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Ade CM, Sporn MJ, Das S, Yu Z, Hanada KI, Qi YA, Maity T, Zhang X, Guha U, Andresson T, Yang JC. Identification of neoepitope reactive T-cell receptors guided by HLA-A*03:01 and HLA-A*11:01 immunopeptidomics. J Immunother Cancer 2023; 11:e007097. [PMID: 37758652 PMCID: PMC10537849 DOI: 10.1136/jitc-2023-007097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Tumor-specific mutated proteins can create immunogenic non-self, mutation-containing 'neoepitopes' that are attractive targets for adoptive T-cell therapies. To avoid the complexity of defining patient-specific, private neoepitopes, there has been major interest in targeting common shared mutations in driver genes using off-the-shelf T-cell receptors (TCRs) engineered into autologous lymphocytes. However, identifying the precise naturally processed neoepitopes to pursue is a complex and challenging process. One method to definitively demonstrate whether an epitope is presented at the cell surface is to elute peptides bound to a specific major histocompatibility complex (MHC) allele and analyze them by mass spectrometry (MS). These MS data can then be prospectively applied to isolate TCRs specific to the neoepitope. METHODS We created mono-allelic cell lines expressing one class I HLA allele and one common mutated oncogene in order to eliminate HLA deconvolution requirements and increase the signal of recovered peptides. MHC-bound peptides on the surface of these cell lines were immunoprecipitated, purified, and analyzed using liquid chromatography-tandem mass spectrometry, producing a list of mutation-containing minimal epitopes. To validate the immunogenicity of these neoepitopes, HLA-transgenic mice were vaccinated using the minimal peptides identified by MS in order to generate neoepitope-reactive TCRs. Specificity of these candidate TCRs was confirmed by peptide titration and recognition of transduced targets. RESULTS We identified precise neoepitopes derived from mutated isoforms of KRAS, EGFR, BRAF, and PIK3CA presented by HLA-A*03:01 and/or HLA-A*11:01 across multiple biological replicates. From our MS data, we were able to successfully isolate murine TCRs that specifically recognize four HLA-A*11:01 restricted neoepitopes (KRAS G13D, PIK3CA E545K, EGFR L858R and BRAF V600E) and three HLA-A*03:01 restricted neoepitopes (KRAS G12V, EGFR L858R and BRAF V600E). CONCLUSIONS Our data show that an MS approach can be used to demonstrate which shared oncogene-derived neoepitopes are processed and presented by common HLA alleles, and those MS data can rapidly be used to develop TCRs against these common tumor-specific antigens. Although further characterization of these neoepitope-specific murine TCRs is required, ultimately, they have the potential to be used clinically for adoptive cell therapy.
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Affiliation(s)
- Catherine M Ade
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Matthew J Sporn
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Sudipto Das
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Ken-Ichi Hanada
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Yue A Qi
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Tapan Maity
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD, USA
| | - Xu Zhang
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, National Cancer Institute, Bethesda, Maryland, USA
- NextCure Inc, Beltsville, MD, USA
| | - Thorkell Andresson
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - James C Yang
- Surgery Branch, National Cancer Institute, Bethesda, Maryland, USA
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Ade CM, Qi YA, Das S, Hanada KI, Maity T, Zhang X, Andresson T, Guha U, Yang JC. Abstract 273: A mass spectrometry survey of frequent HLA alleles successfully presenting common tumor specific mutations for immune recognition. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Tumor-specific mutated proteins can create non-self, mutation-containing ‘neoepitopes' that are immunogenic and are attractive targets for adoptive T-cell therapies. To avoid the complexity of patient-specific, private neoepitopes and their T-cell responses, there has been major interest in targeting common shared mutations in driver genes using off-the-shelf T-cell receptors engineered into autologous lymphocytes. The diversity of MHC alleles which could present these select neoantigens is an obstacle to this strategy. Most neoepitopes will not be successfully presented by most HLA alleles, and algorithms predicting epitope-HLA binding will either miss valid epitopes or identify too many candidate alleles to investigate thoroughly. One method to definitively demonstrate that an MHC allele can successfully present an epitope is to elute peptides bound to that MHC allele on the cell surface and analyze them by mass spectrometry (MS). It has the additional advantages of defining the precise epitope processed from an antigen and estimating its abundance. We undertook a comprehensive analysis by MS of several common shared mutations in driver oncogenes and their presentation by common Class I HLA alleles. To overcome the low sensitivity of MS (compared to T-cells), we created mono-allelic cell lines expressing one Class I HLA allele and one common mutated oncogene. Peptides bound to MHC on the surface of these cell lines were immunoprecipitated, eluted, and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). As expected, most HLA alleles could not present a detectable neoepitope from the candidate antigens. Our system was able to identify precise neoepitopes derived from four commonly mutated oncogenes (KRAS, EGFR, BRAF, and PIK3CA) presented by the HLA-A*03 HLA superfamily. The majority of mutated peptides were consistently found in biological replicates, demonstrating the reproducibility of our system. By evaluating intensities and fragmentation data for mutated peptides, we were able to improve the reliability of detection of neoepitopes at the cell surface. Although most of the identified epitopes were predicted to bind using the canonical NetMHCpan algorithm, many epitopes predicted to bind with high affinity were not observed using our pipeline. HLA-A*0201 has been intensely studied because of its high frequency in the U.S. population but we have not found it to consistently present mutated peptides from our candidate oncogenes. Our data show that we could utilize a MS approach to demonstrate which shared oncogene-derived neoepitopes are unequivocally processed and presented by common HLA alleles, which will allow greater focused efforts on developing TCRs against these promising HLA-neoantigen pairs.
