Single amino acid fingerprinting of the human antibody repertoire with high density peptide arrays

Weber, Laura K.; Palermo, Andrea; Kügler, Jonas; Armant, Olivier; Isse, Awale; Rentschler, Simone; Jaenisch, Thomas; Hubbuch, Jürgen; Dübel, Stefan; Nesterov‐Mueller, Alexander; Breitling, F.; Loeffler, Felix F.

doi:10.1016/j.jim.2017.01.012

Cited by 39 publications

(48 citation statements)

References 35 publications

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“…We show that it is possible to produce 9‐mer peptides with this simple setup, which is comparable to the high‐resolution LIFT method, reproducibly enabling a resolution of 250 µm (1600 spots cm −2 ). Peptide arrays are becoming increasingly important in research, and several applications in immunology and diagnostics have been shown recently, for example, the development of therapeutic antibodies or diagnostic biomarkers …”

Section: Resultsmentioning

confidence: 99%

A Low‐Cost Laser‐Based Nano‐3D Polymer Printer for Rapid Surface Patterning and Chemical Synthesis of Peptide and Glycan Microarrays

Eickelmann

Tsouka

Heidepriem

et al. 2019

Adv Materials Technologies

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A low‐cost laser‐based printing setup is presented, which allows for the spot‐wise patterning of surfaces with defined polymer nanolayers. These nanolayer spots serve as a “solid solvent,” embedding different chemicals, chemical building blocks, materials, or precursors and can be stacked on top of each other. By melting the spot pattern, the polymer‐embedded molecules are released for chemical reaction. This enables researchers to quickly pattern a surface with different molecules and materials, mixing them directly on the surface for high‐throughput chemical synthesis to generate and screen diverse microarray libraries. In contrast to expensive ink‐jet or contact printing, this approach does not require premixing of inks, which enables in situ combinatorial mixing. Easy access and versatility of this patterning approach are shown by generating microarrays of various biomolecules, such as glycans for the first time, to screen interactions of antibodies and lectins. In addition, a layer‐by‐layer solid‐phase synthesis of peptides directly on the microarray is presented. Amino acid–containing nanolayers are repeatedly laser‐transferred and reacted with the functionalized acceptor surface in defined patterns. This simple system enables a reproducible array production, down to spot‐to‐spot distances of 100 µm, and offers a flexible and cheap alternative to expensive spotting robot technology.

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Section: Resultsmentioning

confidence: 99%

A Low‐Cost Laser‐Based Nano‐3D Polymer Printer for Rapid Surface Patterning and Chemical Synthesis of Peptide and Glycan Microarrays

Eickelmann

Tsouka

Heidepriem

et al. 2019

Adv Materials Technologies

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“…Bacterial proteins chosen for validation were Streptolysin O, corresponding to the second most prevalent Streptococcus epitope (Table 2), and Extracellular matrix protein-binding protein emp, corresponding to most prevalent Staphylococcus epitope (Table 2). In all cases, K-TOPE found prominent peaks in the histograms that corresponded to reported epitopes (Fig 4) [6,33,35,40]. Additionally, K-TOPE identified an immunogenic region of GA-repeats from positions 100-350 in the analysis of EBNA1 [23].…”

Section: Resultsmentioning

confidence: 99%

“…KRPSCIGCK was noted as an EBNA1 epitope that was preferentially targeted by pre-eclamptic women, but was also targeted by healthy controls [6]. The motif XPEFXGSXX was discovered and inferred to correspond to VPEFKGSLP in Staphylococcus aureus using protein database searches [40]. For Poliovirus 1 , the epitope PALTAVETGATNPL was found to be a cross-reactive epitope in many enteroviruses [35].…”

