1
|
Zhu X, Zhang W, Yu Z, Yang X, Li L, Chen C, Djumanazarov T, Piquemal D, Yusupbekov AA, Zheng Y. Synergistic action of gemcitabine and celecoxib in promoting the antitumor efficacy of anti-programmed death-1 monoclonal antibody by triggering immunogenic cell death. Transl Cancer Res 2024; 13:3031-3045. [PMID: 38988937 PMCID: PMC11231791 DOI: 10.21037/tcr-24-698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/24/2024] [Indexed: 07/12/2024]
Abstract
Background Emerging evidence suggests that immunogenic chemotherapy not only kills tumor cells but also improves the immune-suppressive tumor microenvironment by inducing immunogenic cell death (ICD), leading to sustained anti-tumor effects. The lack of ICD inducers explored in lung cancer necessitates investigation into new inducers for this context, therefore, this study aims to explore whether the gemcitabine (GEM) and celecoxib can activate the immunogenic chemotherapy progress in lung cancer tissue. Methods We assessed five chemotherapeutic agents for their ability to trigger ICD using ex vivo and in vivo experiments, including western blotting (WB), flow cytometry, and tumor preventive vaccine assays. Additionally, we evaluated the synergistic effects of GEM, celecoxib, and anti-programmed death 1 monoclonal antibody (aPD-1) in tumor-bearing mice to understand how GEM activates antitumor immunity and enhances immunochemotherapy. Results GEM was identified as an effective ICD inducer, showing high expression of calreticulin (CRT) and heat shock protein 90 (HSP90). Co-culture with GEM-treated cells [Lewis lung carcinoma (LLC) and CMT-64] enhanced dendritic cell (DC) activity, evidenced by maturation markers and increased phagocytic capacity. Moreover, celecoxib was found to enhance ICD by reducing indoleamine 2,3-dioxygenase 1 (IDO1) expression and increasing reactive oxygen species (ROS)-based endoplasmic reticulum (ER) stress. The combination therapy [GEM, celecoxib, and aPD-1 (GCP)] exhibited potent and sustained antitumor activity in immunocompetent mice, with enhanced recruitment of tumor-infiltrating lymphocytes. Conclusions These findings support the potential use of GCP therapy as a treatment option for lung cancer patients.
Collapse
Affiliation(s)
- Xiongjie Zhu
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Wenkai Zhang
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Zhongjian Yu
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xia Yang
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Laiqing Li
- Guangzhou Youdi Bio-Technology Co., Ltd., Guangzhou, China
| | - Cuicui Chen
- Guangzhou Youdi Bio-Technology Co., Ltd., Guangzhou, China
| | - Temirbek Djumanazarov
- Republican Specialized Scientific and Practical Medical Center of Oncology and Radiology (National Cancer Center of Uzbekistan), Tashkent, Uzbekistan
| | | | - Abrorjon A. Yusupbekov
- Republican Specialized Scientific and Practical Medical Center of Oncology and Radiology (National Cancer Center of Uzbekistan), Tashkent, Uzbekistan
| | - Yanfang Zheng
- Department of Medical Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
2
|
Sun Y, Xiong B, Shuai X, Li J, Wang C, Guo J, Cheng Z, Liu S. Downregulation of HNRNPA1 induced neoantigen generation via regulating alternative splicing. Mol Med 2024; 30:85. [PMID: 38867190 PMCID: PMC11167825 DOI: 10.1186/s10020-024-00849-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Immunotherapies effectively treat human malignancies, but the low response and resistance are major obstacles. Neoantigen is an emerging target for tumor immunotherapy that can enhance anti-tumor immunity and improve immunotherapy. Aberrant alternative splicing is an important source of neoantigens. HNRNPA1, an RNA splicing factor, was found to be upregulated in the majority of tumors and play an important role in the tumor immunosuppressive microenvironment. METHODS Whole transcriptome sequencing was performed on shHNRNPA1 SKOV3 cells and transcriptomic data of shHNRNPA1 HepG2, MCF-7M, K562, and B-LL cells were downloaded from the GEO database. Enrichment analysis was performed to elucidate the mechanisms underlying the activation of anti-tumor immunity induced by HNRNPA1 knockdown. mRNA alternative splicing was analyzed and neoantigens were predicted by JCAST v.0.3.5 and Immune epitope database. The immunogenicity of candidate neoantigens was calculated by Class I pMHC Immunogenicity and validated by the IFN-γ ELISpot assay. The effect of shHNRNPA1 on tumor growth and immune cells in vivo was evaluated by xenograft model combined with immunohistochemistry. RESULTS HNRNPA1 was upregulated in a majority of malignancies and correlated with immunosuppressive status of the tumor immune microenvironment. Downregulation of HNRNPA1 could induce the activation of immune-related pathways and biological processes. Disruption of HNRNPA1 resulted in aberrant alternative splicing events and generation of immunogenic neoantigens. Downregulation of HNRNPA1 inhibited tumor growth and increased CD8+ T cell infiltration in vivo. CONCLUSION Our study demonstrated that targeting HNRNPA1 could produce immunogenic neoantigens that elicit anti-tumor immunity by inducing abnormal mRNA splicing. It suggests that HNRNPA1 may be a potential target for immunotherapy.
Collapse
Affiliation(s)
- Yaoqi Sun
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Bing Xiong
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Xueqian Shuai
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Jiale Li
- Anhui University of Science and Technology, Huainan, 232001, China
| | - Chunyan Wang
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Jing Guo
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Zhongping Cheng
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
| | - Shupeng Liu
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China.
| |
Collapse
|
3
|
Fu S, Wei J, Li C, Zhang N, Yue H, Yang A, Xu J, Dong K, Xing Y, Tong M, Shi X, Xi Z, Wang H, Hou Y, Zhao Y. Design, synthesis, and biological evaluation of 2,4-diaminopyrimidine derivatives as potent Hematopoietic Progenitor Kinase 1 (HPK1) inhibitors. Bioorg Chem 2024; 148:107454. [PMID: 38795581 DOI: 10.1016/j.bioorg.2024.107454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/10/2024] [Accepted: 05/12/2024] [Indexed: 05/28/2024]
Abstract
HPK1 also referred to as MAP4K1, belongs to the category of mammalian STE20-like protein serine/threonine kinases. Its physiological function involves the down-regulation of T cell signals, and it is regarded as a new immune checkpoint of tumor immunology. In this study, we commenced our investigation with the hit compounds, focusing the efforts on structural optimization and SAR exploration to identify a novel class of 2,4-diaminopyrimidine HPK1 inhibitors. Notably, compound 14g exhibited a remarkable inhibitory effect on HPK1 kinase (IC50 = 0.15 nM), significantly suppressed the phosphorylation of the downstream adaptor protein SLP76 (pSLP76 IC50 = 27.92 nM), and effectively stimulated the secretion of the T cell activation marker IL-2 (EC50 = 46.64 nM). In vitro microsomal stability assay, compound 14g showed moderate stability in HLMs with T1/2 = 38.2 min and CLint = 36.4 µL·min-1·mg-1 proteins. In vivo pharmacokinetic studies, compound 14g demonstrated heightened plasma exposure (AUC0-inf = 644 ng·h·mL-1), extended half-life (T1/2 = 9.98 h), and reduced plasma clearance (CL = 52.3 mL·min-1·kg-1) compared to the reference compound after a single intravenous dose of 2 mg/kg in rats. These results indicated that compound 14g emerged as a promising inhibitor of HPK1.
Collapse
Affiliation(s)
- Siyu Fu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Jiakuan Wei
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Chunting Li
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Na Zhang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Hao Yue
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Ao Yang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Jichang Xu
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Kuan Dong
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Yongpeng Xing
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China
| | - Minghui Tong
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou 215104, China
| | - Xuan Shi
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou 215104, China
| | - Zhiguo Xi
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou 215104, China
| | - Han Wang
- 3D BioOptima, 1338 Wuzhong Avenue, Suzhou 215104, China
| | - Yunlei Hou
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China.
| | - Yanfang Zhao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, Liaoning 110016, China.
| |
Collapse
|
4
|
Marx OM, Mankarious MM, Koltun WA, Yochum GS. Identification of differentially expressed genes and splicing events in early-onset colorectal cancer. Front Oncol 2024; 14:1365762. [PMID: 38680862 PMCID: PMC11047122 DOI: 10.3389/fonc.2024.1365762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
Background The incidence of colorectal cancer (CRC) has been steadily increasing in younger individuals over the past several decades for reasons that are incompletely defined. Identifying differences in gene expression profiles, or transcriptomes, in early-onset colorectal cancer (EOCRC, < 50 years old) patients versus later-onset colorectal cancer (LOCRC, > 50 years old) patients is one approach to understanding molecular and genetic features that distinguish EOCRC. Methods We performed RNA-sequencing (RNA-seq) to characterize the transcriptomes of patient-matched tumors and adjacent, uninvolved (normal) colonic segments from EOCRC (n=21) and LOCRC (n=22) patients. The EOCRC and LOCRC cohorts were matched for demographic and clinical characteristics. We used The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) database for validation. We used a series of computational and bioinformatic tools to identify EOCRC-specific differentially expressed genes, molecular pathways, predicted cell populations, differential gene splicing events, and predicted neoantigens. Results We identified an eight-gene signature in EOCRC comprised of ALDOB, FBXL16, IL1RN, MSLN, RAC3, SLC38A11, WBSCR27 and WNT11, from which we developed a score predictive of overall CRC patient survival. On the entire set of genes identified in normal tissues and tumors, cell type deconvolution analysis predicted a differential abundance of immune and non-immune populations in EOCRC versus LOCRC. Gene set enrichment analysis identified increased expression of splicing machinery in EOCRC. We further found differences in alternative splicing (AS) events, including one within the long non-coding RNA, HOTAIRM1. Additional analysis of AS found seven events specific to EOCRC that encode potential neoantigens. Conclusion Our transcriptome analyses identified genetic and molecular features specific to EOCRC which may inform future screening, development of prognostic indicators, and novel drug targets.