Citation Format: Catherine M. Ade, Yue A. Qi, Sudipto Das, Ken-ichi Hanada, Tapan Maity, Xu Zhang, Thorkell Andresson, Udayan Guha, James C. Yang. A mass spectrometry survey of frequent HLA alleles successfully presenting common tumor specific mutations for immune recognition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 273.
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Ade CM, Derbes RS, Wagstaff BJ, Linker SB, White TB, Deharo D, Belancio VP, Ivics Z, Roy-Engel AM. Evaluating different DNA binding domains to modulate L1 ORF2p-driven site-specific retrotransposition events in human cells. Gene 2017; 642:188-198. [PMID: 29154869 DOI: 10.1016/j.gene.2017.11.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/11/2017] [Indexed: 12/28/2022]
Abstract
DNA binding domains (DBDs) have been used with great success to impart targeting capabilities to a variety of proteins creating highly useful genomic tools. We evaluated the ability of five types of DBDs and strategies (AAV Rep proteins, Cre, TAL effectors, zinc finger proteins, and Cas9/gRNA system) to target the L1 ORF2 protein to drive retrotransposition of Alu inserts to specific sequences in the human genome. First, we find that the L1 ORF2 protein tolerates the addition of protein domains both at the amino- and carboxy-terminus. Although in some instances retrotransposition efficiencies slightly diminished, all fusion proteins containing an intact ORF2 were capable of driving retrotransposition. Second, the stability of individual ORF2 fusion proteins varies and difficult to predict. Third, DBDs that require the formation of multimers for target recognition are unlikely to modify targeting of ORF2p-driven insertions. Fourth, the more components needed to assemble into a complex to drive targeted retrotransposition, the less likely the strategy will increase targeted insertions. Fifth, abundance of target sequences present in the genome will likely dictate the effectiveness and efficiency of targeted insertions. Lastly, the cleavage capabilities of Cas9 (or a Cas9 nickase variant) are unable to substitute for the L1 ORF2 endonuclease domain functions, suggestive that the endonuclease domain has alternate functions needed for retrotransposition. From these studies, we conclude that the most critical component for the modification of the human L1 ORF2 protein to drive targeted insertions is the selection of the DBD due to the varying functional requirements and impacts on protein stability.
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Affiliation(s)
- Catherine M Ade
- Department of Cellular and Molecular Biology, Tulane University, USA
| | - Rebecca S Derbes
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA
| | - Bradley J Wagstaff
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA
| | - Sara B Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, CA 92037-1002, USA
| | - Travis B White
- Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Dawn Deharo
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Astrid M Roy-Engel
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center and LCRC, 1700 Tulane Ave., New Orleans, LA 70112, USA.
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Abstract
Heavy metals such as cadmium, arsenic and nickel are classified as carcinogens. Although the precise mechanism of carcinogenesis is undefined, heavy metal exposure can contribute to genetic damage by inducing double strand breaks (DSBs) as well as inhibiting critical proteins from different DNA repair pathways. Here we take advantage of two previously published culture assay systems developed to address mechanistic aspects of DNA repair to evaluate the effects of heavy metal exposures on competing DNA repair outcomes. Our results demonstrate that exposure to heavy metals significantly alters how cells repair double strand breaks. The effects observed are both specific to the particular metal and dose dependent. Low doses of NiCl2 favored resolution of DSBs through homologous recombination (HR) and single strand annealing (SSA), which were inhibited by higher NiCl2 doses. In contrast, cells exposed to arsenic trioxide preferentially repaired using the "error prone" non-homologous end joining (alt-NHEJ) while inhibiting repair by HR. In addition, we determined that low doses of nickel and cadmium contributed to an increase in mutagenic recombination-mediated by Alu elements, the most numerous family of repetitive elements in humans. Sequence verification confirmed that the majority of the genetic deletions were the result of Alu-mediated non-allelic recombination events that predominantly arose from repair by SSA. All heavy metals showed a shift in the outcomes of alt-NHEJ repair with a significant increase of non-templated sequence insertions at the DSB repair site. Our data suggest that exposure to heavy metals will alter the choice of DNA repair pathway changing the genetic outcome of DSBs repair.
