1
|
Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [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: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
Collapse
Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
| |
Collapse
|
2
|
Li J, Huang HY, Lin YCD, Zuo H, Tang Y, Huang HD. Cinnamomi ramulus inhibits cancer cells growth by inducing G2/M arrest. Front Pharmacol 2023; 14:1121799. [PMID: 37007025 PMCID: PMC10063822 DOI: 10.3389/fphar.2023.1121799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/13/2023] [Indexed: 03/19/2023] Open
Abstract
Introduction:Cinnamomi ramulus (CR) is one of the most widely used traditional Chinese medicine (TCM) with anti-cancer effects. Analyzing transcriptomic responses of different human cell lines to TCM treatment is a promising approach to understand the unbiased mechanism of TCM.Methods: This study treated ten cancer cell lines with different CR concentrations, followed by mRNA sequencing. Differential expression (DE) analysis and gene set enrichment analysis (GSEA) were utilized to analyze transcriptomic data. Finally, the in silico screening results were verified by in vitro experiments.Results: Both DE and GSEA analysis suggested the Cell cycle pathway was the most perturbated pathway by CR across these cell lines. By analyzing the clinical significance and prognosis of G2/M related genes (PLK1, CDK1, CCNB1, and CCNB2) in various cancer tissues, we found that they were up-regulated in most cancer types, and their down-regulation showed better overall survival rates in cancer patients. Finally, in vitro experiments validation on A549, Hep G2, and HeLa cells suggested that CR can inhibit cell growth by suppressing the PLK1/CDK1/ Cyclin B axis.Discussion: This is the first study to apply transcriptomic analysis to investigate the cancer cell growth inhibition of CR on various human cancer cell lines. The core effect of CR on ten cancer cell lines is to induce G2/M arrest by inhibiting the PLK1/CDK1/Cyclin B axis.
Collapse
Affiliation(s)
- Jing Li
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Hsi-Yuan Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Yang-Chi-Dung Lin
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Huali Zuo
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Yun Tang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Hsien-Da Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- *Correspondence: Hsien-Da Huang,
| |
Collapse
|
3
|
Research advances and treatment perspectives of pancreatic adenosquamous carcinoma. Cell Oncol (Dordr) 2023; 46:1-15. [PMID: 36316580 DOI: 10.1007/s13402-022-00732-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND As a malignant tumor, pancreatic cancer has an extremely low overall 5-year survival rate. Pancreatic adenosquamous carcinoma (PASC), a rare pancreatic malignancy, owns clinical presentation similar to pancreatic ductal adenocarcinoma (PDAC), which is the most prevalent pancreatic cancer subtype. PASC is generally defined as a pancreatic tumor consisting mainly of adenocarcinoma tissue and squamous carcinoma tissue. Compared with PDAC, PASC has a higher metastatic potential and worse prognosis, and lacks of effective treatment options to date. However, the pathogenesis and treatment of PASC are not yet clear and are accompanied with difficulties. CONCLUSION The present paper systematically summarizes the possible pathogenesis, diagnosis methods, and further suggests potential new treatment directions through reviewing research results of PASC, including the clinical manifestations, pathological manifestation, the original hypothesis of squamous carcinoma and the potential regulatory mechanism. In short, the present paper provides a systematic review of the research progress and new ideas for the development mechanism and treatment of PASC.
