Combination of IM-Based Approaches to Unravel the Coexistence of Two Conformers on a Therapeutic Multispecific mAb

Multispecific antibodies, which target multiple antigens at once, are emerging as promising therapeutic entities to offer more effective treatment than conventional monoclonal antibodies (mAbs). However, these highly complex mAb formats pose significant analytical challenges. We report here on the characterization of a trispecific antibody (tsAb), which presents two isomeric forms clearly separated and identified with size exclusion chromatography coupled to native mass spectrometry (SEC-nMS). Previous studies showed that these isomers might originate from a proline cis/trans isomerization in one Fab subunit of the tsAb. We combined several innovative ion mobility (IM)-based approaches to confirm the isomeric nature of the two species and to gain new insights into the conformational landscape of both isomers. Preliminary SEC-nIM-MS measurements performed on a low IM resolution instrument provided the first hints of the coexistence of different conformers, while complementary collision-induced unfolding (CIU) experiments evidenced distinct gas-phase unfolding behaviors upon activation for the two isomers. As subtle conformational differences remained poorly resolved on our early generation IM platform, we performed high-resolution cyclic IM (cIM-MS) to unambiguously conclude on the coexistence of two conformers. The cis/trans equilibrium was further tackled by exploiting the IMⁿ slicing capabilities of the cIM-MS instrument. Altogether, our results clearly illustrate the benefits of combining state-of-the-art nMS and IM-MS approaches to address challenging issues encountered in biopharma. As engineered antibody constructs become increasingly sophisticated, CIU and cIM-MS methodologies undoubtedly have the potential to integrate the drug development analytical toolbox to achieve in-depth conformational characterization of these products.

Multi-attribute method based characterization of antibody drug conjugates (ADC) at the intact and subunit levels

Antibody-drug conjugates (ADCs) represent an important class of new biopharmaceutical modalities. ADCs are highly complex and heterogeneous molecules, potentially containing numerous product-related structures, that can contribute to the quality, efficacy and safety of the product. To keep up with product life cycle related changes, wide-range and targeted characterization of product quality attributes (PQA) are of high demand. Multi-attribute methods (MAM) can screen numerous PQAs in a parallel fashion including product properties as well as product and process-related impurities. MAM is usually based on a bottom-up approach relying on the enzymatic digestion of the protein into peptides prior to mass spectrometry (MS). However, this processing workflow can result in considerable information loss, such as the drug distribution profile of an antibody-drug conjugate. Therefore, complementary MAM approaches, based on subunit and intact mass analyses, are necessary approaches offering the advantage of product identity confirmation, quantification of the different conjugated species and monitoring the drug-to-antibody ratio at the same time. In this work we introduce a high throughput MS based attribute tracking method for ADC characterization at the intact and subunit levels by simultaneously monitoring multiple PQAs. The workflow includes sample preparation and MS instrument suitability testing for heterogeneous lysine-linked ADCs, software solutions for routine PQAs tracking, method repeatability and an easy data review fitting perfectly into high throughput analyses. As methionine oxidation is one of the modifications that should be closely monitored at any step of process development, an important application to oxidative stress evaluation using forced degradation demonstrated the applicability of the workflow.

A combined transcriptome and proteome analysis extends the allergome of house dust mite Dermatophagoides species

Background

House dust mites (HDMs) such as Dermatophagoides farinae and D. pteronyssinus represent major causes of perennial allergy. HDM proteomes are currently poorly characterized, with information mostly restricted to allergens. As of today, 33 distinct allergen groups have been identified for these 2 mite species, with groups 1 and 2 established as major allergens. Given the multiplicity of IgE-reactive mite proteins, potential additional allergens have likely been overlooked.

Objective

To perform a comprehensive characterization of the transcriptomes, proteomes and allergomes of D. farinae and D. pteronyssinus in order to identify novel allergens.

Methods

Transcriptomes were analyzed by RNA sequencing and de novo assembly. Comprehensive mass spectrometry-based analyses proteomes were combined with two-dimensional IgE reactivity profiling.

