Polypeptide Immunogenicity Prediction via APC Internalization Index

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Solution Overview

Problem

Current methods for determining the propensity of polypeptides to elicit anti-drug antibodies (ADAs) are labor-intensive, time-consuming, and costly, requiring extensive equipment, limiting their efficiency in preclinical drug development.

Innovation Solution

A method involving contacting antigen-presenting cells (APCs) with polypeptides, measuring surface and total associated polypeptide amounts, calculating an internalization index, and comparing it to a reference index to predict ADA production, using techniques such as flow cytometry and permeabilization to assess polypeptide immunogenicity.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If traditional cell-based techniques (MAPPs, T cell proliferation assay) are used to determine immunogenic potential, then measurement precision and reliability are improved, but device complexity, loss of time, and loss of energy increase significantly

Engineering Contradiction:

Improveimmunogenicity prediction accuracyVSAvoidequipment requirements

Core Design Contradiction:

Measurement precisionVSDevice complexity

Solution Approach 1:

The patent extracts and focuses solely on measuring polypeptide internalization by APCs, eliminating the need for complex MHC-peptide complex analysis, T cell proliferation measurements, and multiple specialized equipment systems. This selective extraction of the critical internalization parameter simplifies the assay while maintaining predictive accuracy for immunogenicity.

Inventive Principle:

Principle #2Taking out (Extraction)

Solution Approach 2:

The patent uses flow cytometry to create a simplified digital copy of the internalization process, replacing the need for physical complex equipment systems. The flow cytometric measurement provides a quantitative proxy for internalization that captures the essential information without requiring the complex infrastructure of traditional MAPPs and proliferation assays.

Inventive Principle:

Principle #26Copying

2Measurement precision

If traditional cell-based techniques are used to determine immunogenic potential, then measurement precision is improved, but loss of time increases significantly

Engineering Contradiction:

Improveimmunogenicity prediction accuracyVSAvoidassay duration

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent performs preliminary measurement of surface-bound polypeptide before permeabilization, allowing the internalization calculation to be based on a single rapid flow cytometric reading rather than requiring extended incubation periods for complete internalization and processing. This preliminary measurement approach accelerates the assay timeline while maintaining measurement precision.

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent skips the time-consuming steps of complete peptide processing, MHC loading, and T cell proliferation that characterize traditional assays. By directly measuring polypeptide internalization through flow cytometry and permeabilization, the patent rushes through the essential measurement phase in a fraction of the time required by conventional methods.

Inventive Principle:

Principle #21Skipping (Rushing through)

3Reliability

If traditional cell-based techniques are used to determine immunogenic potential, then reliability is improved, but loss of energy and cost-effectiveness worsen

Engineering Contradiction:

Improveimmunogenicity prediction accuracyVSAvoidresource consumption

Core Design Contradiction:

ReliabilityVSLoss of energy

Solution Approach 1:

The patent employs disposable flow cytometry samples and standard laboratory reagents instead of requiring expensive, specialized equipment systems. The methodology uses readily available APCs, standard fluorescent antibodies, and conventional flow cytometers, dramatically reducing the energy and financial resources required while maintaining reliable immunogenicity prediction through the internalization index calculation.

Inventive Principle:

Principle #27Cheap short-living objects (Disposable)

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 provides a cost-effective and time-efficient method to predict ADA production, distinguishing between high and low immunogenic polypeptides, aiding in drug development by identifying potential immunogenic risks early in the process.

Implementation Method 1

The APCs will internalize and process the therapeutic into short peptides

Methodology Applied

Scientific EffectEndocytosis:

Implementation Method 2

measuring the amount of polypeptide, or fragment thereof, present on an outer surface of the APC; measuring the total amount of polypeptide, or fragment thereof, associated with the APC

Methodology Applied

Scientific EffectFlow cytometry:

Data Source

PatentUS20230160907A1Cell-based methods for predicting polypeptide immunogenicity

Publication Date: 2023.05.25 GENENTECH INC

AI summary

The presently disclosed subject matter provides methods for determining the propensity of a polypeptide or a fragment thereof, e.g., an antibody or a fragment thereof, to elicit production of anti-drug antibodies (ADAs) and kits for performing such methods.