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Li L, Zhang X, Wang X, Kim SW, Herndon JM, Becker-Hapak MK, Carreno BM, Myers NB, Sturmoski MA, McLellan MD, Miller CA, Johanns TM, Tan BR, Dunn GP, Fleming TP, Hansen TH, Goedegebuure SP, Gillanders WE. Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation. Genome Med 2021; 13:56. [PMID: 33879241 PMCID: PMC8059244 DOI: 10.1186/s13073-021-00872-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/17/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Preclinical studies and early clinical trials have shown that targeting cancer neoantigens is a promising approach towards the development of personalized cancer immunotherapies. DNA vaccines can be rapidly and efficiently manufactured and can integrate multiple neoantigens simultaneously. We therefore sought to optimize the design of polyepitope DNA vaccines and test optimized polyepitope neoantigen DNA vaccines in preclinical models and in clinical translation. METHODS We developed and optimized a DNA vaccine platform to target multiple neoantigens. The polyepitope DNA vaccine platform was first optimized using model antigens in vitro and in vivo. We then identified neoantigens in preclinical breast cancer models through genome sequencing and in silico neoantigen prediction pipelines. Optimized polyepitope neoantigen DNA vaccines specific for the murine breast tumor E0771 and 4T1 were designed and their immunogenicity was tested in vivo. We also tested an optimized polyepitope neoantigen DNA vaccine in a patient with metastatic pancreatic neuroendocrine tumor. RESULTS Our data support an optimized polyepitope neoantigen DNA vaccine design encoding long (≥20-mer) epitopes with a mutant form of ubiquitin (Ubmut) fused to the N-terminus for antigen processing and presentation. Optimized polyepitope neoantigen DNA vaccines were immunogenic and generated robust neoantigen-specific immune responses in mice. The magnitude of immune responses generated by optimized polyepitope neoantigen DNA vaccines was similar to that of synthetic long peptide vaccines specific for the same neoantigens. When combined with immune checkpoint blockade therapy, optimized polyepitope neoantigen DNA vaccines were capable of inducing antitumor immunity in preclinical models. Immune monitoring data suggest that optimized polyepitope neoantigen DNA vaccines are capable of inducing neoantigen-specific T cell responses in a patient with metastatic pancreatic neuroendocrine tumor. CONCLUSIONS We have developed and optimized a novel polyepitope neoantigen DNA vaccine platform that can target multiple neoantigens and induce antitumor immune responses in preclinical models and neoantigen-specific responses in clinical translation.
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Affiliation(s)
- Lijin Li
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Xiuli Zhang
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Xiaoli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Samuel W Kim
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - John M Herndon
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | | | - Beatriz M Carreno
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Present Address: Parker Institute for Cancer Immunotherapy, Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy B Myers
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Mark A Sturmoski
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Michael D McLellan
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Christopher A Miller
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
- The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA
| | - Tanner M Johanns
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Benjamin R Tan
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Gavin P Dunn
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Timothy P Fleming
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
- The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA
- Present Address: Norton Thoracic Institute, St. Joseph Hospital and Medical Center, Phoenix, AZ, USA
| | - Ted H Hansen
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
- The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA.
- The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA.
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George RJ, Sturmoski MA, May R, Sureban SM, Dieckgraefe BK, Anant S, Houchen CW. Loss of p21Waf1/Cip1/Sdi1 enhances intestinal stem cell survival following radiation injury. Am J Physiol Gastrointest Liver Physiol 2009; 296:G245-54. [PMID: 19056768 PMCID: PMC2643902 DOI: 10.1152/ajpgi.00021.2008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The microcolony assay following gamma irradiation (IR) is a functional assay of intestinal stem cell fate. The cyclin-dependent kinase (CDK) inhibitor p21(Waf1/Cip1/Sdi1) (p21) regulates cell cycle arrest following DNA damage. To explore the role of p21 on stem cell fate, we examined the effects of p21 deletion on intestinal crypt survival following IR and expression of the stem/progenitor cell marker Musashi-1 (Msi-1) and the antiapoptotic gene survivin. Intestinal stem cell survival in adult wild-type (WT) and p21(-/-) mice was measured using the microcolony assay. Msi-1, p21, and survivin mRNA were measured using real-time PCR and immunohistochemical analysis. Laser capture microdissection (LCM) was used to isolate mRNA from the crypt stem cell zone. No differences in radiation-induced apoptosis were observed between WT and p21(-/-) mice. However, increased crypt survival (3.0-fold) was observed in p21(-/-) compared with WT mice 3.5 days after 13 Gy. Msi-1 and survivin mRNA were elevated 12- and 7.5-fold, respectively, in LCM-dissected crypts of p21(-/-) compared with WT mice. In conclusion, deletion of p21 results in protection of crypt stem/progenitor cells from IR-induced cell death. Furthermore, the increase in crypt survival is associated with increased numbers of Msi-1- and survivin-expressing cells in regenerative crypts.
