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Wang HY, Xie Y, Du H, Luo B, Li Z. High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration. PeerJ 2023; 11:e16104. [PMID: 37810780 PMCID: PMC10557942 DOI: 10.7717/peerj.16104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/25/2023] [Indexed: 10/10/2023] Open
Abstract
Background Many researches proved that non-coding RNAs are important in glioma development. We screened the differentially expressed genes through The Cancer Genome Atlas (TCGA) database and identified the molecule LYRM4-AS1 associated with prognosis. As a lncRNA, the expression level and role of LYRM4-AS1 in glioma are inconclusive. Therefore, we attempted to assess the clinical significance, expression and related mechanisms of LYRM4-AS1 in glioma by employing cell experiments and an integrative in silico methodology. Methods RNA-seq data were obtained from UCSC XENA and TCGA datasets. The Gene Expression Omnibus (GEO) database was used to download glioma-related expression profile data. The LYRM4-AS1 expression level was evaluated. Survival curves were constructed by the Kaplan-Meier method. Cox regression analysis was used to analyze independent variables. Patients were divided into high and low expression group base on the median LYRM4-AS1 expression value in glioma tissues. The DESeq2 R package was used to identify differentially expressed genes (DEGs) between two different expression LYRM4-AS1 groups. Gene set enrichment analysis (GSEA) was conducted. Next, the single-sample Gene Set Enrichment Analysis (ssGSEA) was done to quantify the immune infiltration of immune cells in glioma tissues. Gene expression profiles for glioma tumor tissues were used to quantify the relative enrichment score for each immune cell. Spearman correlation analysis was used to analyze the correlation between LYRM4-AS1 and biomarkers of immune cells as well as immune checkpoints in glioma. Finally, assays for cell apoptosis, cell viability and wound healing were conducted to evaluate the function on U87 MG and U251 cells after knocking down LYRM4-AS1. Results We found that LYRM4-AS1 was upregulated and related to the grade and malignancy of glioma. Survival analyses showed that high expression LYRM4-AS1 patients had poor clinical outcomes (P < 0.01). Cox regression analyses demonstrated that LYRM4-AS1 was an independent risk factor for overall survival (OS) in glioma (HR: 274 1.836; CI [1.278-2.639]; P = 0.001). Enrichment and immune infiltration analysis showed interferon signaling and cytokine-cytokine receptor interaction enriched in the LYRM4-AS1 high-expression phenotype, and LYRM4-AS1 showed significantly positively related to immune infiltration as well as immune checkpoints (P < 0.01). The knockdown of LYRM4-AS1 in U87 MG and U251 cells can inhibit migration and proliferation of cells (P < 0.05). Conclusions These findings indicated that the increased LYRM4-AS1 may be useful for the diagnosis and prognosis of glioma and might participate in the immune infiltration.
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Affiliation(s)
- Hai yue Wang
- Department of Nutrition, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Nutrition and Health, Shijiazhuang, Hebei, China
| | - Ying Xie
- Department of Nutrition, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Nutrition and Health, Shijiazhuang, Hebei, China
| | - Hongzhen Du
- Department of Nutrition, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Nutrition and Health, Shijiazhuang, Hebei, China
| | - Bin Luo
- Department of Nutrition, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Nutrition and Health, Shijiazhuang, Hebei, China
| | - Zengning Li
- Department of Nutrition, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Nutrition and Health, Shijiazhuang, Hebei, China
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Herzog RW, Cooper M, Perrin GQ, Biswas M, Martino AT, Morel L, Terhorst C, Hoffman BE. Regulatory T cells and TLR9 activation shape antibody formation to a secreted transgene product in AAV muscle gene transfer. Cell Immunol 2017; 342:103682. [PMID: 28888664 DOI: 10.1016/j.cellimm.2017.07.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/15/2017] [Accepted: 07/31/2017] [Indexed: 12/21/2022]
Abstract
Adeno-associated viral (AAV) gene delivery to skeletal muscle is being explored for systemic delivery of therapeutic proteins. To better understand the signals that govern antibody formation against secreted transgene products in this approach, we administered an intramuscular dose of AAV1 vector expressing human coagulation factor IX (hFIX), which does not cause antibody formation against hFIX in C57BL/6 mice. Interestingly, co-administration of a TLR9 agonist (CpG-deoxyoligonucleotide, ODN) but not of lipopolysaccharide, caused a transient anti-hFIX response. ODN activated monocyte-derived dendritic cells and enhanced T follicular helper cell responses. While depletion of regulatory T cells (Tregs) also caused an antibody response, TLR9 activation combined with Treg depletion instead resulted in prolonged CD8+ T cell infiltration of transduced muscle. Thus, Tregs modulate the response to the TLR9 agonist. Further, Treg re-population eventually resolved humoral and cellular immune responses. Therefore, specific modes of TLR9 activation and Tregs orchestrate antibody formation in muscle gene transfer.
