronic vascular inflammation, such as atherosclerosis. Binding of cytoplasmic tail RAGE (ctRAGE) to diaphanous-related formin 1 (Diaph1) is known to yield RAGE intracellular signal transduction and subsequent cellular responses. However, the effectiveness of an inhibitor of the ctRAGE/Diaph1 interaction in attenuating the development of atherosclerosis is unclear. In this study, using macrophages from Ager+/+ and Ager-/- mice, we validated the effects of an inhibitor on AGEs-RAGE-induced foam cell formation. The inhibitor significantly suppressed AGEs-RAGE-evoked Rac1 activity, cell invasion, and uptake of oxidized low-density lipoprotein, as well as AGEs-induced NF-κB activation and upregulation of proinflammatory gene expression. Moreover, expression of Il-10, an anti-inflammatory gene, was restored by this antagonist. These findings suggest that the RAGE-Diaph1 inhibitor could be a potential therapeutic drug against RAGE-related diseases, such as chronic inflammation and atherosclerosis.
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Affiliation(s)
- Nontaphat Leerach
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Seiichi Munesue
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Ai Harashima
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Kumi Kimura
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Yu Oshima
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Shuhei Kawano
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Mariko Tanaka
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Akane Niimura
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Natthiya Sakulsak
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Hiroshi Yamamoto
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan; Komatsu University, Komatsu, 923-0921, Japan
| | - Osamu Hori
- Department of Neuroanatomy, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan
| | - Yasuhiko Yamamoto
- Department of Biochemistry and Molecular Vascular Biology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, 920-8640, Japan.
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Haebe S, Shree T, Sathe A, Day G, Czerwinski DK, Grimes SM, Lee H, Binkley MS, Long SR, Martin B, Ji HP, Levy R. Single-cell analysis can define distinct evolution of tumor sites in follicular lymphoma. Blood 2021; 137:2869-2880. [PMID: 33728464 PMCID: PMC8160505 DOI: 10.1182/blood.2020009855] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Tumor heterogeneity complicates biomarker development and fosters drug resistance in solid malignancies. In lymphoma, our knowledge of site-to-site heterogeneity and its clinical implications is still limited. Here, we profiled 2 nodal, synchronously acquired tumor samples from 10 patients with follicular lymphoma (FL) using single-cell RNA, B-cell receptor (BCR) and T-cell receptor sequencing, and flow cytometry. By following the rapidly mutating tumor immunoglobulin genes, we discovered that BCR subclones were shared between the 2 tumor sites in some patients, but in many patients, the disease had evolved separately with limited tumor cell migration between the sites. Patients exhibiting divergent BCR evolution also exhibited divergent tumor gene-expression and cell-surface protein profiles. While the overall composition of the tumor microenvironment did not differ significantly between sites, we did detect a specific correlation between site-to-site tumor heterogeneity and T follicular helper (Tfh) cell abundance. We further observed enrichment of particular ligand-receptor pairs between tumor and Tfh cells, including CD40 and CD40LG, and a significant correlation between tumor CD40 expression and Tfh proliferation. Our study may explain discordant responses to systemic therapies, underscores the difficulty of capturing a patient's disease with a single biopsy, and furthers our understanding of tumor-immune networks in FL.