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Affiliation(s)
- Robert J. George
- Department of Medicine, Division of Digestive Diseases and Nutrition, and Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; Department of Internal Medicine, Division of Gastroenterology, and Department of Surgery, Washington University School of Medicine, St. Louis, Missouri; OU Cancer Institute, Oklahoma City; and Department of Veteran Affairs Medical Center, Oklahoma City, Oklahoma
| | - Mark A. Sturmoski
- Department of Medicine, Division of Digestive Diseases and Nutrition, and Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; Department of Internal Medicine, Division of Gastroenterology, and Department of Surgery, Washington University School of Medicine, St. Louis, Missouri; OU Cancer Institute, Oklahoma City; and Department of Veteran Affairs Medical Center, Oklahoma City, Oklahoma
| | - Randal May
- Department of Medicine, Division of Digestive Diseases and Nutrition, and Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; Department of Internal Medicine, Division of Gastroenterology, and Department of Surgery, Washington University School of Medicine, St. Louis, Missouri; OU Cancer Institute, Oklahoma City; and Department of Veteran Affairs Medical Center, Oklahoma City, Oklahoma
| | - Sripathi M. Sureban
- Department of Medicine, Division of Digestive Diseases and Nutrition, and Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; Department of Internal Medicine, Division of Gastroenterology, and Department of Surgery, Washington University School of Medicine, St. Louis, Missouri; OU Cancer Institute, Oklahoma City; and Department of Veteran Affairs Medical Center, Oklahoma City, Oklahoma
| | - Brian K. Dieckgraefe
- Department of Medicine, Division of Digestive Diseases and Nutrition, and Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; Department of Internal Medicine, Division of Gastroenterology, and Department of Surgery, Washington University School of Medicine, St. Louis, Missouri; OU Cancer Institute, Oklahoma City; and Department of Veteran Affairs Medical Center, Oklahoma City, Oklahoma
| | - Shrikant Anant
- Department of Medicine, Division of Digestive Diseases and Nutrition, and Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; Department of Internal Medicine, Division of Gastroenterology, and Department of Surgery, Washington University School of Medicine, St. Louis, Missouri; OU Cancer Institute, Oklahoma City; and Department of Veteran Affairs Medical Center, Oklahoma City, Oklahoma
| | - Courtney W. Houchen
- Department of Medicine, Division of Digestive Diseases and Nutrition, and Department of Cell Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; Department of Internal Medicine, Division of Gastroenterology, and Department of Surgery, Washington University School of Medicine, St. Louis, Missouri; OU Cancer Institute, Oklahoma City; and Department of Veteran Affairs Medical Center, Oklahoma City, Oklahoma
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George RJ, Sturmoski MA, Anant S, Houchen CW. EP4 mediates PGE2 dependent cell survival through the PI3 kinase/AKT pathway. Prostaglandins Other Lipid Mediat 2007; 83:112-20. [PMID: 17259077 PMCID: PMC1886004 DOI: 10.1016/j.prostaglandins.2006.10.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Revised: 09/12/2006] [Accepted: 10/24/2006] [Indexed: 12/13/2022]
Abstract
The anti-apoptotic effect of PGE(2) was examined in Jurkat cells (human T-cell leukemia) by incubation with PGE(2) (5 nM) prior to treatment with the cancer chemotherapeutic agent camptothecin. Apoptosis was evaluated by caspase-3 activity in cell extracts and flow cytometry of propidium iodide-labeled cells. Pre-incubation with PGE(2) reduced camptothecin-induced caspase activity by 30% and apoptosis by 35%, respectively. Pharmacological data demonstrate that the EP4 receptor is responsible for mediating the protection from camptothecin-induced apoptosis. Pre-treatment of the cells with the EP4 antagonist (EP4A) prior to PGE(2) and camptothecin abolished the increased survival effect of PGE(2). Specific inhibition of the downstream of PI3 kinase or AKT/protein kinase but not protein kinase A prevents the observed increase in cell survival elicited by PGE(2). These findings have critical implications regarding the mechanism and potential application of PGE(2) receptor specific inhibition in cancer therapy.
