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Luo R, Liu J, Wen J, Zhou X. Single-cell Landscape of Malignant Transition: Unraveling Cancer Cell-of-Origin and Heterogeneous Tissue Microenvironment. RESEARCH SQUARE 2024:rs.3.rs-4085185. [PMID: 38645221 PMCID: PMC11030487 DOI: 10.21203/rs.3.rs-4085185/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Understanding disease progression and sophisticated tumor ecosystems is imperative for investigating tumorigenesis mechanisms and developing novel prevention strategies. Here, we dissected heterogeneous microenvironments during malignant transitions by leveraging data from 1396 samples spanning 13 major tissues. Within transitional stem-like subpopulations highly enriched in precancers and cancers, we identified 30 recurring cellular states strongly linked to malignancy, including hypoxia and epithelial senescence, revealing a high degree of plasticity in epithelial stem cells. By characterizing dynamics in stem-cell crosstalk with the microenvironment along the pseudotime axis, we found differential roles of ANXA1 at different stages of tumor development. In precancerous stages, reduced ANXA1 levels promoted monocyte differentiation toward M1 macrophages and inflammatory responses, whereas during malignant progression, upregulated ANXA1 fostered M2 macrophage polarization and cancer-associated fibroblast transformation by increasing TGF-β production. Our spatiotemporal analysis further provided insights into mechanisms responsible for immunosuppression and a potential target to control evolution of precancer and mitigate the risk for cancer development.
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Affiliation(s)
| | - Jiajia Liu
- The University of Texas Health Science Center at Houston
| | - Jianguo Wen
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston
| | - Xiaobo Zhou
- School of Biomedical Informatics, The University of Texas Health Science Center at Houston
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Kumar H, Luo R, Wen J, Yang C, Zhou X, Kim P. FusionNeoAntigen: a resource of fusion gene-specific neoantigens. Nucleic Acids Res 2024; 52:D1276-D1288. [PMID: 37870454 PMCID: PMC10767944 DOI: 10.1093/nar/gkad922] [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: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
Among the diverse sources of neoantigens (i.e. single-nucleotide variants (SNVs), insertions or deletions (Indels) and fusion genes), fusion gene-derived neoantigens are generally more immunogenic, have multiple targets per mutation and are more widely distributed across various cancer types. Therefore, fusion gene-derived neoantigens are a potential source of highly immunogenic neoantigens and hold great promise for cancer immunotherapy. However, the lack of fusion protein sequence resources and knowledge prevents this application. We introduce 'FusionNeoAntigen', a dedicated resource for fusion-specific neoantigens, accessible at https://compbio.uth.edu/FusionNeoAntigen. In this resource, we provide fusion gene breakpoint crossing neoantigens focused on ∼43K fusion proteins of ∼16K in-frame fusion genes from FusionGDB2.0. FusionNeoAntigen provides fusion gene information, corresponding fusion protein sequences, fusion breakpoint peptide sequences, fusion gene-derived neoantigen prediction, virtual screening between fusion breakpoint peptides having potential fusion neoantigens and human leucocyte antigens (HLAs), fusion breakpoint RNA/protein sequences for developing vaccines, information on samples with fusion-specific neoantigen, potential CAR-T targetable cell-surface fusion proteins and literature curation. FusionNeoAntigen will help to develop fusion gene-based immunotherapies. We will report all potential fusion-specific neoantigens from all possible open reading frames of ∼120K human fusion genes in future versions.
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Affiliation(s)
- Himansu Kumar
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ruihan Luo
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianguo Wen
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Chengyuan Yang
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Haynes T, Gilbert MR, Breen K, Yang C. Pathways to hypermutation in high-grade gliomas: Mechanisms, syndromes, and opportunities for immunotherapy. Neurooncol Adv 2024; 6:vdae105. [PMID: 39022645 PMCID: PMC11252568 DOI: 10.1093/noajnl/vdae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024] Open
Abstract
Despite rapid advances in the field of immunotherapy, including the success of immune checkpoint inhibition in treating multiple cancer types, clinical response in high-grade gliomas (HGGs) has been disappointing. This has been in part attributed to the low tumor mutational burden (TMB) of the majority of HGGs. Hypermutation is a recently characterized glioma signature that occurs in a small subset of cases, which may open an avenue to immunotherapy. The substantially elevated TMB of these tumors most commonly results from alterations in the DNA mismatch repair pathway in the setting of extensive exposure to temozolomide or, less frequently, from inherited cancer predisposition syndromes. In this review, we discuss the genetics and etiology of hypermutation in HGGs, with an emphasis on the resulting genomic signatures, and the state and future directions of immuno-oncology research in these patient populations.