Results

Transcripts from D. farinae and D. pteronyssinus were assembled, translated into protein sequences and used to populate derived sequence databases in order to inform immunoproteomic analyses. A total of 527 and 157 proteins were identified by bottom-up MS analyses in aqueous extracts from purified HDM bodies and fecal pellets, respectively. Based on high sequence similarities (>71% identity), we also identified 2 partial and 11 complete putative sequences of currently undisclosed D. pteronyssinus counterparts of D. farinae registered allergens. Immunoprofiling on 2D-gels revealed the presence of unknown 23 kDa IgE reactive proteins in both species. Following expression of non-glycosylated recombinant forms of these molecules, we confirm that these new allergens react with serum IgEs from 42% (8/19) of HDM-allergic individuals.

Conclusions

Using combined transcriptome and immunoproteome approaches, we provide a comprehensive characterization of D. farinae and D. pteronyssinus allergomes. We expanded the known allergen repertoire for D. pteronyssinus and identified two novel HDM allergens, now officially referred by the International Union of Immunological Societies (IUIS) Nomenclature Subcommittee as Der f 36 and Der p 36.

Patterns of IgE sensitization in house dust mite-allergic patients: implications for allergen immunotherapy

BACKGROUND

Understanding patterns of IgE sensitization in Dermatophagoides-allergic patients living in various geographical areas is necessary to design a product suitable for worldwide allergen immunotherapy (AIT).

METHODS

Using a HIFI Allergy customized microarray assay, IgEs specific for 12 purified allergens from Dermatophagoides pteronyssinus or D. farinae were assessed in sera from 1302 house dust mite (HDM)-allergic patients living in various areas. Comprehensive mass spectrometric (MS) analyses were conducted to characterize HDM extracts, as well as purified bodies and feces.

RESULTS

Patterns of IgE reactivity to HDM allergens are comparable in all cohorts of patients analyzed, encompassing adults and 5- to 17-year-old children, as well as American, Canadian, European, and Japanese patients. Overall, >70% and >80% of HDM-allergic patients are sensitized to group 1 and group 2 allergens, respectively, from D. pteronyssinus and/or D. farinae species. Furthermore, 20-47% of patients also have IgEs to allergens from groups 4, 5, 7, 13, 15, 21, and 23. All patients have IgEs to allergens present in mite bodies and feces. MS-based analyses confirmed the presence of mite allergens recorded by IUIS in D. pteronyssinus and D. farinae extracts, with groups 2, 8, 10, 11, 14, and 20 prominent in bodies and groups 1, 6, 18, and 23 well represented in feces.

CONCLUSIONS

Mite-specific AIT should rely upon a mixture of D. pteronyssinus and D. farinae extracts, manufactured from both feces and bodies. Such a combination is appropriate to treat children and adult Dermatophagoides-allergic patients from Asia, Europe, and North America.

Allergen extracts for immunotherapy: to mix or not to mix?

Allergen immunotherapy (AIT) is established as a curative treatment for allergic rhinitis, asthma, as well as insect venom allergy. AIT is based on the administration of natural allergen extracts via the subcutaneous or sublingual routes to reorient the immune system towards tolerogenic mechanisms. In this regard, since many patients are poly-allergic, mixtures of allergen extracts are often used with a potential risk to cause allergen degradation, thereby affecting treatment efficacy. Herein, we discuss the advantages and drawbacks of mixing homologous (i.e., related) or heterogeneous (i.e., unrelated) allergen extracts. We provide evidence for incompatibilities between mixes of grass pollen and house dust mite extracts containing bodies and feces, and summarize critical points to consider when mixing allergen extracts for AIT.

Comparison of approaches for purifying and desalting polymerase chain reaction products prior to electrospray ionization mass spectrometry

We have compared the recovery and desalting efficiency of different methods (ethanol precipitation, dialysis/ultrafiltration, purification with commercial kits, anion-exchange chromatography) of purifying and desalting PCR products prior to analysis by high-resolution/high mass accuracy electrospray ionization mass spectrometry (LTQ-Orbitrap). The results support the use of anion-exchange chromatography, which shows excellent desalting efficiency with almost no adducts observed, along with a recovery of approximately 70% and the ability to purify approximately 10 samples in 45 min.