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Affiliation(s)
- Robert J George
- Washington University School of Medicine, Department of Internal Medicine, St. Louis, Missouri 63110, USA
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Riehl TE, George RJ, Sturmoski MA, May R, Dieckgraefe B, Anant S, Houchen CW. Azoxymethane protects intestinal stem cells and reduces crypt epithelial mitosis through a COX-1-dependent mechanism. Am J Physiol Gastrointest Liver Physiol 2006; 291:G1062-70. [PMID: 17038629 DOI: 10.1152/ajpgi.00129.2006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Azoxymethane (AOM) is a potent DNA-damaging agent and carcinogen that induces intestinal and colonic tumors in rodents. Evaluation of the stem cell population by colony formation assay reveals that, within 8 h after treatment, AOM (10 mg/kg) elicited a prosurvival response. In wild-type (WT) mice, AOM treatment induced a 2.5-fold increase in intestinal crypt stem cell survival. AOM treatment increased stem cell survival in cyclooxygenase (COX)-2(-/-) but not COX-1(-/-) mice, confirming a role of COX-1 in the AOM-induced increase in stem cell survival. COX-1 mRNA and protein expression as well as COX-1-derived PGE(2) synthesis were increased 8 h after AOM treatment. Immunohistochemical staining of COX-1 demonstrated expression of the enzyme in the crypt epithelial cells, especially in the columnar epithelial cells between the Paneth cells adjacent to the stem cell zone. WT mice receiving AOM exhibited increased intestinal apoptosis and a simultaneous reduction in crypt mitotic figures within 8 h of injection. There were no significant differences in baseline or AOM-induced intestinal epithelial apoptosis between WT and COX-1(-/-) mice, but there was a complete reversal of the AOM-mediated reduction in mitosis in COX-1(-/-) mice. This suggests that COX-1-derived PGE(2) may play a key role in the early phase of intestinal tumorigenesis in response to DNA damage and suggests that COX-1 may be a potential therapeutic target in this model of colon cancer.
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Affiliation(s)
- Terrence E Riehl
- Division of Gastroenterology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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Houchen CW, Sturmoski MA, Anant S, Breyer RM, Stenson WF. Prosurvival and antiapoptotic effects of PGE2 in radiation injury are mediated by EP2 receptor in intestine. Am J Physiol Gastrointest Liver Physiol 2003; 284:G490-8. [PMID: 12431904 DOI: 10.1152/ajpgi.00240.2002] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The biological activities of PGE(2) are mediated through EP receptors (EP(1)-EP(4)), plasma membrane G protein-coupled receptors that differ in ligand binding and signal-transduction pathways. We investigated gastrointestinal EP(2) receptor expression in adult mice before and after radiation injury and evaluated intestinal stem cell survival and crypt epithelial apoptosis after radiation injury in EP(2) null mice. EP(2) was expressed throughout the gut. Intestinal EP(2) mRNA increased fivefold after gamma-irradiation. Crypt survival was diminished in EP(2)-/- mice (4.06 crypts/cross section) compared with wild-type littermates (8.15 crypts/cross section). Radiation-induced apoptosis was significantly increased in EP(2)-/- mice compared with wild-type littermates. Apoptosis was 1.6-fold higher in EP(2) (-/-) mice (5.9 apoptotic cells/crypt) than in wild-type mice (3.5 apoptotic cells/crypt). The EP(2) receptor is expressed in mouse gastrointestinal epithelial cells and is upregulated following radiation injury. The effects of PGE(2) on both crypt epithelial apoptosis and intestinal crypt stem cell survival are mediated through the EP(2) receptor.