Collapse
Affiliation(s)
- Olivia M. Marx
- Koltun and Yochum Laboratory, Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Marc M. Mankarious
- Koltun and Yochum Laboratory, Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Walter A. Koltun
- Koltun and Yochum Laboratory, Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Gregory S. Yochum
- Koltun and Yochum Laboratory, Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| |
Collapse
|
5
|
Wang Y, Xie Z, Kutschera E, Adams JI, Kadash-Edmondson KE, Xing Y. rMATS-turbo: an efficient and flexible computational tool for alternative splicing analysis of large-scale RNA-seq data. Nat Protoc 2024; 19:1083-1104. [PMID: 38396040 DOI: 10.1038/s41596-023-00944-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 11/02/2023] [Indexed: 02/25/2024]
Abstract
Pre-mRNA alternative splicing is a prevalent mechanism for diversifying eukaryotic transcriptomes and proteomes. Regulated alternative splicing plays a role in many biological processes, and dysregulated alternative splicing is a feature of many human diseases. Short-read RNA sequencing (RNA-seq) is now the standard approach for transcriptome-wide analysis of alternative splicing. Since 2011, our laboratory has developed and maintained Replicate Multivariate Analysis of Transcript Splicing (rMATS), a computational tool for discovering and quantifying alternative splicing events from RNA-seq data. Here we provide a protocol for the contemporary version of rMATS, rMATS-turbo, a fast and scalable re-implementation that maintains the statistical framework and user interface of the original rMATS software, while incorporating a revamped computational workflow with a substantial improvement in speed and data storage efficiency. The rMATS-turbo software scales up to massive RNA-seq datasets with tens of thousands of samples. To illustrate the utility of rMATS-turbo, we describe two representative application scenarios. First, we describe a broadly applicable two-group comparison to identify differential alternative splicing events between two sample groups, including both annotated and novel alternative splicing events. Second, we describe a quantitative analysis of alternative splicing in a large-scale RNA-seq dataset (~1,000 samples), including the discovery of alternative splicing events associated with distinct cell states. We detail the workflow and features of rMATS-turbo that enable efficient parallel processing and analysis of large-scale RNA-seq datasets on a compute cluster. We anticipate that this protocol will help the broad user base of rMATS-turbo make the best use of this software for studying alternative splicing in diverse biological systems.
Collapse
Affiliation(s)
- Yuanyuan Wang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA, USA
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zhijie Xie
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jenea I Adams
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn E Kadash-Edmondson
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| |
Collapse
|
6
|
Ren Y, Manoharan T, Liu B, Cheng CZM, En Siew B, Cheong WK, Lee KY, Tan IJW, Lieske B, Tan KK, Chia G. Circular RNA as a source of neoantigens for cancer vaccines. J Immunother Cancer 2024; 12:e008402. [PMID: 38508656 PMCID: PMC10952939 DOI: 10.1136/jitc-2023-008402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The effectiveness of somatic neoantigen-based immunotherapy is often hindered by the limited number of mutations in tumors with low to moderate mutation burden. Focusing on microsatellite-stable colorectal cancer (CRC), this study investigates the potential of tumor-associated circular RNAs (circRNAs) as an alternative source of neoepitopes in CRC. METHODS Tumor-associated circRNAs in CRC were identified using the MiOncoCirc database and ribo-depletion RNA sequencing of paired clinical normal and tumor samples. Candidate circRNA expression was validated by quantitative real-time PCR (RT-qPCR) using divergent primers. TransCirc database was used for translation prediction. Human leukocyte antigen binding affinity of open reading frames from potentially translatable circRNA was predicted using pVACtools. Strong binders from messenger RNA-encoded proteins were excluded using BlastP. The immunogenicity of the candidate antigens was functionally validated through stimulation of naïve CD8+ T cells against the predicted neoepitopes and subsequent analysis of the T cells through enzyme-linked immunospot (ELISpot) assay, intracellular cytokine staining (ICS) and granzyme B (GZMB) reporter. The cytotoxicity of T cells trained with antigen peptides was further tested using patient-derived organoids. RESULTS We identified a neoepitope from circRAPGEF5 that is upregulated in CRC tumor samples from MiOncoCirc database, and two neoepitopes from circMYH9, which is upregulated across various tumor samples from our matched clinical samples. The translation potential of candidate peptides was supported by Clinical Proteomic Tumor Analysis Consortium database using PepQuery. The candidate peptides elicited antigen-specific T cells response and expansion, evidenced by various assays including ELISpot, ICS and GZMB reporter. Furthermore, T cells trained with circMYH9 peptides were able to specifically target and eliminate tumor-derived organoids but not match normal organoids. This observation underscores the potential of circRNAs as a source of immunogenic neoantigens. Lastly, circMYH9 was enriched in the liquid biopsies of patients with CRC, thus enabling a detection-to-vaccination treatment strategy for patients with CRC. CONCLUSIONS Our findings underscore the feasibility of tumor-associated circRNAs as an alternative source of neoantigens for cancer vaccines targeting tumors with moderate mutation levels.
Collapse
Affiliation(s)
- Yi Ren
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Thamizhanban Manoharan
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Beijia Liu
- Department of Pharmacy, National University of Singapore, Singapore
| | - Cyrus Zai Ming Cheng
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| | - Bei En Siew
- Department of Surgery, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Wai-Kit Cheong
- Department of Surgery, National University Hospital, Singapore
| | - Kai Yin Lee
- Department of Surgery, National University Hospital, Singapore
| | - Ian Jse-Wei Tan
- Department of Surgery, National University Hospital, Singapore
| | - Bettina Lieske
- Department of Surgery, National University Hospital, Singapore
| | - Ker-Kan Tan
- Department of Surgery, National University of Singapore, Singapore
- Department of Surgery, National University Hospital, Singapore
| | - Gloryn Chia
- Department of Pharmacy, National University of Singapore, Singapore
- NUS iHealthtech, Singapore
| |
Collapse
|
7
|
Yan Y, Ren Y, Bao Y, Wang Y. RNA splicing alterations in lung cancer pathogenesis and therapy. CANCER PATHOGENESIS AND THERAPY 2023; 1:272-283. [PMID: 38327600 PMCID: PMC10846331 DOI: 10.1016/j.cpt.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/25/2023] [Accepted: 04/29/2023] [Indexed: 02/09/2024]
Abstract
RNA splicing alterations are widespread and play critical roles in cancer pathogenesis and therapy. Lung cancer is highly heterogeneous and causes the most cancer-related deaths worldwide. Large-scale multi-omics studies have not only characterized the mutational landscapes but also discovered a plethora of transcriptional and post-transcriptional changes in lung cancer. Such resources have greatly facilitated the development of new diagnostic markers and therapeutic options over the past two decades. Intriguingly, altered RNA splicing has emerged as an important molecular feature and therapeutic target of lung cancer. In this review, we provide a brief overview of splicing dysregulation in lung cancer and summarize the recent progress on key splicing events and splicing factors that contribute to lung cancer pathogenesis. Moreover, we describe the general strategies targeting splicing alterations in lung cancer and highlight the potential of combining splicing modulation with currently approved therapies to combat this deadly disease. This review provides new mechanistic and therapeutic insights into splicing dysregulation in cancer.
Collapse
Affiliation(s)
- Yueren Yan
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yunpeng Ren
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yufang Bao
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| |
Collapse
|
8
|
Zhou L, Ye X, Wang K, Shen H, Wang T, Zhang X, Jiang S, Xiao Y, Zhang K. Discovery of diaminotriazine carboxamides as potent inhibitors of hematopoetic progenitor kinase 1. Bioorg Chem 2023; 138:106682. [PMID: 37339563 DOI: 10.1016/j.bioorg.2023.106682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 06/01/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023]
Abstract
Hematopoietic progenitor kinase 1 (HPK1), a member of mitogen-activated protein kinase kinase kinase kinase (MAP4K) family of Ste20 serine/threonine kinases, is a negative regulator of T-cell receptor (TCR) signaling. Inactivating HPK1 kinase has been reported to be sufficient to elicit antitumor immune response. Therefore, HPK1 has attracted much attention as a promising target for tumor immunotherapy. A few of HPK1 inhibitors have been reported, and none of them have been approved for clinical applications. Hence, more effective HPK1 inhibitors are needed. Herein, a series of structurally novel diaminotriazine carboxamides were rationally designed, synthesized and evaluated for their inhibitory activity against HPK1 kinase. Most of them exhibited potent inhibitory potency against HPK1 kinase. In particular, compound 15b showed more robust HPK1 inhibitory activity than that of 11d developed by Merck in kinase activity assay (IC50 = 3.1 and 8.2 nM, respectively). The significant inhibitory potency against SLP76 phosphorylation in Jurkat T cells further confirmed the efficacy of compound 15b. In human peripheral blood mononuclear cell (PBMC) functional assays, compound 15b more significantly induced the production of interleukin 2 (IL-2) and interferon γ (IFN-γ) relative to 11d. Furthermore, 15b alone or in combination with anti-PD-1 antibodies showed potent in vivo antitumor efficacy in MC38 tumor-bearing mice. Compound 15b represents a promising lead for the development of effective HPK1 small-molecule inhibitors.