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Affiliation(s)
- Maria E Morales
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Rebecca S Derbes
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Catherine M Ade
- Department of Cellular and Molecular Biology, Tulane University, 6400 Freret Street, New Orleans, LA 70118, United States of America
| | - Jonathan C Ortego
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Jeremy Stark
- Department of Radiation Biology, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, United States of America
| | - Prescott L Deininger
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Astrid M Roy-Engel
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
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Morales ME, Derbes RS, Ade CM, Ortego JC, Stark J, Deininger PL, Roy-Engel AM. Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes. PLoS One 2016; 11:e0151367. [PMID: 26966913 PMCID: PMC4788447 DOI: 10.1371/journal.pone.0151367] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/26/2016] [Indexed: 11/22/2022] Open
Abstract
Heavy metals such as cadmium, arsenic and nickel are classified as carcinogens. Although the precise mechanism of carcinogenesis is undefined, heavy metal exposure can contribute to genetic damage by inducing double strand breaks (DSBs) as well as inhibiting critical proteins from different DNA repair pathways. Here we take advantage of two previously published culture assay systems developed to address mechanistic aspects of DNA repair to evaluate the effects of heavy metal exposures on competing DNA repair outcomes. Our results demonstrate that exposure to heavy metals significantly alters how cells repair double strand breaks. The effects observed are both specific to the particular metal and dose dependent. Low doses of NiCl2 favored resolution of DSBs through homologous recombination (HR) and single strand annealing (SSA), which were inhibited by higher NiCl2 doses. In contrast, cells exposed to arsenic trioxide preferentially repaired using the “error prone” non-homologous end joining (alt-NHEJ) while inhibiting repair by HR. In addition, we determined that low doses of nickel and cadmium contributed to an increase in mutagenic recombination-mediated by Alu elements, the most numerous family of repetitive elements in humans. Sequence verification confirmed that the majority of the genetic deletions were the result of Alu-mediated non-allelic recombination events that predominantly arose from repair by SSA. All heavy metals showed a shift in the outcomes of alt-NHEJ repair with a significant increase of non-templated sequence insertions at the DSB repair site. Our data suggest that exposure to heavy metals will alter the choice of DNA repair pathway changing the genetic outcome of DSBs repair.
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Affiliation(s)
- Maria E. Morales
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Rebecca S. Derbes
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Catherine M. Ade
- Department of Cellular and Molecular Biology, Tulane University, 6400 Freret Street, New Orleans, LA 70118, United States of America
| | - Jonathan C. Ortego
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Jeremy Stark
- Department of Radiation Biology, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, United States of America
| | - Prescott L. Deininger
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
| | - Astrid M. Roy-Engel
- Department of Epidemiology and Tulane Cancer Center, and Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, United States of America
- * E-mail:
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Abstract
OBJECTIVES The null hypothesis is that there is no difference in outcome when pregnancies with ultrasonographically documented subchorionic hemorrhages are compared with those without these hemorrhages. STUDY DESIGN We performed a case-control study, utilizing our computerized ultrasonographic database. Cases were matched with two or three controls in two separate control groups. Matching criteria were maternal age, gestational age at scan, and invasive procedures (chorionic villus sampling or amniocentesis). General exclusion criteria were absence of fetal heart motion and fetal anomalies. Presence of subchorionic hemorrhage was an exclusion criterion for both control groups; however, in addition, presence of vaginal bleeding was a further criterion for one of the two. Statistical analysis was performed with chi2 analysis and Yates' correction. Odd ratios and 95% confidence intervals were calculated. RESULTS There was no difference in maternal characteristics between the cases and controls. The incidence of subchorionic hemorrhage was 1.3%. There was an increased risk of miscarriage (odds ratio 2.8, 95% confidence interval 1.7 to 7.4), stillbirth (4.5, 1.5 to 13.2), abruptio placentae (11.2, 2.7 to 46.4), and preterm labor (2.6, 1.5 to 4.6) when cases were compared with controls without subchorionic hemorrhage or bleeding. These risks were also increased in comparison with the control group with bleeding, except with respect to miscarriage. In this case the risks were similar in both cases and controls but increased with respect to the controls without bleeding. The mean birth weight was lower in the cases than in both control groups. CONCLUSION The presence of an ultransonographically detected subchorionic hemorrhage increases the risk of miscarriage, stillbirth, abruptio placentae, and preterm labor. The presence of bleeding alone appears to increase the risk of miscarriage. It is unclear whether the subchorionic hemorrhage is causative or whether it is simply a sign of an underlying process that produces these negative effects.
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Affiliation(s)
- R H Ball
- Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, USA
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