Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation
Abstract
:1. Introduction
2. Results
2.1. Identification of Immunogenic Peptides Assembled in HLA-I
2.2. Effect of Protein Extraction Strategy on Immunopeptidome Characterization
2.3. Effect of the Immunoaffinity Matrix on Immunopeptidome Characterization
2.4. Quality Control in Immunopeptidome Analysis
2.5. Design and Development of an Immunopeptidome Score
2.6. Immunopeptidome Score Evaluation
3. Discussion
4. Materials and Methods
4.1. Preparation of Peptide-MHC (pMHC) Samples
4.2. Sample Preparation
4.2.1. Cell Lines
4.2.2. Cell Culture Conditions
4.3. Antibody Coupling to Immunoaffinity Matrix
4.3.1. Immunoaffinity Matrix #1
4.3.2. Immunoaffinity Matrix #2
4.4. Immunoprecipitation (IP) Method
4.4.1. Protein Extraction
Immunoaffinity Matrix #1
Immunoaffinity Matrix #2
4.4.2. Immunoprecipitation (IP)
Immunoaffinity Matrix #1
Immunoaffinity Matrix #2
4.4.3. HLA-I Molecule Enrichment and Peptide Elution
Immunoaffinity Matrix #1
Immunoaffinity Matrix #2
4.5. Peptide Cleanup for LC-MS/MS Analysis
4.5.1. LC-MS/MS-Based Acquisition and Detection of Immunopeptidomes
4.5.2. Database Search
4.5.3. Data Analysis
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- Tron Cell Line Portal or TCLP (http://celllines.tron-mainz.de/ accessed on 11 March 2021): Database that integrates public RNA-Seq data from 1082 cell lines and determines the type and abundance of human leukocyte antigen (HLA), predicted neoepitopes, virus, and gene expression of all of them [103]. In this work, it has been used to identify the different HLA molecule alleles in the analyzed tumor cell lines;
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- NetMHCpan-4.1 (https://services.healthtech.dtu.dk/service.php?NetMHCpan-4.1 accessed on 11 March 2021): Prediction server for the pan-specific binding prediction of peptides to the MHC-I molecule using artificial neural networks [17]. In this study, it was used for such peptide binding prediction of all the samples. The corresponding MS peptide list in the FASTA format was employed and multiple lengths (8–12 mer peptides) and alleles specific to the corresponding cell line were selected. The following settings and thresholds were determined: threshold for the strong binder: 0.5% rank; threshold for the weak binder: 2% rank; filtering threshold for %Rank (leave −99 to print all): −99;
- -
- Class I Immunogenicity by The Immune Epitope Database (IEDB) (http://tools.iedb.org/immunogenicity/ accessed on 11 March 2021): This database predicts the immunogenicity of a peptide-MHC complex based on both the properties and position of the amino acids within the peptide [104]. This database was used to predict the immunogenicity of all peptides identified in each of the studied samples. The input is the MS peptide list in FASTA format and the obtained output is a resulting score, positive (>0) if the peptide is reported as immunogenic and negative (<0) if it is not immunogenic.
4.6. Biostatistics and Data Visualization
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | #Proteins | #Proteins without Repetitions or Contaminants | #Peptide | #Peptides without Repetitions or Contaminants |
---|---|---|---|---|
H460_1A | 737 | 732 | 5736 | 5592 |
H460_1B | 619 | 603 | 3699 | 3157 |
JURKAT_1A | 539 | 525 | 2884 | 2700 |
JURKAT_1B | 116 | 105 | 646 | 526 |
H460_2B | 2321 | 2291 | 8263 | 7832 |