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MESH Headings
- Adult
- Aged
- Antigens, Neoplasm/biosynthesis
- Antigens, Neoplasm/genetics
- Biopsy, Fine-Needle
- CD40 Antigens/biosynthesis
- CD40 Antigens/genetics
- CD40 Ligand/biosynthesis
- CD40 Ligand/genetics
- Clonal Evolution/genetics
- DNA, Neoplasm/genetics
- Disease Progression
- Female
- Flow Cytometry
- Gene Rearrangement, B-Lymphocyte, Light Chain
- Gene Rearrangement, T-Lymphocyte
- Humans
- Lymph Nodes/chemistry
- Lymph Nodes/ultrastructure
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphoma, Follicular/chemistry
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/pathology
- Male
- Middle Aged
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Phylogeny
- RNA, Neoplasm/genetics
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Single-Cell Analysis
- T Follicular Helper Cells/immunology
- T Follicular Helper Cells/metabolism
- Transcriptome
- Tumor Microenvironment
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Affiliation(s)
- Sarah Haebe
- Division of Oncology, Department of Medicine, School of Medicine
| | - Tanaya Shree
- Division of Oncology, Department of Medicine, School of Medicine
| | - Anuja Sathe
- Division of Oncology, Department of Medicine, School of Medicine
| | - Grady Day
- Division of Oncology, Department of Medicine, School of Medicine
| | | | | | - HoJoon Lee
- Division of Oncology, Department of Medicine, School of Medicine
| | | | - Steven R Long
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA
| | - Brock Martin
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, School of Medicine
- Stanford Genome Technology Center
| | - Ronald Levy
- Division of Oncology, Department of Medicine, School of Medicine
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193
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Mukherjee K, Sur D, Singh A, Rai S, Das N, Sekar R, Narindi S, Dhingra VK, Jat B, Balraam KVV, Agarwal SP, Mandal PK. Robust expression of LINE-1 retrotransposon encoded proteins in oral squamous cell carcinoma. BMC Cancer 2021; 21:628. [PMID: 34044801 PMCID: PMC8161598 DOI: 10.1186/s12885-021-08174-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/07/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Oral Squamous Cell Carcinoma (OSCC) results from a series of genetic alteration in squamous cells. This particular type of cancer considers one of the most aggressive malignancies to control because of its frequent local invasions to the regional lymph node. Although several biomarkers have been reported, the key marker used to predict the behavior of the disease is largely unknown. Here we report Long INterpersed Element-1 (LINE1 or L1) retrotransposon activity in post-operative oral cancer samples. L1 is the only active retrotransposon occupying around 17% of the human genome with an estimated 500,000 copies. An active L1 encodes two proteins (L1ORF1p and L1ORF2p); both of which are critical in the process of retrotransposition. Several studies report that the L1 retrotransposon is highly active in many cancers. L1 activity is generally determined by assaying L1ORF1p because of its high expression and availability of the antibody. However, due to its lower expression and unavailability of a robust antibody, detection of L1ORF2p has been limited. L1ORF2p is the crucial protein in the process of retrotransposition as it provides endonuclease and reverse transcriptase (RT) activity. METHODS Immunohistochemistry and Western blotting were performed on the post-operative oral cancer samples and murine tissues. RESULTS Using in house novel antibodies against both the L1 proteins (L1ORF1p and L1ORF2p), we found L1 retrotransposon is extremely active in post-operative oral cancer tissues. Here, we report a novel human L1ORF2p antibody generated using an 80-amino-acid stretch from the RT domain, which is highly conserved among different species. The antibody detects significant L1ORF2p expression in human oral squamous cell carcinoma (OSCC) samples and murine germ tissues. CONCLUSIONS We report exceptionally high L1ORF1p and L1ORF2p expression in post-operative oral cancer samples. The novel L1ORF2p antibody reported in this study will serve as a useful tool to understand why L1 activity is deregulated in OSCC and how it contributes to the progression of this particular cancer. Cross-species reactivity of L1ORF2p antibody due to the conserved epitope will be useful to study the retrotransposon biology in mice and rat germ tissues.
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Affiliation(s)
- Koel Mukherjee
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | - Debpali Sur
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | - Abhijeet Singh
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | - Sandhya Rai
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | | | - Rakshanya Sekar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Vandana Kumar Dhingra
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | - Bhinyaram Jat
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | | | - Satya Prakash Agarwal
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
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194
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Markey FB, Romero B, Parashar V, Batish M. Identification of a New Transcriptional Co-Regulator of STEAP1 in Ewing's Sarcoma. Cells 2021; 10:cells10061300. [PMID: 34073779 PMCID: PMC8225120 DOI: 10.3390/cells10061300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 12/28/2022] Open
Abstract
Ewing’s sarcoma (ES) is caused by a chromosomal translocation leading to the formation of the fused EWSFLI1 gene, which codes for an aberrant transcription factor EWSFLI1. The transcriptional targets of EWSFLI1 have been viewed as promising and novel drug targets in the treatment of ES. One such target is six transmembrane epithelial antigen of the prostate 1 (STEAP1), a transmembrane protein that is upregulated by EWSFLI1 in ES. STEAP1 is a hallmark of tumor invasiveness and an indicator of tumor responsiveness to therapy. EWSFLI1 binds to the STEAP1 promoter region, but the mechanism of action by which it upregulates STEAP1 expression in ES is not entirely understood. Upon analysis of the STEAP1 promoter, we predicted two binding sites for NKX2.2, another crucial transcription factor involved in ES pathogenesis. We confirmed the interaction of NKX2.2 with the STEAP1 promoter using chromatin immunoprecipitation (ChIP) analysis. We used single-molecule RNA imaging, biochemical, and genetic studies to identify the novel role of NKX2.2 in regulating STEAP1 expression in ES. Our results show that NKX2.2 is a co-regulator of STEAP1 expression and functions by interacting with the STEAP1 promoter at sites proximal to the reported EWSFLI1 sites. The co-operative interaction of NKX2.2 with EWSFLI1 in regulating STEAP1 holds potential as a new target for therapeutic interventions for ES.
