HLA-DM Assisted Epitope Identification via Conformational Selection

Resolve Bottlenecks,
Find Innovative SolutionsGenerate Solutions

Solution Overview

Problem

Current methods for identifying immunogenic and immunodominant epitopes, particularly helper T cell epitopes, are tedious, costly, and unreliable, often failing to detect naturally occurring ligands due to limitations in peptide sequencing and prediction algorithms.

Innovation Solution

A cell-free method involving soluble HLA-DR1 and HLA-DM proteins, along with endosomal proteases, is used to form complexes with peptides, which are then analyzed by mass spectrometry to identify immunodominant epitopes, exploiting the role of HLA-DM in selecting peptides insensitive to dissociation.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If peptide mapping and synthetic peptide library screening are used to identify helper T cell epitopes, then information about potential epitopes can be obtained, but the methods are tedious, costly, and unreliable in identifying naturally occurring ligands

Engineering Contradiction:

Improveepitope identification accuracyVSAvoidtime required for epitope identification

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent introduces HLA-DM as an intermediary molecule that mediates the selection process between peptides and MHC class II molecules. HLA-DM acts as a chaperone that facilitates peptide loading and selection, enabling the identification of immunodominant epitopes through its preferential binding to certain peptide-MHC complexes. This intermediary approach replaces tedious peptide mapping with a more efficient HLA-DM assisted binding assay.

Inventive Principle:

Principle #24Intermediary (Mediator)

Solution Approach 2:

The patent replaces mechanical peptide mapping and library screening methods with a biochemical assay system based on HLA-DM protein interactions. Instead of physically mapping peptides or screening synthetic libraries, the method uses HLA-DM's natural biochemical properties to selectively bind and present immunodominant epitopes, which can then be detected through standard immunological assays.

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

2Reliability

If HLA-DM assisted class II binding assay is used to identify immunodominant epitopes, then identification efficiency and reliability are improved, but the device complexity and methodology complexity increase

Engineering Contradiction:

Improveepitope identification reliabilityVSAvoidmethodology complexity

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The patent employs HLA-DM's inherent self-service capability to automatically select and present immunodominant epitopes without requiring complex external selection mechanisms. HLA-DM naturally performs peptide editing and selection based on its structural properties and binding preferences, eliminating the need for complex device systems while maintaining high reliability in epitope identification.

Inventive Principle:

Principle #25Self-service

3Loss of information

If conventional peptide sequencing methods are used, then peptide sequences can be determined, but naturally occurring ligands are often missed due to method limitations

Engineering Contradiction:

Improvenatural ligand detection completenessVSAvoidmethod simplicity

Core Design Contradiction:

Loss of informationVSEase of manufacture

Solution Approach 1:

The patent applies preliminary action by using HLA-DM to pre-select and enrich immunodominant epitopes before detection. HLA-DM's preferential binding to certain peptide-MHC complexes occurs prior to the actual detection step, ensuring that naturally occurring ligands are captured and presented in a form that is easily detectable by standard assays, thus preventing information loss.

Inventive Principle:

Principle #10Preliminary action

Applied Scientific Principles

This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.

Function Achieved in This Case

This approach allows for the efficient identification of physiologically relevant immunogenic helper T cell epitopes, enabling the development of vaccines and immunotherapies by capturing the repertoire of peptides bound to MHC class II molecules, thereby overcoming the limitations of existing methods.

Implementation Method 1

DM distinguishes its substrates based on conformational differences between peptide/MHC complexes

Methodology Applied

Scientific EffectConformational selection:

Implementation Method 2

which are then analyzed by mass spectrometry to identify immunodominant epitopes

Methodology Applied

Scientific EffectMass spectrometry:

Implementation Method 3

A cell-based method has been developed that utilizes the endosomal proteases, HLA-DM and MHC class II

Methodology Applied

Scientific EffectProteolytic cleavage: Enzyme

Data Source

PatentUS8916340B2Method for identifying and validating dominant T helper cell epitopes using an HLA-DM-assisted class II binding assay

Publication Date: 2014.12.23 JOHNS HOPKINS UNIVERSITY

AI summary

Rational design of immunotherapeutics relies on clear knowledge of the immunodominant epitopes of antigens. Current methods for identifying kinetically stable peptide-MHC complexes are in many cases inadequate for a number of reasons. Disclosed herein is a reductionistic system incorporating known participants of MHC class II antigen processing in solution to generate peptide pools from antigens, including those for which no immunodominant epitope has yet been identified, that are highly enriched for proteolytic fragments containing their immunodominant epitopes. HLA-DM-mediated editing contributes significantly to immunodominance and is exploited in discovering immunodominant epitopes from novel or previously uncharacterized antigens, particularly antigens associated with pathogens, tumors or autoimmune diseases.