Collapse
|
4
|
Meraviglia-Crivelli D, Villanueva H, Zheleva A, Villalba-Esparza M, Moreno B, Menon AP, Calvo A, Cebollero J, Barainka M, de los Mozos IR, Huesa-Berral C, Pastor F. IL-6/STAT3 signaling in tumor cells restricts the expression of frameshift-derived neoantigens by SMG1 induction. Mol Cancer 2022; 21:211. [PMID: 36443756 PMCID: PMC9703761 DOI: 10.1186/s12943-022-01679-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/21/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The quality and quantity of tumor neoantigens derived from tumor mutations determines the fate of the immune response in cancer. Frameshift mutations elicit better tumor neoantigens, especially when they are not targeted by nonsense-mediated mRNA decay (NMD). For tumor progression, malignant cells need to counteract the immune response including the silencing of immunodominant neoantigens (antigen immunoediting) and promoting an immunosuppressive tumor microenvironment. Although NMD inhibition has been reported to induce tumor immunity and increase the expression of cryptic neoantigens, the possibility that NMD activity could be modulated by immune forces operating in the tumor microenvironment as a new immunoediting mechanism has not been addressed. METHODS We study the effect of SMG1 expression (main kinase that initiates NMD) in the survival and the nature of the tumor immune infiltration using TCGA RNAseq and scRNAseq datasets of breast, lung and pancreatic cancer. Different murine tumor models were used to corroborate the antitumor immune dependencies of NMD. We evaluate whether changes of SMG1 expression in malignant cells impact the immune response elicited by cancer immunotherapy. To determine how NMD fluctuates in malignant cells we generated a luciferase reporter system to track NMD activity in vivo under different immune conditions. Cytokine screening, in silico studies and functional assays were conducted to determine the regulation of SMG1 via IL-6/STAT3 signaling. RESULTS IL-6/STAT3 signaling induces SMG1, which limits the expression of potent frameshift neoantigens that are under NMD control compromising the outcome of the immune response. CONCLUSION We revealed a new neoantigen immunoediting mechanism regulated by immune forces (IL-6/STAT3 signaling) responsible for silencing otherwise potent frameshift mutation-derived neoantigens.
Collapse
Affiliation(s)
- Daniel Meraviglia-Crivelli
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.508840.10000 0004 7662 6114Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Helena Villanueva
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.508840.10000 0004 7662 6114Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Angelina Zheleva
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.508840.10000 0004 7662 6114Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - María Villalba-Esparza
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.508840.10000 0004 7662 6114Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain ,grid.47100.320000000419368710Department of Pathology, Yale University School of Medicine, New Haven, CT 06510 USA
| | - Beatriz Moreno
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain
| | - Ashwathi Puravankara Menon
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.508840.10000 0004 7662 6114Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Alfonso Calvo
- grid.5924.a0000000419370271IDISNA, CIBERONC, Program in Solid Tumors (CIMA), Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Avenida Pío XII, 55, 31008 Pamplona, Spain
| | - Javier Cebollero
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.508840.10000 0004 7662 6114Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Martin Barainka
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.508840.10000 0004 7662 6114Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Igor Ruiz de los Mozos
- grid.5924.a0000000419370271Gene Therapy Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.424222.00000 0001 2242 5374Department of Personalized Medicine, NASERTIC, Government of Navarra, 31008 Pamplona, Spain
| | - Carlos Huesa-Berral
- grid.5924.a0000000419370271Department of Physics and Applied Mathematics, School of Science, University of Navarra, E-31008 Pamplona, Navarra Spain
| | - Fernando Pastor
- grid.5924.a0000000419370271Molecular Therapeutics Program, Center for Applied Medical Research, CIMA, University of Navarra, 31008 Pamplona, Spain ,grid.508840.10000 0004 7662 6114Instituto de Investigación Sanitaria de Navarra (IDISNA), Recinto de Complejo Hospitalario de Navarra, 31008 Pamplona, Spain ,grid.5924.a0000000419370271Department of Molecular Therapies, CIMA (Center for Applied Medical Research) University of Navarre, Av. de Pío XII, 55, 31008 Pamplona, Spain
| |
Collapse
|
5
|
A pan-tumor-siRNA aptamer chimera to block nonsense-mediated mRNA decay inflames and suppresses tumor progression. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:413-425. [PMID: 35991316 PMCID: PMC9379514 DOI: 10.1016/j.omtn.2022.07.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/15/2022] [Indexed: 12/21/2022]
Abstract
Immune-checkpoint blockade (ICB) therapy has changed the clinical outcome of many types of aggressive tumors, but there still remain many cancer patients that do not respond to these treatments. There is an unmet need to develop a feasible clinical therapeutic platform to increase the rate of response to ICB. Here we use a previously described clinically tested aptamer (AS1411) conjugated with SMG1 RNAi (AS1411-SMG1 aptamer-linked siRNA chimeras [AsiCs]) to inhibit the nonsense-mediated RNA decay pathway inducing tumor inflammation and improving response to ICB. The aptamer AS1411 shows binding to numerous mouse and human tumor cell lines tested. AS1411 induces tumor cytotoxicity in long incubation times, which allows for the use of the aptamer as a carrier to target the RNAi inhibition to the tumor. The AS1411-SMG1 AsiCs induce a strong antitumor response in local and systemic treatment in different types of tumors. Finally, AS1411-SMG1 AsiCs are well tolerated with no detected side effects.