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Affiliation(s)
- Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103, USA;
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19713, USA; (B.R.); (V.P.)
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19713, USA; (B.R.); (V.P.)
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ 07103, USA;
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19713, USA; (B.R.); (V.P.)
- Correspondence: ; Tel.: +1-302-831-8591
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Kim YR, Kim KU, Lee JH, Kim DW, Chung JH, Kim YD, Shin DH, Lee MK, Shin YI, Lee SY. Cancer Testis Antigen, NOL4, Is an Immunogenic Antigen Specifically Expressed in Small-Cell Lung Cancer. ACTA ACUST UNITED AC 2021; 28:1927-1937. [PMID: 34065612 PMCID: PMC8161805 DOI: 10.3390/curroncol28030179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Accepted: 05/09/2021] [Indexed: 11/17/2022]
Abstract
To identify cancer/testis (CT) antigens and immunogenic proteins, immunoscreening of testicular and small-cell lung cancer cell line NCI-H889 cDNA libraries was performed using serum obtained from a small-cell lung cancer (SCLC) patient. We obtained 113 positive cDNA clones comprised of 74 different genes, designated KP-SCLC-1 through KP-SCLC-74. Of these genes, 59 genes were found to be related to cancers by EMBASE analysis. Three of these antigens, including KP-SCLC-29 (NOL4), KP-SCLC-59 (CCDC83), and KP-SCLC-69 (KIF20B), were CT antigens. RT-PCR and western blot analysis showed that NOL4 was frequently present in small-cell lung cancer cell lines (8/9, 8/9). In addition, NOL4 mRNA was weakly, or at a low frequency, or not detected in various cancer cell lines. Our results reveal that NOL4 was expressed at protein levels in small-cell lung cancer tissues (10/10) but not detected in lung adenocarcinoma and squamous cell carcinoma by immunohistochemical analysis. Serological response to NOL4 was also evaluated by western blot assay using NOL4 recombinant protein. A humoral response against NOL4 proteins was detected in 75% (33/44) of small-cell lung cancer patients and in 65% (13/20) of healthy donors by a serological western blot assay. These data suggest that NOL4 is a specific target that may be useful for diagnosis and immunotherapy in SCLC.
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Affiliation(s)
- Ye-Rin Kim
- Department of Biochemistry, School of Medicine, Pusan National University, Beomeo-ri, Mulgeum-eup, Yangsan 50612, Korea; (Y.-R.K.); (D.-W.K.)
| | - Ki-Uk Kim
- Department of Internal Medicine, Pusan National University Hospital, 1-10 Ami-dong, Seo-gu, Busan 49241, Korea; (K.-U.K.); (M.-K.L.)
| | - Jung-Hee Lee
- Department of Pathology, School of Medicine, Pusan National University, Beomeo-ri, Mulgeum-eup, Yangsan 50612, Korea; (J.-H.L.); (D.-H.S.)
| | - Deok-Won Kim
- Department of Biochemistry, School of Medicine, Pusan National University, Beomeo-ri, Mulgeum-eup, Yangsan 50612, Korea; (Y.-R.K.); (D.-W.K.)
| | - Jae-Heun Chung
- Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan 50612, Korea;
| | - Yeong-Dae Kim
- Department of Thoracic Surgery, Pusan National University Hospital, 1-10 Ami-dong, Seo-gu, Busan 49241, Korea;
| | - Dong-Hoon Shin
- Department of Pathology, School of Medicine, Pusan National University, Beomeo-ri, Mulgeum-eup, Yangsan 50612, Korea; (J.-H.L.); (D.-H.S.)
| | - Min-Ki Lee
- Department of Internal Medicine, Pusan National University Hospital, 1-10 Ami-dong, Seo-gu, Busan 49241, Korea; (K.-U.K.); (M.-K.L.)
| | - Yong-Il Shin
- Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Korea;
| | - Sang-Yull Lee
- Department of Biochemistry, School of Medicine, Pusan National University, Beomeo-ri, Mulgeum-eup, Yangsan 50612, Korea; (Y.-R.K.); (D.-W.K.)
