T and B cell epitope analysis for the immunogenicity evaluation and mitigation of antibody-based therapeutics

Figures & data

Figure 1. The effects of immunogenicity on antibody-based therapeutics. (A) The structural diagrams of different antibody-based therapeutics. mAb, monoclonal antibodies. KIH, knob-into-hole. BiTE, bispecific T cell engagers. ADC, antibody-drug conjugate. Fv, variable fragment. (B) The impacts on antibody-based therapeutics. The ADA bound to the paratope of mAb elicit neutralization capacity and therefore lead to the attenuation of therapeutic efficacy. The ADA may also trigger the onset of type I (IgE-mediated) and II (IgG-mediated) hypersensitivity. Once immunocomplexes are formed by ADAs (IgM or IgG) and therapeutics, the adverse events associated with type III hypersensitivity may take place. The large sizes of immunocomplexes also lead to faster clearance of therapeutics from blood stream. The graph was created on BioRender.com.

Figure 2. The schematic illustration of T cell-dependent and -independent B cell activation pathways. DC, dendritic cell. pMHC II, peptide-MHC II complex. TCR, T cell receptor. BCR, B cell receptor. The graph was created on BioRender.com.

Table 1. Summarization and comparison of various strategies applied for TCE identification.

Category	Method	Cost	Time	Commercial availability	Ref
In vitro binding	HLA binding assay	++	+	Yes	^Citation32–35
Immunopeptidomics	MAPPs	+++	++	Yes	^Citation35–41
Cell-based functional assay	ELISpot	++	++	Yes	^Citation34,Citation38,Citation42
	T cell proliferation assay	++	++	Yes	^Citation38–40,Citation43

Table 2. The summary and comparison of various strategies applied for pBCEs identification.

Category	Name of methods	Epitope type		Cost	Time	Commercial availability	Ref
		Linear	Conformational
LBA	Domain specificity	No	No	+	+	Yes*	^Citation59–61
	Peptide screening	Yes	No	++	++	Yes	^Citation62–65
	Peptide display	Yes	No	++	++	Yes	^Citation66,Citation67
	DMS	Yes	Yes	+++	+++	No	^Citation68–72
MS	PROTEX	Yes	No	++	++	No	^Citation73,Citation74
	HDX-MS	Yes	Yes	++	++	Yes	^Citation75
	FPOP-MS	Yes	Yes	++	++	Yes	^Citation76
Structure biology	nsEMPEM	Yes	Yes	+++	+++	Yes	^Citation77–80

*Domain specificity analysis can be incorporated into the validated ADA/Nab assay and executed by facilities compliant with regulatory standards, but it is usually not provided as a service independently.

Figure 3. The recommended schedule of actions to be conducted for immunogenicity assessment of TPs. Different computational and experimental strategies can be performed to support the investigation of immunogenicity from early discovery to marketing stages. Note: the in silico BCE analysis is outlined in dashed line due to the lack of solid evidence justifying its value in candidate evaluation.

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