Collapse
Affiliation(s)
- Lixin Zhou
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiuquan Ye
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kaizhen Wang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Hongtao Shen
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Tianyu Wang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiangyu Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Sheng Jiang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Yibei Xiao
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| | - Kuojun Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China.
| |
Collapse
|
9
|
Xing S, Zhu Y, You Y, Wang S, Wang H, Ning M, Jin H, Liu Z, Zhang X, Yu C, Lu ZJ. Cell-free RNA for the liquid biopsy of gastrointestinal cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1791. [PMID: 37086051 DOI: 10.1002/wrna.1791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
Gastrointestinal (GI) cancer includes many cancer types, such as esophageal, liver, gastric, pancreatic, and colorectal cancer. As the cornerstone of personalized medicine for GI cancer, liquid biopsy based on noninvasive biomarkers provides promising opportunities for early diagnosis and dynamic treatment management. Recently, a growing number of studies have demonstrated the potential of cell-free RNA (cfRNA) as a new type of noninvasive biomarker in body fluids, such as blood, saliva, and urine. Meanwhile, transcriptomes based on high-throughput RNA detection technologies keep discovering new cfRNA biomarkers. In this review, we introduce the origins and applications of cfRNA, describe its detection and qualification methods in liquid biopsy, and summarize a comprehensive list of cfRNA biomarkers in different GI cancer types. Moreover, we also discuss perspective studies of cfRNA to overcome its current limitations in clinical applications. This article is categorized under: RNA in Disease and Development > RNA in Disease.
Collapse
Affiliation(s)
- Shaozhen Xing
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute for Precision Medicine, Tsinghua University, Beijing, China
| | - Yumin Zhu
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Population Health and Aristogenics, Department of Maternal & Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Yaxian You
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Siqi Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongke Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Meng Ning
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Heyue Jin
- MOE Key Laboratory of Population Health Across Life Cycle, Anhui Provincial Key Laboratory of Population Health and Aristogenics, Department of Maternal & Child and Adolescent Health, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Zhengxia Liu
- Department of General Surgery, SIR RUN RUN Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xinhua Zhang
- Department of Health Care, Jiangsu Women and Children Health Hospital, the First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), Nanjing, Jiangsu, China
| | - Chunzhao Yu
- Department of General Surgery, SIR RUN RUN Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Geriatrics, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Institute for Precision Medicine, Tsinghua University, Beijing, China
| |
Collapse
|
10
|
Wang F, Xu Y, Wang R, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson KE, Xing Y, Lin L. TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing. Nat Commun 2023; 14:4760. [PMID: 37553321 PMCID: PMC10409798 DOI: 10.1038/s41467-023-40083-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 07/11/2023] [Indexed: 08/10/2023] Open
Abstract
Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. One strategy for overcoming this bottleneck is targeted long-read RNA-seq for preselected gene panels. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq utilizing isothermally linear-amplified capture probes. When performed on the Oxford nanopore platform with multiple gene panels of varying sizes, TEQUILA-seq consistently and substantially enriches transcript coverage while preserving transcript quantification. We profile full-length transcript isoforms of 468 actionable cancer genes across 40 representative breast cancer cell lines. We identify transcript isoforms enriched in specific subtypes and discover novel transcript isoforms in extensively studied cancer genes such as TP53. Among cancer genes, tumor suppressor genes (TSGs) are significantly enriched for aberrant transcript isoforms targeted for degradation via mRNA nonsense-mediated decay, revealing a common RNA-associated mechanism for TSG inactivation. TEQUILA-seq reduces the per-reaction cost of targeted capture by 2-3 orders of magnitude, as compared to a standard commercial solution. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
Collapse
Affiliation(s)
- Feng Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yang Xu
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Wang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Beatrice Zhang
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Noah Smith
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amber Notaro
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samantha Gaerlan
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kathryn E Kadash-Edmondson
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Lan Lin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| |
Collapse
|
11
|
Tretter C, de Andrade Krätzig N, Pecoraro M, Lange S, Seifert P, von Frankenberg C, Untch J, Zuleger G, Wilhelm M, Zolg DP, Dreyer FS, Bräunlein E, Engleitner T, Uhrig S, Boxberg M, Steiger K, Slotta-Huspenina J, Ochsenreither S, von Bubnoff N, Bauer S, Boerries M, Jost PJ, Schenck K, Dresing I, Bassermann F, Friess H, Reim D, Grützmann K, Pfütze K, Klink B, Schröck E, Haller B, Kuster B, Mann M, Weichert W, Fröhling S, Rad R, Hiltensperger M, Krackhardt AM. Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nat Commun 2023; 14:4632. [PMID: 37532709 PMCID: PMC10397250 DOI: 10.1038/s41467-023-39570-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
Collapse
Affiliation(s)
- Celina Tretter
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Niklas de Andrade Krätzig
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Matteo Pecoraro
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Munich, Germany
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Sebastian Lange
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Philipp Seifert
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Clara von Frankenberg
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Johannes Untch
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Gabriela Zuleger
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Mathias Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
- Technical University of Munich, TUM School of Life Sciences, Computational Mass Spectrometry, Freising, Germany
| | - Daniel P Zolg
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
| | - Florian S Dreyer
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Eva Bräunlein
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Thomas Engleitner
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Sebastian Uhrig
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Precision Oncology Program, NCT Heidelberg, Heidelberg, Germany
| | - Melanie Boxberg
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Julia Slotta-Huspenina
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Sebastian Ochsenreither
- German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nikolas von Bubnoff
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Hematology and Oncology, Medical Center, University of Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Sebastian Bauer
- German Cancer Consortium (DKTK), partner site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp J Jost
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
- Clinical Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- University Comprehensive Cancer Center Graz, Medical University of Graz, Graz, Austria
| | - Kristina Schenck
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Iska Dresing
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Helmut Friess
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Daniel Reim
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Konrad Grützmann
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Core Unit Molecular Tumor Diagnostics (CMTD), NCT Dresden, Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Katrin Pfütze
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Klink
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Evelin Schröck
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), Dresden, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bernhard Haller
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of AI and Informatics in Medicine, Munich, Germany
| | - Bernhard Kuster
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
- Technical University of Munich, TUM School of Life Sciences, Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Freising, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Munich, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Michael Hiltensperger
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Angela M Krackhardt
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany.
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany.
- Malteser Krankenhaus St. Franziskus-Hospital, Flensburg, Germany.
| |
Collapse
|
12
|
Zhen N, Zhu J, Mao S, Zhang Q, Gu S, Ma J, Zhang Y, Yin M, Li H, Huang N, Wu H, Sun F, Ying B, Zhou L, Pan Q. Alternative Splicing of lncRNAs From SNHG Family Alters snoRNA Expression and Induces Chemoresistance in Hepatoblastoma. Cell Mol Gastroenterol Hepatol 2023; 16:735-755. [PMID: 37478905 PMCID: PMC10520360 DOI: 10.1016/j.jcmgh.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND & AIMS Hepatoblastoma (HB) is a common pediatric malignant liver tumor that is characterized by a low level of genetic mutations. Alternative splicing (AS) has been shown to be closely associated with cancer progression, especially in tumors with a low mutational burden. However, the role of AS in HB remains unknown. METHODS Transcriptome sequencing was performed on 5 pairs of HB tissues and matched non-tumor tissues to delineate the AS landscape in HB. AS events were validated in 92 samples from 46 patients. RNA pull-down and RNA immunoprecipitation assays were carried out to identify splicing factors that regulate the AS of small nucleolar RNA host genes (SNHG). Patient-derived organoids (PDOs) were established to investigate the role of the splicing factor polyadenylate-binding nuclear protein 1 (PABPN1). RESULTS This study uncovered aberrant alternative splicing in HB, including lncRNAs from SNHG family that undergo intron retention in HB. Further investigations revealed that PABPN1, a significantly upregulated RNA binding protein, interacts with splicing machinery in HB, inducing the intron retention of these SNHG RNAs and the downregulation of intronic small nucleolar RNAs (snoRNAs). Functionally, PABPN1 acts as an oncofetal splicing regulator in HB by promoting cell proliferation and DNA damage repair via inducing the intron retention of SNHG19. Knock-down of PABPN1 increases the cisplatin sensitivity of HB PDOs. CONCLUSIONS Our findings revealed the role of intron retention in regulating snoRNA expression in hepatoblastoma, explained detailed regulatory mechanism between PABPN1 and the intron retention of SNHG RNAs, and provided insight into the development of new HB treatment options.