Collapse
|
6
|
Tan K, Stupack DG, Wilkinson MF. Nonsense-mediated RNA decay: an emerging modulator of malignancy. Nat Rev Cancer 2022; 22:437-451. [PMID: 35624152 PMCID: PMC11009036 DOI: 10.1038/s41568-022-00481-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that selectively degrades RNAs harbouring truncating mutations that prematurely terminate translation, including nonsense, frameshift and some splice-site mutations. Recent studies show that NMD shapes the mutational landscape of tumours by selecting for mutations that tend to downregulate the expression of tumour suppressor genes but not oncogenes. This suggests that NMD can benefit tumours, a notion further supported by the finding that mRNAs encoding immunogenic neoantigen peptides are typically targeted for decay by NMD. Together, this raises the possibility that NMD-inhibitory therapy could be of therapeutic benefit against many tumour types, including those with a high load of neoantigen-generating mutations. Complicating this scenario is the evidence that NMD can also be detrimental for many tumour types, and consequently tumours often have perturbed NMD. NMD may suppress tumour generation and progression by degrading subsets of specific normal mRNAs, including those encoding stress-response proteins, signalling factors and other proteins beneficial for tumours, as well as pro-tumour non-coding RNAs. Together, these findings suggest that NMD-modulatory therapy has the potential to provide widespread therapeutic benefit against diverse tumour types. However, whether NMD should be stimulated or repressed requires careful analysis of the tumour to be treated.
Collapse
Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
7
|
Polaski JT, Udy DB, Escobar-Hoyos LF, Askan G, Leach SD, Ventura A, Kannan R, Bradley RK. The origins and consequences of UPF1 variants in pancreatic adenosquamous carcinoma. eLife 2021; 10:e62209. [PMID: 33404013 PMCID: PMC7846273 DOI: 10.7554/elife.62209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic adenosquamous carcinoma (PASC) is an aggressive cancer whose mutational origins are poorly understood. An early study reported high-frequency somatic mutations affecting UPF1, a nonsense-mediated mRNA decay (NMD) factor, in PASC, but subsequent studies did not observe these lesions. The corresponding controversy about whether UPF1 mutations are important contributors to PASC has been exacerbated by a paucity of functional studies. Here, we modeled two UPF1 mutations in human and mouse cells to find no significant effects on pancreatic cancer growth, acquisition of adenosquamous features, UPF1 splicing, UPF1 protein, or NMD efficiency. We subsequently discovered that 45% of UPF1 mutations reportedly present in PASCs are identical to standing genetic variants in the human population, suggesting that they may be non-pathogenic inherited variants rather than pathogenic mutations. Our data suggest that UPF1 is not a common functional driver of PASC and motivate further attempts to understand the genetic origins of these malignancies.
Collapse
Affiliation(s)
- Jacob T Polaski
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Molecular and Cellular Biology Graduate Program, University of WashingtonSeattleUnited States
| | - Luisa F Escobar-Hoyos
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Department of Pathology, Stony Brook UniversityNew YorkUnited States
- Yale University School of MedicineNew HavenUnited States
| | - Gokce Askan
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Steven D Leach
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Department of Surgery, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
- Dartmouth Norris Cotton Cancer CenterLebanonUnited States
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Ram Kannan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| |
Collapse
|