CACO-2_2B | 1532 | 1493 | 7091 | 6607 |
MDA-MB-231_2B | 2261 | 2223 | 9824 | 9389 |
Cell-Line | Reference ATCC | Organism | Tissue | Disease | Cell Type | HLA Genotyping (TRON Cell Line Portal) | |||
---|---|---|---|---|---|---|---|---|---|
Allele 1 | Allele 2 | RPKM | Source | ||||||
JURKAT (CLONE E6-1) | TIB-152 | Homo sapiens | Peripheral blood | T Acute Lymphoblastic Leukemia | T lymphoblast | HLA-A * 03:01 | HLA-A * 03:01 | 49.09 | seq2HLA |
HLA-B * 07:02 | HLA-B * 35:03 | 12.64 | |||||||
HLA-C * 04:01 | HLA-C * 07:02 | 26.29 | |||||||
HLA-DQB1 * 06:11′ | HLA-DQB1 * 06:11 | 0.22 | |||||||
HLA-DRB1 * 15:01 | HLA-DRB1 * 14:18′ | 0.3 | |||||||
H460 (NCIH460) | HTB-177 | Homo sapiens | Lung; Pleural effusion | Large Cell Lung Carcinoma | epithelial | HLA-A * 68:01′ | HLA-A * 24:02 | 127.74 | seq2HLA |
HLA-B * 51:01′ | HLA-B * 35:01 | 15.95 | |||||||
HLA-C * 15:02 | HLA-C * 03:03 | 47.06 | |||||||
HLA-DQB1 * 05:01 | HLA-DQB1 * 05:01 | 0.1 | |||||||
HLA-DRB1 * 01:01 | HLA-DRB1 * 01:01 | 0.34 | |||||||
Caco-2 (Caco2) | HTB-37 | Homo sapiens | Large intestine; Colon | Colorectal Adenocarcinoma | epithelial | HLA-A * 02:01 | HLA-A * 02:01 | 103.06 | seq2HLA |
HLA-B * 15:01′ | HLA-B * 15:01 | 9.09 | |||||||
HLA-C * 04:01 | HLA-C * 04:01 | 58.08 | |||||||
HLA-DRB1 * 04:05′ | HLA-DRB1 * 04:05 | 0.06 | |||||||
MDA-MB-231 | CRM-HTB-26 | Homo sapiens | Breast; Mammary gland | Breast Adenocarcinoma | epithelial | HLA-A * 02:17′ | HLA-A * 02:17 | 492.2 | seq2HLA |
HLA-B * 41:01 | HLA-B * 40:02′ | 186.94 | |||||||
HLA-C * 02:02 | HLA-C * 17:01 | 123.07 | |||||||
HLA-DQA1 * 01:02′ | HLA-DQA1 * 01:02 | 0.08 | |||||||
HLA-DQB1 * 02:02′ | HLA-DQB1 * 03:04′ | 0.07 |
Sample | Immunoaffinity Matrix | Antibody Anti-HLA Class I (Clone W6/32) | Protein Extraction Protocol | Peptide Cleanup | Immunopeptidome Score |
---|---|---|---|---|---|
H460_1A | Immunoaffinity Matrix #1 Magnetic microspheres QuantumPlex M SP Carboxyl | 1 mg/mL | Protocol A | STOP-GO microcolumns | Test |
H460_1B | Protocol B | ||||
JURKAT_1A | Protocol A | ||||
JURKAT_1B | Protocol B | ||||
H460_2B | Immunoaffinity Matrix #2 CNBr-activated Sepharose® 4B beads | 2 mg/mL | Protocol B | ||
CACO-2_2B | |||||
MDA-MB-231_2B | |||||
MM1S_Control_2B | Empore SDB-XC | Evaluation | |||
MM1S_3nM_Btz_2B | |||||
MM1S_4nM_Btz_2B |
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Juanes-Velasco, P.; Arias-Hidalgo, C.; García-Vaquero, M.L.; Sotolongo-Ravelo, J.; Paíno, T.; Lécrevisse, Q.; Landeira-Viñuela, A.; Góngora, R.; Hernández, Á.-P.; Fuentes, M. Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation. Int. J. Mol. Sci. 2024, 25, 9564. https://doi.org/10.3390/ijms25179564
Juanes-Velasco P, Arias-Hidalgo C, García-Vaquero ML, Sotolongo-Ravelo J, Paíno T, Lécrevisse Q, Landeira-Viñuela A, Góngora R, Hernández Á-P, Fuentes M. Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation. International Journal of Molecular Sciences. 2024; 25(17):9564. https://doi.org/10.3390/ijms25179564
Chicago/Turabian StyleJuanes-Velasco, Pablo, Carlota Arias-Hidalgo, Marina L. García-Vaquero, Janet Sotolongo-Ravelo, Teresa Paíno, Quentin Lécrevisse, Alicia Landeira-Viñuela, Rafael Góngora, Ángela-Patricia Hernández, and Manuel Fuentes. 2024. "Crucial Parameters for Immunopeptidome Characterization: A Systematic Evaluation" International Journal of Molecular Sciences 25, no. 17: 9564. https://doi.org/10.3390/ijms25179564