Collapse
Affiliation(s)
- Ni Zhen
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiabei Zhu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Siwei Mao
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Song Gu
- Department of Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Ma
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- Department of Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People's Hospital, Shanghai, China
| | - Minzhi Yin
- Department of Pathology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haojie Li
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Nan Huang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Han Wu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fenyong Sun
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Lin Zhou
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China; Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Hainan, China.
| |
Collapse
|
13
|
Chen X, Yang HT, Zhang B, Phillips JW, Cheng D, Rigo F, Witte ON, Xing Y, Black DL. The RNA-binding proteins hnRNP H and F regulate splicing of a MYC-dependent HRAS exon in prostate cancer cells. Proc Natl Acad Sci U S A 2023; 120:e2220190120. [PMID: 37399401 PMCID: PMC10334793 DOI: 10.1073/pnas.2220190120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/31/2023] [Indexed: 07/05/2023] Open
Abstract
The MYC proto-oncogene contributes to the pathogenesis of more than half of human cancers. Malignant transformation by MYC transcriptionally up-regulates the core pre-mRNA splicing machinery and causes misregulation of alternative splicing. However, our understanding of how splicing changes are directed by MYC is limited. We performed a signaling pathway-guided splicing analysis to identify MYC-dependent splicing events. These included an HRAS cassette exon repressed by MYC across multiple tumor types. To molecularly dissect the regulation of this HRAS exon, we used antisense oligonucleotide tiling to identify splicing enhancers and silencers in its flanking introns. RNA-binding motif prediction indicated multiple binding sites for hnRNP H and hnRNP F within these cis-regulatory elements. Using siRNA knockdown and cDNA expression, we found that both hnRNP H and F activate the HRAS cassette exon. Mutagenesis and targeted RNA immunoprecipitation implicate two downstream G-rich elements in this splicing activation. Analyses of ENCODE RNA-seq datasets confirmed hnRNP H regulation of HRAS splicing. Analyses of RNA-seq datasets across multiple cancers showed a negative correlation of HNRNPH gene expression with MYC hallmark enrichment, consistent with the effect of hnRNP H on HRAS splicing. Interestingly, HNRNPF expression showed a positive correlation with MYC hallmarks and thus was not consistent with the observed effects of hnRNP F. Loss of hnRNP H/F altered cell cycle progression and induced apoptosis in the PC3 prostate cancer cell line. Collectively, our results reveal mechanisms for MYC-dependent regulation of splicing and point to possible therapeutic targets in prostate cancers.
Collapse
Affiliation(s)
- Xinyuan Chen
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, CA90095
| | - Harry Taegyun Yang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA90095
| | - Beatrice Zhang
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - John W. Phillips
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Donghui Cheng
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Frank Rigo
- Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA92010
| | - Owen N. Witte
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA90095
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Douglas L. Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
| |
Collapse
|
14
|
Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
Collapse
Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| |
Collapse
|
15
|
Pan Y, Phillips JW, Zhang BD, Noguchi M, Kutschera E, McLaughlin J, Nesterenko PA, Mao Z, Bangayan NJ, Wang R, Tran W, Yang HT, Wang Y, Xu Y, Obusan MB, Cheng D, Lee AH, Kadash-Edmondson KE, Champhekar A, Puig-Saus C, Ribas A, Prins RM, Seet CS, Crooks GM, Witte ON, Xing Y. IRIS: Discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing. Proc Natl Acad Sci U S A 2023; 120:e2221116120. [PMID: 37192158 PMCID: PMC10214192 DOI: 10.1073/pnas.2221116120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/05/2023] [Indexed: 05/18/2023] Open
Abstract
Alternative splicing (AS) is prevalent in cancer, generating an extensive but largely unexplored repertoire of novel immunotherapy targets. We describe Isoform peptides from RNA splicing for Immunotherapy target Screening (IRIS), a computational platform capable of discovering AS-derived tumor antigens (TAs) for T cell receptor (TCR) and chimeric antigen receptor T cell (CAR-T) therapies. IRIS leverages large-scale tumor and normal transcriptome data and incorporates multiple screening approaches to discover AS-derived TAs with tumor-associated or tumor-specific expression. In a proof-of-concept analysis integrating transcriptomics and immunopeptidomics data, we showed that hundreds of IRIS-predicted TCR targets are presented by human leukocyte antigen (HLA) molecules. We applied IRIS to RNA-seq data of neuroendocrine prostate cancer (NEPC). From 2,939 NEPC-associated AS events, IRIS predicted 1,651 epitopes from 808 events as potential TCR targets for two common HLA types (A*02:01 and A*03:01). A more stringent screening test prioritized 48 epitopes from 20 events with "neoantigen-like" NEPC-specific expression. Predicted epitopes are often encoded by microexons of ≤30 nucleotides. To validate the immunogenicity and T cell recognition of IRIS-predicted TCR epitopes, we performed in vitro T cell priming in combination with single-cell TCR sequencing. Seven TCRs transduced into human peripheral blood mononuclear cells (PBMCs) showed high activity against individual IRIS-predicted epitopes, providing strong evidence of isolated TCRs reactive to AS-derived peptides. One selected TCR showed efficient cytotoxicity against target cells expressing the target peptide. Our study illustrates the contribution of AS to the TA repertoire of cancer cells and demonstrates the utility of IRIS for discovering AS-derived TAs and expanding cancer immunotherapies.
Collapse
Affiliation(s)
- Yang Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA90095
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - John W. Phillips
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Beatrice D. Zhang
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Miyako Noguchi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Eric Kutschera
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Jami McLaughlin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | | | - Zhiyuan Mao
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Nathanael J. Bangayan
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Robert Wang
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Wendy Tran
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Harry T. Yang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA90095
| | - Yuanyuan Wang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA90095
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Yang Xu
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA19104
| | - Matthew B. Obusan
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Donghui Cheng
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
| | - Alex H. Lee
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Kathryn E. Kadash-Edmondson
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Ameya Champhekar
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Cristina Puig-Saus
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Robert M. Prins
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Christopher S. Seet
- Molecular Biology Institute, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
| | - Gay M. Crooks
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Owen N. Witte
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA90095
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA90095
- Parker Institute for Cancer Immunotherapy, David Geffen School of Medicine, University of California, Los Angeles, CA90095
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| |
Collapse
|
16
|
Zhu Z, Lu H, Zhao X, Sun Y, Yao J, Xue C, Huang B. circDYRK1A tethers biological behaviors of gastric carcinoma using novel bioinformatics analysis and experimental validations. Sci Rep 2023; 13:8265. [PMID: 37217530 DOI: 10.1038/s41598-023-33861-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Gastric cancer has been one of the wide public health burdens with its high morbidity and mortality over several decades. As the unconventional modules among RNA families, circular RNAs present their blazing biological effects during gastric carcinogenesis. Though diverse hypothetical mechanisms were reported, further tests were necessitated for authentication. Herein, this study pinpointed a representative circDYRK1A which screened from vast amounts of public data sets using surprisingly novel bioinformatics approaches together with validations from the in vitro findings and then concluded that circDYRK1A tethered the biological behavior and swayed the clinicopathological features with gastric cancer patients thus providing an in-depth awareness for gastric carcinoma.
Collapse
Affiliation(s)
- Zirui Zhu
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors (China Medical University), Ministry of Education, No.155 Nanjing North Street, Heping District, Shenyang, 110001, China
- School of Medicine, Xiamen University, Xiamen, 361000, China
| | - Huiwen Lu
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors (China Medical University), Ministry of Education, No.155 Nanjing North Street, Heping District, Shenyang, 110001, China
| | - Xu Zhao
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors (China Medical University), Ministry of Education, No.155 Nanjing North Street, Heping District, Shenyang, 110001, China
| | - Yimeng Sun
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors (China Medical University), Ministry of Education, No.155 Nanjing North Street, Heping District, Shenyang, 110001, China
| | - Junqiao Yao
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors (China Medical University), Ministry of Education, No.155 Nanjing North Street, Heping District, Shenyang, 110001, China
| | - Chi Xue
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors (China Medical University), Ministry of Education, No.155 Nanjing North Street, Heping District, Shenyang, 110001, China
| | - Baojun Huang
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors (China Medical University), Ministry of Education, No.155 Nanjing North Street, Heping District, Shenyang, 110001, China.
| |
Collapse
|
17
|
Lu L, Zeng Y, Yu Z, Chen S, Xie J, Rao B, Yang B, Qiu F, Lu J, Yang L. EIF4a3-regulated circRABL2B regulates cell stemness and drug sensitivity of lung cancer via YBX1-dependent downregulation of MUC5AC expression. Int J Biol Sci 2023; 19:2725-2739. [PMID: 37324942 PMCID: PMC10266078 DOI: 10.7150/ijbs.78588] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/11/2023] [Indexed: 06/17/2023] Open
Abstract
Identification of mucin modulators is of remarkable significance to facilitate mucin-based antineoplastic therapy. However, little is known about circular RNAs (circRNAs) on regulating mucins. Dysregulated mucins and circRNAs were identified via high-throughput sequencing and their relationships with lung cancer survival were analyzed in tumor samples of 141 patients. The biological functions of circRABL2B were determined via gain- and loss-of-function experiments and exosome-packaged circRABL2B treatment in cells, patient-derived lung cancer organoids and nude mice. We identified that circRABL2B was negatively correlated with MUC5AC. Patients with low circRABL2B and high MUC5AC displayed the poorest survival (HR=2.00; 95% CI=1.12-3.57). Overexpressed circRABL2B significantly inhibited cell malignant phenotypes, while it knock-down exerted opposite effects. CircRABL2B interacted with YBX1 to inhibit MUC5AC, and subsequently suppressed integrin β4/pSrc/p53 signaling and impoverished cell stemness, and promoted erlotinib sensitivity. Exosome-packaged circRABL2B exerted significant anti-cancer actions in cells, patient-derived lung cancer organoids and nude mice. Meanwhile, circRABL2B in plasma exosomes could distinguish early-stage lung cancer patients from healthy controls. Finally, we found circRABL2B was downregulated at the transcriptional level, and EIF4a3 involved the formation of circRABL2B. In conclusion, our data suggest that circRABL2B counteracts lung cancer progression via MUC5AC/integrin β4/pSrc/p53 axis, which provides a rationale to enhance the efficacy of anti-MUCs treatment in lung cancer.