Section: Methodsmentioning

confidence: 99%

A general approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes

Paull

Johnston

Ibsen

et al. 2019

Preprint

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28Antibodies are essential to functional immunity, yet the epitopes targeted by antibody 29 repertoires remain largely uncharacterized. To aid in characterization, we developed a 30 generalizable strategy to identify antibody-binding epitopes within individual proteins and entire 31 proteomes. Specifically, we selected antibody-binding peptides for 273 distinct sera out of a 32 random library and identified the peptides using next-generation sequencing. To identify 33 antibody-binding epitopes and the antigens from which these epitopes were derived, we tiled the 34 sequences of candidate antigens into short overlapping subsequences of length k (k-mers). We 35 used the enrichment over background of these k-mers in the antibody-binding peptide dataset to 36 identify antibody-binding epitopes. As a positive control, we used this approach, termed K-mer 37 Tiling of Protein Epitopes (K-TOPE), to identify epitopes targeted by monoclonal and polyclonal 38 antibodies of well-characterized specificity, accurately recovering their known epitopes. K-39 TOPE characterized a commonly targeted antigen from Rhinovirus A, identifying three epitopes 40 recognized by antibodies present in 83% of sera (n = 250). An analysis of 2,908 proteins from 41 400 viral taxa that infect humans revealed seven enterovirus epitopes and five Epstein-Barr virus 42 epitopes recognized by >30% of specimens. Analysis of Staphylococcus and Streptococcus 43 proteomes similarly revealed six epitopes recognized by >40% of specimens. These common 44 viral and bacterial epitopes exhibited excellent agreement with previously mapped epitopes.45 Additionally, we identified 30 HSV2-specific epitopes that were 100% specific against HSV1 in 46 novel and previously reported antigens. The K-TOPE approach thus provides a powerful new 47 tool to elucidate the organisms, antigens, and epitopes targeted by human antibody repertoires. 48 49 50 Introduction 51 52 Immunological memory allows for rapid antibody responses towards diverse antigens 53 long after initial exposure. For example, the adaptive immune response to many vaccinations is 54 often sustained throughout an individual's lifetime [1]. This immunological information is 55 archived within the genes encoding B-cell and T-cell receptors along with the corresponding 56 receptor structures, but has proven difficult to characterize in a comprehensive manner. The 57 ability to more fully interrogate immunological memory could reveal exposures to pathogens, 58 commensal organisms, and allergens. Such information has proven useful for correlating 59 antibody responses with disease outcomes to design more effective vaccines [2]. A detailed 60 record of immune exposures can also facilitate the identification of biomarkers to diagnose 61 infectious [3], autoimmune [4], and allergic conditions [5]. Furthermore, the capability to 62 broadly characterize antibody repertoires at the epitope level could be used to identify conserved 63 pathogen epitopes [6] and tumor specific antigen epitopes [7] to aid in therapeutic disco...

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“…With substitution analyses, we have investigated the role of single amino acids regarding their importance for antibody binding to immunodominant epitopes (also see [39]). In this study, we demonstrated for the first time that, if the same VlsE epitope is targeted by antibodies, almost identical amino acids of the epitope are crucial for the formation of the antibody-antigen complex in different individuals.…”

Section: Discussionmentioning

confidence: 99%

Antibody fingerprints in lyme disease deciphered with high density peptide arrays

Weber

Isse

Rentschler

et al. 2017

Engineering in Life Sciences

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Lyme disease is the most common tick‐borne infectious disease in Europe and North America. Previous studies discovered the immunogenic role of a surface‐exposed lipoprotein (VlsE) of Borreliella burgdorferi. We employed high density peptide arrays to investigate the antibody response to the VlsE protein in VlsE‐positive patients by mapping the protein as overlapping peptides and subsequent in‐depth epitope substitution analyses. These investigations led to the identification of antibody fingerprints represented by a number of key residues that are indispensable for the binding of the respective antibody. This approach allows us to compare the antibody specificities of different patients to the resolution of single amino acids. Our study revealed that the sera of VlsE‐positive patients recognize different epitopes on the protein. Remarkably, in those cases where the same epitope is targeted, the antibody fingerprint is almost identical. Furthermore, we could correlate two fingerprints with human autoantigens and an Epstein‐Barr virus epitope; yet, the link to autoimmune disorders seems unlikely and must be investigated in further studies. The other three fingerprints are much more specific for B. burgdorferi. Since antibody fingerprints of longer sequences have proven to be highly disease specific, our findings suggest that the fingerprints could function as diagnostic markers that can reduce false positive test results.

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Single amino acid fingerprinting of the human antibody repertoire with high density peptide arrays

Cited by 39 publications

References 35 publications

A Low‐Cost Laser‐Based Nano‐3D Polymer Printer for Rapid Surface Patterning and Chemical Synthesis of Peptide and Glycan Microarrays

A Low‐Cost Laser‐Based Nano‐3D Polymer Printer for Rapid Surface Patterning and Chemical Synthesis of Peptide and Glycan Microarrays

A general approach for identifying protein epitopes targeted by antibody repertoires using whole proteomes

Antibody fingerprints in lyme disease deciphered with high density peptide arrays

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