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Affiliation(s)
- Tuesday Haynes
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Kevin Breen
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Chunzhang Yang
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, Maryland, USA
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Luo N, Mei Z, Zhang Q, Tang H, Wan R, Deng A, Zou X, Lv C. TMX family genes and their association with prognosis, immune infiltration, and chemotherapy in human pan-cancer. Aging (Albany NY) 2023; 15:15064-15083. [PMID: 38147024 PMCID: PMC10781458 DOI: 10.18632/aging.205332] [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: 07/13/2023] [Accepted: 11/10/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND The thioredoxin (TMX) system, an important redox system, plays crucial roles in several immune-related diseases. However, there is limited research on the correlation of TMX family gene expression with human pan-cancer prognosis, tumor microenvironment (TME), and immunotherapy. METHODS Based on the integration of several bioinformatics analysis methods, we explored the expression levels and prognostic value of TMX family members in pan-cancer and analyzed their association between TME, immune infiltration, stemness scores, and drug sensitivity. Using KEGG enrichment analysis, we explored the potential signaling pathways of their regulation. Additionally, we conducted a transwell assay to verify the relationship between TMX family gene expression and epithelial-mesenchymal transition (EMT) in liver cancer. RESULTS Expression of the TMX family genes was shown to have an obvious intratumoral heterogeneity. In some cancers, TMX family members expression was also been found to correlate with poor prognosis of patients. Furthermore, TMX family genes may serve important roles in TME. The expression of TMX family genes was found to have a strong correlation with the stromal scores, immune scores, DNAss and RNAss in pan-cancer. Specifically, the expression levels of TMX family genes have been found to be associated with immune subtypes of renal clear cell carcinoma and liver hepatocellular carcinoma. High TMX2 expression promote EMT in liver cancer. CONCLUSIONS The findings of this study may elucidate the biological roles of TMX family genes as potential targets for pan-cancer and also offer valuable insights for further investigating how these genes function in the development and spreading of cancer.
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Affiliation(s)
- Na Luo
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
- School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Zhiqiang Mei
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Qiqi Zhang
- Degree Office, The Graduate School of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Hong Tang
- Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Runlan Wan
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Anni Deng
- Department of Pediatrics, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Xiaopan Zou
- Breast and Thyroid Surgery, Renmin Hospital, Jilin University, Changchun 130024, Jilin, China
| | - Chaoxiang Lv
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
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Sandbank E, Eckerling A, Margalit A, Sorski L, Ben-Eliyahu S. Immunotherapy during the Immediate Perioperative Period: A Promising Approach against Metastatic Disease. Curr Oncol 2023; 30:7450-7477. [PMID: 37623021 PMCID: PMC10453707 DOI: 10.3390/curroncol30080540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
Tumor excision is a necessary life-saving procedure in most solid cancers. However, surgery and the days before and following it, known as the immediate perioperative period (IPP), entail numerous prometastatic processes, including the suppression of antimetastatic immunity and direct stimulation of minimal residual disease (MRD). Thus, the IPP is pivotal in determining long-term cancer outcomes, presenting a short window of opportunity to circumvent perioperative risk factors by employing several therapeutic approaches, including immunotherapy. Nevertheless, immunotherapy is rarely examined or implemented during this short timeframe, due to both established and hypothetical contraindications to surgery. Herein, we analyze how various aspects of the IPP promote immunosuppression and progression of MRD, and how potential IPP application of immunotherapy may interact with these deleterious processes. We discuss the feasibility and safety of different immunotherapies during the IPP with a focus on the latest approaches of immune checkpoint inhibition. Last, we address the few past and ongoing clinical trials that exploit the IPP timeframe for anticancer immunotherapy. Accordingly, we suggest that several specific immunotherapies can be safely and successfully applied during the IPP, alone or with supporting interventions, which may improve patients' resistance to MRD and overall survival.
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Affiliation(s)
- Elad Sandbank
- Neuro-Immunology Research Unit, School of Psychological Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (E.S.); (A.E.); (L.S.)
| | - Anabel Eckerling
- Neuro-Immunology Research Unit, School of Psychological Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (E.S.); (A.E.); (L.S.)
| | - Adam Margalit
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel;
| | - Liat Sorski
- Neuro-Immunology Research Unit, School of Psychological Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (E.S.); (A.E.); (L.S.)
| | - Shamgar Ben-Eliyahu
- Neuro-Immunology Research Unit, School of Psychological Sciences, Tel Aviv University, Tel Aviv 69978, Israel; (E.S.); (A.E.); (L.S.)
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel;
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