Collapse
Affiliation(s)
- Liming Lu
- The State Key Lab of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| | - Yuyuan Zeng
- The State Key Lab of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| | - Ziqi Yu
- The State Key Lab of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| | - Shizhen Chen
- The State Key Lab of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| | - Jianjiang Xie
- Department of Pulmonary and Critical Care Medicine, Guangzhou First People's Hospital, the Second Affiliated Hospital of South China University of Technology, Guangzhou 510080, China
| | - Boqi Rao
- The State Key Lab of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| | - Binyao Yang
- Innovation center for Advanced Interdisciplinary Medicine, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510735, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou 511436, China
- The State Key Lab of Respiratory Disease, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou 511436, China
| |
Collapse
|
18
|
Admon A. The biogenesis of the immunopeptidome. Semin Immunol 2023; 67:101766. [PMID: 37141766 DOI: 10.1016/j.smim.2023.101766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
The immunopeptidome is the repertoire of peptides bound and presented by the MHC class I, class II, and non-classical molecules. The peptides are produced by the degradation of most cellular proteins, and in some cases, peptides are produced from extracellular proteins taken up by the cells. This review attempts to first describe some of its known and well-accepted concepts, and next, raise some questions about a few of the established dogmas in this field: The production of novel peptides by splicing is questioned, suggesting here that spliced peptides are extremely rare, if existent at all. The degree of the contribution to the immunopeptidome by degradation of cellular protein by the proteasome is doubted, therefore this review attempts to explain why it is likely that this contribution to the immunopeptidome is possibly overstated. The contribution of defective ribosome products (DRiPs) and non-canonical peptides to the immunopeptidome is noted and methods are suggested to quantify them. In addition, the common misconception that the MHC class II peptidome is mostly derived from extracellular proteins is noted, and corrected. It is stressed that the confirmation of sequence assignments of non-canonical and spliced peptides should rely on targeted mass spectrometry using spiking-in of heavy isotope-labeled peptides. Finally, the new methodologies and modern instrumentation currently available for high throughput kinetics and quantitative immunopeptidomics are described. These advanced methods open up new possibilities for utilizing the big data generated and taking a fresh look at the established dogmas and reevaluating them critically.
Collapse
Affiliation(s)
- Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Israel.
| |
Collapse
|
19
|
Liu M, Zhang S, Zhou H, Hu X, Li J, Fu B, Wei M, Huang H, Wu H. The interplay between non-coding RNAs and alternative splicing: from regulatory mechanism to therapeutic implications in cancer. Theranostics 2023; 13:2616-2631. [PMID: 37215575 PMCID: PMC10196821 DOI: 10.7150/thno.83920] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
Alternative splicing (AS) is a common and conserved process in eukaryotic gene regulation. It occurs in approximately 95% of multi-exon genes, greatly enriching the complexity and diversity of mRNAs and proteins. Recent studies have found that in addition to coding RNAs, non-coding RNAs (ncRNAs) are also inextricably linked with AS. Multiple different types of ncRNAs are generated by AS of precursor long non-coding (pre-lncRNAs) or precursor messenger RNAs (pre-mRNAs). Furthermore, ncRNAs, as a novel class of regulators, can participate in AS regulation by interacting with the cis-acting elements or trans-acting factors. Several studies have implicated abnormal expression of ncRNAs and ncRNA-related AS events in the initiation, progression, and therapy resistance in various types of cancers. Therefore, owing to their roles in mediating drug resistance, ncRNAs, AS-related factors and AS-related novel antigens may serve as promising therapeutic targets in cancer treatment. In this review, we summarize the interaction between ncRNAs and AS processes, emphasizing their great influences on cancer, especially on chemoresistance, and highlighting their potential values in clinical treatment.
Collapse
Affiliation(s)
- Min Liu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Subo Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Heng Zhou
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P. R. China
| | - Xiaoyun Hu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Jianing Li
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Boshi Fu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Shenyang Kangwei Medical Laboratory Analysis Co. LTD, Shenyang, Liaoning, P. R. China
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning 110122, P. R. China
- Liaoning Key Laboratory of molecular targeted anti-tumor drug development and evaluation, Liaoning Cancer immune peptide drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, P. R. China
| |
Collapse
|
20
|
Zhu Q, Xu H, Huang L, Luo J, Li H, Yang R, Liu X, Liu F. Identification and detection of plasma extracellular vesicles-derived biomarkers for esophageal squamous cell carcinoma diagnosis. Biosens Bioelectron 2023; 225:115088. [PMID: 36739741 DOI: 10.1016/j.bios.2023.115088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Esophageal cancer is a malignant tumor with two-thirds of patients having a local recurrence or distant metastasis. To date, diagnostic biomarkers with high sensitivity and specificity are lacking. Extracellular vesicles (EVs) have shown their potential values as disease biomarkers as they carry specific proteins and RNAs derived from cancer cells. In this study, we investigate ESCC precision diagnostics from the insights of circulating EVs, and integrate the ultrafast EV isolation approach (EXODUS) and ELISA for fast detection and screening of ESCC patients. First, we isolate and characterize the high-purity plasma EVs with EXODUS and identify 401 proteins and 372 proteins from ESCC patient and healthy individuals, respectively. Further looking into the differentially expressed proteins (DEPs) of ESCC patients and enriched KEGG pathways, we discover EV-CD14 as a potential diagnostic biomarker for ESCC, which has been further validated as a significantly differentially expressed protein by Western Blot and immunogold labelling TEM. For fast screening and detection of ESCC towards clinical applications, we apply ELISA method to diagnose ESCC from 60 clinical samples based on circulating EV-CD14, which shows a high AUC value up to 96.0% for detection of ESCC in a test set (30 samples), and displays a high accuracy rate up to 90% for prediction of ESCC in a screening test (30 samples). Our results suggest that the circulating EV-CD14 may highly be related to the initiation and progression of ESCC, providing a novel method for the diagnosis and prognosis of ESCC towards clinical translations.
Collapse
Affiliation(s)
- Qingfu Zhu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hao Xu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Liu Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Jiaxin Luo
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengrui Li
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Rui Yang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiaoling Liu
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, China
| | - Fei Liu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| |
Collapse
|
21
|
Du JR, Wang Y, Yue ZH, Zhang HY, Wang H, Sui GQ, Sun ZX. Recent advances in sonodynamic immunotherapy. J Cancer Res Clin Oncol 2023; 149:1645-1656. [PMID: 35831762 DOI: 10.1007/s00432-022-04190-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/06/2022] [Indexed: 12/07/2022]
Abstract
Tumor immunotherapy has become an important means of tumor therapy by enhancing the immune response and triggering the activation of immune cells. However, currently, only a small number of patients respond to immunotherapy alone, and patients may experience immune-related adverse events (irAEs) during the course of treatment. Sonodynamic therapy (SDT) can produce cytotoxic substances to tumor tissue, induce apoptosis and enhance immunity. SDT combined with immunotherapy is considered a promising strategy for cancer treatment. In this mini review, we summarize the role of SDT in immunotherapy in recent years, including the application of SDT-triggered immunotherapy and the combination of SDT and immunotherapy.
Collapse
Affiliation(s)
- Jia-Rui Du
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Street, Changchun and Jilin, 130000, China
| | - Yang Wang
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Street, Changchun and Jilin, 130000, China
| | - Zong-Hua Yue
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Street, Changchun and Jilin, 130000, China
| | - Han-Yu Zhang
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Street, Changchun and Jilin, 130000, China
| | - Hui Wang
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Street, Changchun and Jilin, 130000, China.
| | - Guo-Qing Sui
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Street, Changchun and Jilin, 130000, China.
| | - Zhi-Xia Sun
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, No. 126, Xian Tai Street, Changchun and Jilin, 130000, China.
| |
Collapse
|
22
|
Yang J, Chen Y, Jing Y, Green MR, Han L. Advancing CAR T cell therapy through the use of multidimensional omics data. Nat Rev Clin Oncol 2023; 20:211-228. [PMID: 36721024 DOI: 10.1038/s41571-023-00729-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 02/01/2023]
Abstract
Despite the notable success of chimeric antigen receptor (CAR) T cell therapies in the treatment of certain haematological malignancies, challenges remain in optimizing CAR designs and cell products, improving response rates, extending the durability of remissions, reducing toxicity and broadening the utility of this therapeutic modality to other cancer types. Data from multidimensional omics analyses, including genomics, epigenomics, transcriptomics, T cell receptor-repertoire profiling, proteomics, metabolomics and/or microbiomics, provide unique opportunities to dissect the complex and dynamic multifactorial phenotypes, processes and responses of CAR T cells as well as to discover novel tumour targets and pathways of resistance. In this Review, we summarize the multidimensional cellular and molecular profiling technologies that have been used to advance our mechanistic understanding of CAR T cell therapies. In addition, we discuss current applications and potential strategies leveraging multi-omics data to identify optimal target antigens and other molecular features that could be exploited to enhance the antitumour activity and minimize the toxicity of CAR T cell therapy. Indeed, fully utilizing multi-omics data will provide new insights into the biology of CAR T cell therapy, further accelerate the development of products with improved efficacy and safety profiles, and enable clinicians to better predict and monitor patient responses.