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Affiliation(s)
- Roland W Herzog
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL, United States.
| | - Mario Cooper
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL, United States
| | - George Q Perrin
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL, United States
| | - Moanaro Biswas
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL, United States
| | - Ashley T Martino
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL, United States
| | - Laurence Morel
- Department of Pathology, Immunology, and Laboratory Investigation, University of Florida, Gainesville, FL, United States
| | - Cox Terhorst
- Division of Immunology, BIDMC, Harvard Medical School, Boston, MA, United States
| | - Brad E Hoffman
- Department of Pediatrics, Division of Cellular and Molecular Therapy, University of Florida, Gainesville, FL, United States.
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Robert MA, Chahal PS, Audy A, Kamen A, Gilbert R, Gaillet B. Manufacturing of recombinant adeno-associated viruses using mammalian expression platforms. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600193] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/08/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Marc-André Robert
- Département de génie chimique; Université Laval; Québec QC Canada
- National Research Council Canada; Montréal QC Canada
| | | | - Alexandre Audy
- Département de génie chimique; Université Laval; Québec QC Canada
- National Research Council Canada; Montréal QC Canada
| | - Amine Kamen
- Department of Bioengineering; McGill University; Montréal QC Canada
| | | | - Bruno Gaillet
- Département de génie chimique; Université Laval; Québec QC Canada
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Mays LE, Wang L, Lin J, Bell P, Crawford A, Wherry EJ, Wilson JM. AAV8 induces tolerance in murine muscle as a result of poor APC transduction, T cell exhaustion, and minimal MHCI upregulation on target cells. Mol Ther 2013; 22:28-41. [PMID: 23778424 DOI: 10.1038/mt.2013.134] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 04/24/2013] [Indexed: 12/20/2022] Open
Abstract
Following gene transfer of adeno-associated virus 2/8 (AAV2/8) to the muscle, C57BL/6 mice show long-term expression of a nuclear-targeted LacZ (nLacZ) transgene with minimal immune activation. Here, we show that pre-exposure to AAV2/8 can also induce tolerance to the more immunogenic AAV2/rh32.33 vector, preventing otherwise robust T-cell activation and allowing stable transgene expression. Depletion and adoptive transfer studies showed that a suppressive factor was not sufficient to account for AAV2/8-induced tolerance, whereas further characterization of the T-cell population showed upregulation of the exhaustion markers PD1, 2B4, and LAG3. Furthermore, systemic administration of Toll-like receptor (TLR) ligands at the time of AAV2/rh32.33-administration broke AAV2/8-induced tolerance, restoring T-cell activation and β-gal clearance. As such, AAV2/8 transduction appears to lack the inflammatory signals necessary to prime a functional cytotoxic T-cell response. Inadequate T-cell priming could be explained upstream by AAV2/8's poor transduction and activation of antigen-presenting cells (APCs). Immunohistochemical analysis indicates that AAV2/8 transduction also fails to upregulate major histocompatibility complex class I (MHCI) expression on the surface of myocytes, rendering transduced cells poor targets for T-cell-mediated destruction. Overall, AAV2/8-induced tolerance in the muscle is multifactorial, spanning from poor APC transduction and activation to the subsequent priming of functionally exhausted T-cells, while simultaneously avoiding upregulation of MHCI on potential targets.
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Affiliation(s)
- Lauren E Mays
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lili Wang
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jianping Lin
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Peter Bell
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Alison Crawford
- Present address: Regeneron Pharmaceutical, Tarrytown, New York, USA
| | - E John Wherry
- Department of Microbiology and Institute for Immunology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - James M Wilson
- Gene Therapy Program, Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Steel JC, Di Pasquale G, Ramlogan CA, Patel V, Chiorini JA, Morris JC. Oral vaccination with adeno-associated virus vectors expressing the Neu oncogene inhibits the growth of murine breast cancer. Mol Ther 2013; 21:680-7. [PMID: 23295951 DOI: 10.1038/mt.2012.260] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Recombinant adeno-associated viruses (AAV) have been used for therapeutic gene transfer. These vectors offer a number of advantages including resistance to the effects of pH, a broad cellular tropism, efficient gene transfer, persistence of gene expression, and little toxicity. AAV vectors; however, at high doses can induce humoral and cellular immune responses. While potentially problematic for replacement gene therapy, this effect may be advantageous for antitumor vaccination. We examined the activity of an oral and intramuscular antitumor vaccination using AAV serotypes 5 and 6 expressing a truncated neu oncogene in a neu-positive murine TUBO breast cancer model. Mice receiving a single oral administration of AAV5-neu or AAV6-neu demonstrated improved survival. Oral vaccination significantly improved survivals compared with intramuscular vaccination. Mice vaccinated with AAV6-neu survived longer than those treated with AAV5-neu. Vaccination with AAV5-neu or AAV6-neu induced both humoral and cellular immune responses against the NEU antigen. These responses were more robust in the mice undergoing oral vaccination compared with mice receiving the intramuscular vaccination. Protection from tumor was long lasting with 80% of the animals treated with oral AAV6-neu surviving a re-challenge with TUBO cells at 120 and 320 days post-vaccination. Further evaluation of AAV-based vectors as tumor vaccines is warranted.
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Affiliation(s)
- Jason C Steel
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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