To meet the challenging requirements, Creative Biolabs has equipped a team of experienced scientists with facilities and processes designed specifically to provide the best strategy and protocols customized to neoantigen/HLA complexes analysis services for cancer therapy. We have accomplished many projects and have delivered numerous novel or validated neoantigen/HLA complexes in a range of therapeutic areas.
In the past few decades, several cancer-related mutant peptides (neoantigens or neopeptides) have been used as novel targets for T cell immunity research. But determining which specific peptides can be presented by MHC molecules and trigger T cells has been a major issue. At present, although there are algorithms for predicting MHC binding, they still have serious shortcomings in predicting and distinguishing complex kinetic stability. Therefore, we have developed a fast, high-throughput neoantigen/HLA complexes analysis technology platform to determine various binding parameters of peptide /HLA complexes simultaneously through in silico and in vivo testing.
Fig. 1 The Workflow of Neoantigen/HLA Complexes Analysis Technology.
In our laboratory, CBLMHC 6.0 software will be used to target peptides of different lengths (8-mer, 9-mer, 10-mer, or 11-mer) in a variety of tumor sample types to predict their binding affinity to specific MHC molecules. Then, the best candidate peptides are further synthesized and tested by a series of techniques, such as UV-peptide exchange assay, flow cytometry, as well as differential scanning fluorescence (DSF), to determine the Tm value of these neoantigen complexes.
Creative Biolabs has developed an extensive collection of peptide/HLA complexes from various species, such as humans, mice, rabbits, and monkeys. This growing list of complexes includes more than 600 different MHC I and 15 MHC II alleles that are uniquely suitable for evaluating epitope immunogenicity.
Fig. 2 The Example Binding Profiles on the Linear Peptide Arrays.
Nowadays, we provide advanced neo-peptide/MHC affinity and stability detection assays. These assays include but are not limited to, Kd values for peptide-MHC under different gradients and conditions, and Tm values for MHC/peptide complexes under different stress-induced conditions.
In addition, we offer a series of combined neoantigen/HLA complexes analyses with high sensitivity and accuracy that can greatly reduce the inaccuracies and false positives of single analyses. At the same time, these data can also be further used to evaluate MHC/epitope complexes, opening up unique possibilities for immunogenicity analysis.
In Silico MHC Class II alleles binding prediction
Sample ID: CB1 and CB2
Methods:
The prediction model was built by using a machine learning method based on the affinities between different peptides and MHC molecules, and 27 common MHC Class II alleles were included in the immunogenicity prediction for CB1 and CB2. In detail, the Fv region sequences of CB1 and CB2 were divided into multiple 15-aa peptides (14-aa overlapping), and the affinity for those peptides and the 27 common MHC Class II alleles were predicted. The predicted output is given in units of IC50 nM, and a lower number indicates higher affinity. As a rough guideline, if the predicted IC50 was <50 nM, the peptide was considered to be Strong Binder (or risk site), if the predicted IC50 was >50 nM, the peptide is considered to be Weak Binder.
Example Results:
| Sample ID | CB1 (IC50, nM) | CB2 (IC50, nM) |
|---|---|---|
| 1 | 80YLQXXXXXA88 (10.9) | 80YLQLNSLRA88 (10.8) |
| 2 | 27FNXXXXXXH35 (31.68) | 27FXXXXXXX35 (13.27) |
| 3 | 29VXXXXXXXV37 (23.15) | 29IKXXXXXXV37 (11.48) |
Tab. 1 Predicted Results for HLA-DR Alleles.
Equipped with our advanced technologies and platforms, Creative Biolabs now offers a panel of services to develop well-validated and high-throughput neoantigen/HLA complex development and analysis services with your epitope of interest. Our mission is to help you meet current and future MHC-restricted epitopes mapping and demand and clear the path to commercialization to help you stay at the forefront of cancer therapy. If you are interested in our services, please contact us for more details.
For Research Use Only | Not For Clinical Use
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