Collapse
Affiliation(s)
- Jingwen Yang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yamei Chen
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
| |
Collapse
|
23
|
Li T, Li Y, Zhu X, He Y, Wu Y, Ying T, Xie Z. Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol 2023; 91:50-69. [PMID: 36870459 DOI: 10.1016/j.semcancer.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the body's cancer-immunity cycle and restoring its antitumor immune response. The increased availability of data, combined with advancements in high-performance computing and innovative artificial intelligence (AI) technology, has resulted in a rise in the use of AI in oncology research. State-of-the-art AI models for functional classification and prediction in immunotherapy research are increasingly used to support laboratory-based experiments. This review offers a glimpse of the current AI applications in immunotherapy, including neoantigen recognition, antibody design, and prediction of immunotherapy response. Advancing in this direction will result in more robust predictive models for developing better targets, drugs, and treatments, and these advancements will eventually make their way into the clinical setting, pushing AI forward in the field of precision oncology.
Collapse
Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yupeng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Zhu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China.
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
24
|
Wang H, Guo M, Wei H, Chen Y. Targeting p53 pathways: mechanisms, structures, and advances in therapy. Signal Transduct Target Ther 2023; 8:92. [PMID: 36859359 PMCID: PMC9977964 DOI: 10.1038/s41392-023-01347-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/19/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023] Open
Abstract
The TP53 tumor suppressor is the most frequently altered gene in human cancers, and has been a major focus of oncology research. The p53 protein is a transcription factor that can activate the expression of multiple target genes and plays critical roles in regulating cell cycle, apoptosis, and genomic stability, and is widely regarded as the "guardian of the genome". Accumulating evidence has shown that p53 also regulates cell metabolism, ferroptosis, tumor microenvironment, autophagy and so on, all of which contribute to tumor suppression. Mutations in TP53 not only impair its tumor suppressor function, but also confer oncogenic properties to p53 mutants. Since p53 is mutated and inactivated in most malignant tumors, it has been a very attractive target for developing new anti-cancer drugs. However, until recently, p53 was considered an "undruggable" target and little progress has been made with p53-targeted therapies. Here, we provide a systematic review of the diverse molecular mechanisms of the p53 signaling pathway and how TP53 mutations impact tumor progression. We also discuss key structural features of the p53 protein and its inactivation by oncogenic mutations. In addition, we review the efforts that have been made in p53-targeted therapies, and discuss the challenges that have been encountered in clinical development.
Collapse
Affiliation(s)
- Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics, Laboratory of Structural Biology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| |
Collapse
|
25
|
Zhou JG, Liang R, Wang HT, Jin SH, Hu W, Frey B, Fietkau R, Hecht M, Ma H, Gaipl US. Identification and characterization of circular RNAs as novel putative biomarkers to predict anti-PD-1 monotherapy response in metastatic melanoma patients - Knowledge from two independent international studies. Neoplasia 2023; 37:100877. [PMID: 36696838 PMCID: PMC9879779 DOI: 10.1016/j.neo.2023.100877] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/29/2022] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
Melanoma is the most aggressive skin malignancy with high morbidity. Anti-programmed cell death protein 1 (PD-1) monotherapy has been applied in metastatic melanoma. However, still most of the patients do not respond to anti-PD-1 and the availability of the present approved biomarkers therefore is limited. Here we combined the transcriptomic and clinical data of 163 advanced melanoma patients receiving anti-PD-1 from NIH Melanoma Genome Sequencing Project (phs000452, 122 patients) as the training and internal validation cohort, and Melanoma Institute Australia cohort (PRJEB23709, 41 patients) as the external validation cohort, respectively. Circular RNAs (circRNAs) are an evolutionarily conserved novel class of noncoding endogenous RNAs (ncRNAs) found in the eukaryotic transcriptome and were used based on RNAseq data for our analyses. 74,243 circular RNAs (circRNAs) were identified with NCLscan and CIRCexplorer2. Thereof, 70 circRNAs significantly associated with progression-free survival and overall survival. Further, a prognostic circRNAs signature consisting of HSA_CIRCpedia_1497, HSA_CIRCpedia_12559, HSA_CIRCpedia_43640, HSA_CIRCpedia_43070, and HSA_CIRCpedia_21660 could be determined with LASSO regression. This signature was a prognostic factor of overall survival and progression-free survival among the analyzed advanced melanoma patients. The concordance indexes (C-index of OStraining: 0.61, C-index of PFStraining: 0.68) also confirmed its credibility and accuracy. First enrichment analysis indicated that immune response and pathways related to tumor immune microenvironment were enriched. In conclusion, we succeeded to construct and validate novel prognostic circRNAs signature for advanced melanoma patients treated with anti-PD-1 immunotherapy.
Collapse
Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China,Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Rui Liang
- Biomedical Engineering College of Bioengineering, Chongqing University, Chongqing, China
| | - Hai-Tao Wang
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Su-Han Jin
- Department of Orthodontic, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Wei Hu
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Benjamin Frey
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Rainer Fietkau
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Markus Hecht
- Department of Radiotherapy and Radiation Oncology, Saarland University Medical Center, Homburg, Germany
| | - Hu Ma
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China.
| | - Udo S. Gaipl
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany,Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany,Corresponding author at: Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstraße 27, 91054 Erlangen, Germany.
| |
Collapse
|
26
|
Deng J, Lin J, Liu C, Li J, Cai J, Zhou X, Li X. N7-methylguanosine methylation-related regulator genes as biological markers in predicting prognosis for melanoma. Sci Rep 2022; 12:21082. [PMID: 36473947 PMCID: PMC9726938 DOI: 10.1038/s41598-022-25698-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The aim of this study is to find those N7-methylguanosine (m7G) methylation-related regulator genes (m7GMRRGs) which were associated with melanoma prognosis and use them to develop a prognostic prediction model. Clinical information was retrieved online from The Cancer Gene Atlas (TCGA) and the Gene Expression Omnibus (GEO). R software was used to extract m7GMRRGs by differential expression analysis. To create a prognostic risk model, univariate and multivariate Cox regression analyses were employed for the evaluation of the prognostic significance of m7G methylation modifiers. Internal validation using cohort from TCGA (training set) and external validation using cohort from GEO (validation set) of the model were carried out. The model's predictive performance was confirmed by using the Kaplan-Meier, univariate, and multivariate Cox regression, and receiver operating characteristic curve (ROC) by constructing column line plots incorporating clinical factor characteristics. Immune infiltration analyses were performed to assess the immune function of m7GMRRGs. Drug sensitivity analysis was conducted to study chemotherapeutic drug treatment cues. Prognostic models using four m7GMRRGs (EIF4E3, LARP1, NCBP3, and IFIT5) showed good prognostic power in training and validation sets. The area under the curve (AUC) at 1, 3, and 5 years for GEO-melanoma were 0.689, 0.704, and 0.726, respectively. The prediction model could distinctly classify patients with melanoma into different risk subgroups (P < 0.001 for TCGA-melanoma and P < 0.05 for GEO-melanoma). Clinical characteristics were taken into account in Cox regression and AUC analysis, which highlighted that the risk score served as an independent risk factor determining the prognosis of patients with melanoma. Immuno-infiltration analysis showed that m7GMRRGs could potentially regulate CD8+ T cells as well as regulatory T cells (Treg cells). Results of our study indicate a association between m7GMRRGs and melanoma prognosis, and the prognostic prediction model using m7GMRRGs may predict the prognosis of patients with melanoma well. Nevertheless, these results may provide a clue for potential better options of melanoma treatment but need further validation in futural studies.
Collapse
Affiliation(s)
- Jiehua Deng
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Jiahua Lin
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 China ,Department of Neurosurgery, The 924th Hospital of the Chinese People’s Liberation Army Joint Logistic Support Force, Guilin, 541002 Guangxi Zhuang Autonomous Region China
| | - Chang Liu
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Jiasong Li
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Jun Cai
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Xiyu Zhou
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| | - Xiong Li
- grid.443385.d0000 0004 1798 9548Department of Plastic and Aesthetic Surgery, The Second Affiliated Hospital of Guilin Medical University, No. 212 Renmin Road, Lingui District, Guilin, 541199 Guangxi Zhuang Autonomous Region China
| |
Collapse
|
27
|
Zhou L, Wang T, Zhang K, Zhang X, Jiang S. The development of small-molecule inhibitors targeting HPK1. Eur J Med Chem 2022; 244:114819. [DOI: 10.1016/j.ejmech.2022.114819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/25/2022]
|
28
|
Nagel R, Pataskar A, Champagne J, Agami R. Boosting Antitumor Immunity with an Expanded Neoepitope Landscape. Cancer Res 2022; 82:3637-3649. [PMID: 35904353 PMCID: PMC9574376 DOI: 10.1158/0008-5472.can-22-1525] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 01/07/2023]
Abstract
Immune-checkpoint blockade therapy has been successfully applied to many cancers, particularly tumors that harbor a high mutational burden and consequently express a high abundance of neoantigens. However, novel approaches are needed to improve the efficacy of immunotherapy for treating tumors that lack a high load of classic genetically derived neoantigens. Recent discoveries of broad classes of nongenetically encoded and inducible neoepitopes open up new avenues for therapeutic development to enhance sensitivity to immunotherapies. In this review, we discuss recent work on neoantigen discovery, with an emphasis on novel classes of noncanonical neoepitopes.