- Correspondence: ; Tel.: +82-51-510-8084
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196
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Abstract
Targeting cancer neoantigens generated by tumor-exclusive somatic mutations is an attractive yet challenging strategy for the robust and specific elimination of tumor cells by cellular immunotherapy. In this issue of Cell, Wells et al. describe a consortium-based approach to optimize bioinformatics pipelines to sensitively and accurately predict immunogenic neoantigens from next-generation sequencing data.
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197
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Abstract
The functional repertoire of intratumoral microorganisms and their local effects on the host remain poorly characterized. By revealing potentially immunogenic bacterial peptides on melanoma cells, a Nature paper provides evidence that intratumoral bacteria can directly modulate antitumor immune responses, and it details a new class of therapeutically relevant, non-human tumor antigens.
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Affiliation(s)
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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198
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Davies JA, Marlow G, Uusi-Kerttula HK, Seaton G, Piggott L, Badder LM, Clarkson RWE, Chester JD, Parker AL. Efficient Intravenous Tumor Targeting Using the αvβ6 Integrin-Selective Precision Virotherapy Ad5 NULL-A20. Viruses 2021; 13:864. [PMID: 34066836 PMCID: PMC8151668 DOI: 10.3390/v13050864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
We previously developed a refined, tumor-selective adenovirus, Ad5NULL-A20, harboring tropism ablating mutations in each major capsid protein, to ablate all native means of infection. We incorporated a 20-mer peptide (A20) in the fiber knob for selective infection via αvβ6 integrin, a marker of aggressive epithelial cancers. Methods: To ascertain the selectivity of Ad5NULL-A20 for αvβ6-positive tumor cell lines of pancreatic and breast cancer origin, we performed reporter gene and cell viability assays. Biodistribution of viral vectors in mice harboring xenografts with low, medium, and high αvβ6 levels was quantified by qPCR for viral genomes 48 h post intravenous administration. Results: Ad5NULL-A20 vector transduced cells in an αvβ6-selective manner, whilst cell killing mediated by oncolytic Ad5NULL-A20 was αvβ6-selective. Biodistribution analysis following intravenous administration into mice bearing breast cancer xenografts demonstrated that Ad5NULL-A20 resulted in significantly reduced liver accumulation coupled with increased tumor accumulation compared to Ad5 in all three models, with tumor-to-liver ratios improved as a function of αvβ6 expression. Conclusions: Ad5NULL-A20-based virotherapies efficiently target αvβ6-integrin-positive tumors following intravenous administration, validating the potential of Ad5NULL-A20 for systemic applications, enabling tumor-selective overexpression of virally encoded therapeutic transgenes.
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Affiliation(s)
- James A. Davies
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK; (J.A.D.); (G.M.); (H.K.U.-K.); (L.M.B.); (J.D.C.)
| | - Gareth Marlow
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK; (J.A.D.); (G.M.); (H.K.U.-K.); (L.M.B.); (J.D.C.)
| | - Hanni K. Uusi-Kerttula
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK; (J.A.D.); (G.M.); (H.K.U.-K.); (L.M.B.); (J.D.C.)
| | - Gillian Seaton
- School of Biosciences, Cardiff University, Cardiff CF24 4HQ, UK; (G.S.); (L.P.); (R.W.E.C.)
| | - Luke Piggott
- School of Biosciences, Cardiff University, Cardiff CF24 4HQ, UK; (G.S.); (L.P.); (R.W.E.C.)
| | - Luned M. Badder
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK; (J.A.D.); (G.M.); (H.K.U.-K.); (L.M.B.); (J.D.C.)
| | - Richard W. E. Clarkson
- School of Biosciences, Cardiff University, Cardiff CF24 4HQ, UK; (G.S.); (L.P.); (R.W.E.C.)
| | - John D. Chester
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK; (J.A.D.); (G.M.); (H.K.U.-K.); (L.M.B.); (J.D.C.)