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MESH Headings
- Animals
- Apoptosis/drug effects
- Apoptosis/radiation effects
- Blotting, Western
- Cell Survival/drug effects
- Cell Survival/radiation effects
- Dinoprostone/pharmacology
- Electrophoresis, Polyacrylamide Gel
- Epithelial Cells/pathology
- Immunohistochemistry
- Intestines/pathology
- Intestines/radiation effects
- Mice
- RNA, Messenger/biosynthesis
- Radiation Injuries, Experimental/drug therapy
- Radiation Injuries, Experimental/pathology
- Receptors, Prostaglandin E/drug effects
- Receptors, Prostaglandin E/metabolism
- Receptors, Prostaglandin E, EP2 Subtype
- Receptors, Prostaglandin E, EP4 Subtype
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Affiliation(s)
- Courtney W Houchen
- Department of Medicine, Division of Gastroenterology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
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Houchen CW, George RJ, Sturmoski MA, Cohn SM. FGF-2 enhances intestinal stem cell survival and its expression is induced after radiation injury. Am J Physiol 1999; 276:G249-58. [PMID: 9887002 DOI: 10.1152/ajpgi.1999.276.1.g249] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fibroblast growth factors (FGFs) have mitogenic activity toward a wide variety of cells of mesenchymal, neuronal, and epithelial origin and regulate events in normal embryonic development, angiogenesis, wound repair, and neoplasia. FGF-2 is expressed in many normal adult tissues and can regulate migration and replication of intestinal epithelial cells in culture. However, little is known about the effects of FGF-2 on intestinal epithelial stem cells during either normal epithelial renewal or regeneration of a functional epithelium after injury. In this study, we investigated the expression of FGF-2 in the mouse small intestine after irradiation and determined the effect of exogenous FGF-2 on crypt stem cell survival after radiation injury. Expression of FGF-2 mRNA and protein began to increase at 12 h after gamma-irradiation, and peak levels were observed from 48 to 120 h after irradiation. At all times after irradiation, the higher molecular mass isoform ( approximately 24 kDa) of FGF-2 was the predominant form expressed in the small intestine. Immunohistochemical analysis of FGF-2 expression after radiation injury demonstrated that FGF-2 was predominantly found in the mesenchyme surrounding regenerating crypts. Exogenous recombinant human FGF-2 (rhFGF-2) markedly enhanced crypt stem cell survival when given before irradiation. We conclude that expression of FGF-2 is induced by radiation injury and that rhFGF-2 can enhance crypt stem cell survival after subsequent injury.
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Affiliation(s)
- C W Houchen
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Groisman EA, Sturmoski MA, Solomon FR, Lin R, Ochman H. Molecular, functional, and evolutionary analysis of sequences specific to Salmonella. Proc Natl Acad Sci U S A 1993; 90:1033-7. [PMID: 8430070 PMCID: PMC45805 DOI: 10.1073/pnas.90.3.1033] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In that salmonellae have been implicated in an unprecedented array of diseases, sequences found to be specific to this species are often thought to be involved in the virulence attributes not seen in other enteric bacteria. To identify the molecular, genetic, and phenotypic characteristics that differentiate bacterial species, we analyzed five cloned DNA fragments that were originally described as being confined to Salmonella. Most of these segments mapped to unique positions on the Salmonella typhimurium chromosome indicative of independent evolutionary events, and three had G+C contents considerably lower than that of the Salmonella genome, suggesting that they arose through horizontal transfer. The nucleotide sequence was determined for one of the clones exhibiting an atypical base composition. This 4.9-kb fragment contained an open reading frame with structural similarity to the LysR family of transcriptional regulators. Strains harboring deletions in this region were tested for > 120 phenotypic characteristics including the effects on a collection of environmentally regulated lac gene fusions. In addition, all deletion strains behaved like the wild-type parent when tested for virulence in mice.
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Affiliation(s)
- E A Groisman
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110
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