Collapse
Affiliation(s)
- Remco Nagel
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Abhijeet Pataskar
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Julien Champagne
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.,Corresponding Author: Reuven Agami, Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Phone: 3102-0512-2079; E-mail:
| |
Collapse
|
29
|
Yang Y, Li Y, Yuan H, Liu X, Ren Y, Gao C, Jiao T, Cai Y, Zhao S. Characterization of circRNA–miRNA–mRNA networks regulating oxygen utilization in type II alveolar epithelial cells of Tibetan pigs. Front Mol Biosci 2022; 9:854250. [PMID: 36213124 PMCID: PMC9532862 DOI: 10.3389/fmolb.2022.854250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the signaling pathway regulatory mechanisms in type II alveolar epithelial (ATII) cells, the progenitor cells responsible for proliferating and regenerating type I alveolar epithelial (ATI) and ATII cells, in Tibetan pigs is beneficial for exploring methods of preventing and repairing cellular damage during hypoxia. We simulated a hypoxic environment (2% O2) for culture ATII cells of Tibetan pigs and Landrace pigs, with cells cultured under normoxic conditions (21% O2) as a control group, and performed integrated analysis of circular RNA (circRNA)–microRNA (miRNA)–messenger RNA (mRNA) regulatory axes by whole-transcriptome sequencing. Functional enrichment analysis indicated that the source genes of the differential expressed circRNAs (DEcircRNAs) were primarily involved in cell proliferation, cellular processes, and cell killing. A series of DEcircRNAs were derived from inhibitors of apoptosis proteins and led to a key autonomous effect as modulators of cell repair in Tibetan pigs under hypoxia. The significant higher expression of COL5A1 in TL groups may inhibited apoptosis of ATII cells in Tibetan pigs under lower oxygen concentration, and may lead their better survive in the hypoxia environment. In addition, a competing endogenous RNA (ceRNA) network of functional interactions was constructed that included novel_circ_000898-ssc-miR-199a-5p-CAV1 and novel_circ_000898-ssc-miR-378-BMP2, based on the node genes ssc-miR-199a-5p and ssc-miR-378, which may regulate multiple miRNAs and mRNAs that mediate endoplasmic reticulum (ER) stress-induced apoptosis and inflammation and attenuate hypoxia-induced injury in ATII cells under hypoxic conditions. These results broaden our knowledge of circRNAs, miRNAs, and mRNAs associated with hypoxia and provide new insights into the hypoxic response of ATII cells in Tibetan pigs.
Collapse
Affiliation(s)
- Yanan Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongqing Li
- Xinjiang Academy of Animal Sciences, Ürümqi, Xinjiang, China
| | - Haonan Yuan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xuanbo Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yue Ren
- Academy of Agriculture and Animal Husbandry Sciences, Institute of Animal Husbandry and Veterinary Medicine, Lhasa, China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ting Jiao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- College of Grassland Science, Gansu Agricultural University, Lanzhou, China
| | - Yuan Cai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Shengguo Zhao,
| |
Collapse
|
30
|
Huang X, Yan P, Ding W, Zhou C, Xu Q, Li M, Ye L, Chen W. α-Pinene inhibits the growth of cervical cancer cells through its proapoptotic activity by regulating the miR-34a-5p/Bcl-2 signaling axis. Drug Dev Res 2022; 83:1766-1776. [PMID: 36074793 DOI: 10.1002/ddr.21994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/05/2022] [Accepted: 08/22/2022] [Indexed: 11/05/2022]
Abstract
Among gynecological tumors, cervical cancer (CC) has the second-highest prevalence and mortality rate. α-Pinene is a bicyclic monoterpenoid compound extracted from pine needles that carried promising anticancer properties. Nevertheless, its effect on CC and the underlying mechanism has not yet been elucidated. Therefore, we investigated the effect of α-Pinene on apoptosis in CC via in vitro assays of flow cytometry (FCW), terminal deoxynucleotidyl transferase-mediated nick end labeling (TUNEL) assay, quantitative real-time polymerase chain reaction (qRT-PCR), and Western blot. Following that, we detected the proapoptotic function of α-Pinene on HeLa cells in vivo by TUNEL assay and immunofluorescence staining. Our results displayed that the α-Pinene inhibited the growth of HeLa cells and stalled the cells in the G0/G1 phase. Interestingly, we also detected that α-Pinene induced HeLa cells to apoptosis. The results investigated that α-Pinene induced HeLa cells apoptosis along with up-regulating the expression of Bax, Bid, caspase-9, caspase-3, miR-34a-5p, and down-regulating the expression of Bcl-2 in vitro. At the same time, the expression levels of target genes in vivo were consistent with those in vitro. Our experiment proved that α-Pinene promoted apoptosis, which will be used to hopefully maximize the therapeutic strategies in clinical studies in CC.
Collapse
Affiliation(s)
- Xiaosu Huang
- School of Nursing, Guangdong Pharmaceutical University, Guangdong, China
| | - Pei Yan
- School of Pharmacy, Guangdong Pharmaceutical University, Guangdong, China
| | - Wenqing Ding
- Longgang District Maternity & Child Healthcare Hospital of Shenzhen City, Guangdong, China
| | - Chang Zhou
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangdong, China
| | - Qiuxiang Xu
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangdong, China
| | - Ming Li
- School of Life Science and Biopharmaceutics, Guangdong Pharmaceutical University, Guangdong, China
| | - Lianbao Ye
- School of Pharmacy, Guangdong Pharmaceutical University, Guangdong, China.,Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangdong, China
| | - Weiqiang Chen
- School of Nursing, Guangdong Pharmaceutical University, Guangdong, China.,School of Pharmacy, Guangdong Pharmaceutical University, Guangdong, China
| |
Collapse
|
31
|
Zhang S, Mao M, Lv Y, Yang Y, He W, Song Y, Wang Y, Yang Y, Al Abo M, Freedman JA, Patierno SR, Wang Y, Wang Z. A widespread length-dependent splicing dysregulation in cancer. SCIENCE ADVANCES 2022; 8:eabn9232. [PMID: 35977015 PMCID: PMC9385142 DOI: 10.1126/sciadv.abn9232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Dysregulation of alternative splicing is a key molecular hallmark of cancer. However, the common features and underlying mechanisms remain unclear. Here, we report an intriguing length-dependent splicing regulation in cancers. By systematically analyzing the transcriptome of thousands of cancer patients, we found that short exons are more likely to be mis-spliced and preferentially excluded in cancers. Compared to other exons, cancer-associated short exons (CASEs) are more conserved and likely to encode in-frame low-complexity peptides, with functional enrichment in GTPase regulators and cell adhesion. We developed a CASE-based panel as reliable cancer stratification markers and strong predictors for survival, which is clinically useful because the detection of short exon splicing is practical. Mechanistically, mis-splicing of CASEs is regulated by elevated transcription and alteration of certain RNA binding proteins in cancers. Our findings uncover a common feature of cancer-specific splicing dysregulation with important clinical implications in cancer diagnosis and therapies.
Collapse
Affiliation(s)
- Sirui Zhang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miaowei Mao
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuesheng Lv
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Yingqun Yang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Tech University, Shanghai 200031, China
| | - Weijing He
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muthana Al Abo
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer A. Freedman
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Steven R. Patierno
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| |
Collapse
|
32
|
Inalegwu A, Cuypers B, Claesen J, Janssen A, Coolkens A, Baatout S, Laukens K, De Vos WH, Quintens R. Fractionated irradiation of MCF7 breast cancer cells rewires a gene regulatory circuit towards a treatment-resistant stemness phenotype. Mol Oncol 2022; 16:3410-3435. [PMID: 35579852 PMCID: PMC9533694 DOI: 10.1002/1878-0261.13226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/07/2022] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
Radiotherapy is the standard of care for breast cancer. However, surviving radioresistant cells can repopulate following treatment and provoke relapse. Better understanding of the molecular mechanisms of radiation resistance may help improve treatment of radioresistant tumors. To emulate radiation therapy at the cellular level, we exposed MCF7 breast cancer cells to daily radiation doses of 2 Gy up to an accumulated dose of 20 Gy. Fractionally irradiated cells (FIR20) displayed increased clonogenic survival and population doubling time as compared to age-matched sham-irradiated cells and untreated parental MCF7 cells. RNA-sequencing revealed a core signature of 229 mRNAs and 7 circular RNAs of which the expression was significantly altered in FIR20 cells. Dysregulation of several top genes was mirrored at the protein level. The FIR20 cell transcriptome overlapped significantly with canonical radiation response signatures and demonstrated a remarkable commonality with radiation and endocrine therapy resistance expression profiles, suggesting crosstalk between both acquired resistance pathways, as indicated by reduced sensitivity to tamoxifen cytotoxicity of FIR20 cells. Using predictive analyses and functional enrichment, we identified a gene-regulatory network that promotes stemness and inflammatory signaling in FIR20 cells. We propose that these phenotypic traits render breast cancer cells more radioresistant but may at the same time serve as potential targets for combination therapies.