- Velindre Cancer Centre, Cardiff CF14 2TL, UK
| | - Alan L. Parker
- Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff CF14 4XN, UK; (J.A.D.); (G.M.); (H.K.U.-K.); (L.M.B.); (J.D.C.)
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199
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Dao T, Klatt MG, Korontsvit T, Mun SS, Guzman S, Mattar M, Zivanovic O, Kyi CK, Socci ND, O'Cearbhaill RE, Scheinberg DA. Impact of tumor heterogeneity and microenvironment in identifying neoantigens in a patient with ovarian cancer. Cancer Immunol Immunother 2021; 70:1189-1202. [PMID: 33123756 PMCID: PMC8053669 DOI: 10.1007/s00262-020-02764-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/15/2020] [Indexed: 01/05/2023]
Abstract
Identification of neoepitopes as tumor-specific targets remains challenging, especially for cancers with low mutational burden, such as ovarian cancer. To identify mutated human leukocyte antigen (HLA) ligands as potential targets for immunotherapy in ovarian cancer, we combined mass spectrometry analysis of the major histocompatibility complex (MHC) class I peptidomes of ovarian cancer cells with parallel sequencing of whole exome and RNA in a patient with high-grade serous ovarian cancer. Four of six predicted mutated epitopes capable of binding to HLA-A*02:01 induced peptide-specific T cell responses in blood from healthy donors. In contrast, all six peptides failed to induce autologous peptide-specific response by T cells in peripheral blood or tumor-infiltrating lymphocytes from ascites of the patient. Surprisingly, T cell responses against a low-affinity p53-mutant Y220C epitope were consistently detected in the patient with either unprimed or in vitro peptide-stimulated T cells even though the patient's primary tumor did not bear this mutation. Our results demonstrated that tumor heterogeneity and distinct immune microenvironments within a patient should be taken into consideration for identification of immunogenic neoantigens. T cell responses to a driver gene-derived p53 Y220C mutation in ovarian cancer warrant further study.
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Affiliation(s)
- Tao Dao
- Molecular Pharmacology Program, SKI, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin G Klatt
- Molecular Pharmacology Program, SKI, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tatyana Korontsvit
- Molecular Pharmacology Program, SKI, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sung Soo Mun
- Molecular Pharmacology Program, SKI, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean Guzman
- Molecular Pharmacology Program, SKI, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marissa Mattar
- Molecular Pharmacology Program, SKI, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Oliver Zivanovic
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, NY, USA
| | - Chrisann K Kyi
- Gynecological Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roisin E O'Cearbhaill
- Gynecological Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- National University of Ireland, Galway, Ireland.
| | - David A Scheinberg
- Molecular Pharmacology Program, SKI, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Gynecological Medical Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Experimental Therapeutics Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
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200
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Cideciyan AV, Jacobson SG, Ho AC, Garafalo AV, Roman AJ, Sumaroka A, Krishnan AK, Swider M, Schwartz MR, Girach A. Durable vision improvement after a single treatment with antisense oligonucleotide sepofarsen: a case report. Nat Med 2021; 27:785-789. [PMID: 33795869 PMCID: PMC8127404 DOI: 10.1038/s41591-021-01297-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Leber congenital amaurosis due to CEP290 ciliopathy is being explored by treatment with the antisense oligonucleotide (AON) sepofarsen. One patient who was part of a larger cohort (ClinicalTrials.gov NCT03140969 ) was studied for 15 months after a single intravitreal sepofarsen injection. Concordant measures of visual function and retinal structure reached a substantial efficacy peak near 3 months after injection. At 15 months, there was sustained efficacy, even though there was evidence of reduction from peak response. Efficacy kinetics can be explained by the balance of AON-driven new CEP290 protein synthesis and a slow natural rate of CEP290 protein degradation in human foveal cone photoreceptors.
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Affiliation(s)
- Artur V Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Samuel G Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen C Ho
- Wills Eye Hospital, Thomas Jefferson University, Philadelphia PA, USA
| | - Alexandra V Garafalo
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandro J Roman
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander Sumaroka
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arun K Krishnan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Malgorzata Swider
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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