Collapse
Affiliation(s)
- Auchi Inalegwu
- Radiobiology Unit, SCK CEN, Belgian Nuclear Research Centre, 2400, Mol, Belgium.,Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610, Antwerp, Belgium.,Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020, Antwerp, Belgium.,Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610, Antwerp, Belgium
| | - Bart Cuypers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020, Antwerp, Belgium
| | - Jürgen Claesen
- Department of Epidemiology and Data Science, Amsterdam UMC, VU, Amsterdam, Netherlands
| | - Ann Janssen
- Radiobiology Unit, SCK CEN, Belgian Nuclear Research Centre, 2400, Mol, Belgium
| | - Amelie Coolkens
- Radiobiology Unit, SCK CEN, Belgian Nuclear Research Centre, 2400, Mol, Belgium
| | - Sarah Baatout
- Radiobiology Unit, SCK CEN, Belgian Nuclear Research Centre, 2400, Mol, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020, Antwerp, Belgium
| | - Winnok H De Vos
- Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610, Antwerp, Belgium.,Antwerp Centre for Advanced Microscopy (ACAM), University of Antwerp, Antwerp, Belgium.,µNEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
| | - Roel Quintens
- Radiobiology Unit, SCK CEN, Belgian Nuclear Research Centre, 2400, Mol, Belgium
| |
Collapse
|
33
|
Zhou JG, Ding Z, Shi H, Cheng M. Editorial: The Clinical Application of Neoantigens. Front Immunol 2022; 13:842633. [PMID: 35309343 PMCID: PMC8930198 DOI: 10.3389/fimmu.2022.842633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/07/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany.,Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany.,Comprehensive Cancer Center Erlangen-Europäische Metropolregion Nürnberg (EMN), Erlangen, Germany
| | - Zhenyu Ding
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Huashan Shi
- Department of Biotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Min Cheng
- Department of Physiology, Weifang Medical University, Weifang, China
| |
Collapse
|
34
|
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] [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.
Collapse
Affiliation(s)
- Rui Cheng
- Harbin Institute of Technology, China
| | | | - Meng Luo
- Harbin Institute of Technology, China
| | | | | | | | | | | | | |
Collapse
|
35
|
Li Y, Zhang Y, Pan T, Zhou P, Zhou W, Gao Y, Zheng S, Xu J. Shedding light on the hidden human proteome expands immunopeptidome in cancer. Brief Bioinform 2022; 23:6533503. [PMID: 35189633 DOI: 10.1093/bib/bbac034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/07/2022] [Accepted: 01/25/2022] [Indexed: 01/04/2023] Open
Abstract
Unrestrained cellular growth and immune escape of a tumor are associated with the incidental errors of the genome and transcriptome. Advances in next-generation sequencing have identified thousands of genomic and transcriptomic aberrations that generate variant peptides that assemble the hidden proteome, further expanding the immunopeptidome. Emerging next-generation sequencing technologies and a number of computational methods estimated the abundance of immune infiltration from bulk transcriptome have advanced our understanding of tumor microenvironments. Here, we will characterize several major types of tumor-specific antigens arising from single-nucleotide variants, insertions and deletions, gene fusion, alternative splicing, RNA editing and non-coding RNAs. Finally, we summarize the current state-of-the-art computational and experimental approaches or resources and provide an integrative pipeline for the identification of candidate tumor antigens. Together, the systematic investigation of the hidden proteome in cancer will help facilitate the development of effective and durable immunotherapy targets for cancer.
Collapse
Affiliation(s)
- Yongsheng Li
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tao Pan
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Ping Zhou
- Department of Radiotherapy, the First Affiliated Hospital of Hainan Medical University, Hainan, China
| | - Weiwei Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yueying Gao
- College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou 571199, China
| | - Shaojiang Zheng
- Key Laboratory of Emergency and Trauma of Ministry of Education, Tumor Institute of the First Affiliated Hospital, Hainan Medical University, Haikou, 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| |
Collapse
|
36
|
Karakulak T, Moch H, von Mering C, Kahraman A. Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies. Front Mol Biosci 2021; 8:726902. [PMID: 34888349 PMCID: PMC8650491 DOI: 10.3389/fmolb.2021.726902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/01/2021] [Indexed: 12/03/2022] Open
Abstract
Alternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. In cancer, alternative splicing is frequently disturbed, leading to changes in the expression of alternatively spliced protein isoforms. Advances in sequencing technologies and analysis methods led to new insights into the extent and functional impact of disturbed alternative splicing events. In this review, we give a brief overview of the molecular mechanisms driving alternative splicing, highlight the function of alternative splicing in healthy tissues and describe how alternative splicing is disrupted in cancer. We summarize current available computational tools for analyzing differential transcript usage, isoform switching events, and the pathogenic impact of cancer-specific splicing events. Finally, the strategies of three recent pan-cancer studies on isoform switching events are compared. Their methodological similarities and discrepancies are highlighted and lessons learned from the comparison are listed. We hope that our assessment will lead to new and more robust methods for cancer-specific transcript detection and help to produce more accurate functional impact predictions of isoform switching events.
Collapse
Affiliation(s)
- Tülay Karakulak
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Abdullah Kahraman
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| |
Collapse
|
37
|
Identification of an Immunogenic Medulloblastoma-Specific Fusion Involving EPC2 and GULP1. Cancers (Basel) 2021; 13:cancers13225838. [PMID: 34830991 PMCID: PMC8616194 DOI: 10.3390/cancers13225838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
Medulloblastoma is the most common malignant brain tumor in children. Immunotherapy is yet to demonstrate dramatic results in medulloblastoma, one reason being the low rate of mutations creating new antigens in this entity. In tumors with low mutational burden, gene fusions may represent a source of tumor-specific neoantigens. Here, we reviewed the landscape of fusions in medulloblastoma and analyzed their predicted immunogenicity. Furthermore, we described a new in-frame fusion protein identified by RNA-Seq. The fusion involved two genes on chromosome 2 coding for the enhancer of polycomb homolog 2 (EPC2) and GULP PTB domain containing engulfment adaptor 1 (GULP1) respectively. By qRT-PCR analysis, the fusion was detected in 3 out of 11 medulloblastoma samples, whereby 2 samples were from the same patients obtained at 2 different time points (initial diagnosis and relapse), but not in other pediatric brain tumor entities. Cloning of the full-length sequence indicated that the fusion protein contains the N-terminal enhancer of polycomb-like domain A (EPcA) of EPC2 and the coiled-coil domain of GULP1. In silico analyses predicted binding of the neoantigen-derived peptide to HLA-A*0201. A total of 50% of the fusions described in the literature were also predicted to produce an immunogenic peptide. The EPC2-GULP1 fusion peptide was able to induce a de novo T cell response characterized by interferon gamma release of CD8+ cytotoxic T cells in vitro. While the functional relevance of this fusion in medulloblastoma biology remains to be clarified, our data support an immunotherapeutic approach for pediatric medulloblastoma patients carrying the EPC2-GULP1 fusion and other immunogenic fusions.
Collapse
|
38
|
Zheng L, Guan Z, Xue M. A crucial role for the long non-coding RNA CASC11 in the pathogenesis of human cancers. Am J Transl Res 2021; 13:10922-10932. [PMID: 34650773 PMCID: PMC8507062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs more than 200 nucleotides in length. Although they do not encode proteins, lncRNAs can regulate gene expression at the transcriptional, post-transcriptional, and epigenetic levels. Emerging data show that lncRNAs are important for tumorigenesis and cancer progression. Cancer susceptibility candidate 11 (CASC11) is a prominent lncRNA that is upregulated in various types of cancers. Moreover, its overexpression correlates with larger tumor size, more advanced cancer stages, cancer metastasis, and poor overall survival for most types of cancer. Functionally, the knockdown of CASC11 can inhibit cell proliferation, invasion, and migration, while enhancing apoptosis through its regulation of gene expression and signaling pathways and its interactions with functional proteins. Here, we discuss the identification, expression, and function of CASC11. Additionally, we discuss the potential roles of CASC11 as a diagnostic biomarker, prognostic biomarker, and therapeutic target in various cancers.
Collapse
Affiliation(s)
- Lian Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Zhenjie Guan
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Miaomiao Xue
- Department of General Dentistry, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| |
Collapse
|
39
|
Dorado G, Gálvez S, Rosales TE, Vásquez VF, Hernández P. Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review. Biomolecules 2021; 11:1111. [PMID: 34439777 PMCID: PMC8393538 DOI: 10.3390/biom11081111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.
Collapse
Affiliation(s)
- Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain
| | - Sergio Gálvez
- Dep. Lenguajes y Ciencias de la Computación, Boulevard Louis Pasteur 35, Universidad de Málaga, 29071 Málaga, Spain;
| | - Teresa E. Rosales
- Laboratorio de Arqueobiología, Avda. Universitaria s/n, Universidad Nacional de Trujillo, 13011 Trujillo, Peru;
| | - Víctor F. Vásquez
- Centro de Investigaciones Arqueobiológicas y Paleoecológicas Andinas Arqueobios, Martínez de Companón 430-Bajo 100, Urbanización San Andres, 13088 Trujillo, Peru;
| | - Pilar Hernández
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain;
| |
Collapse
|