Modular binder technology by NGS-aided, high-resolution selection in yeast of designed armadillo modules.

Establishing modular binders as diagnostic detection agents represents a cost- and time-efficient alternative to the commonly used binders that are generated one molecule at a time. In contrast to these conventional approaches, a modular binder can be designed in silico from individual modules to, in principle, recognize any desired linear epitope without going through a selection and hit-validation process, given a set of preexisting, amino acid-specific modules. Designed armadillo repeat proteins (dArmRP) have been developed as modular binder scaffolds, and we report here the generation of highly specific dArmRP modules by yeast surface display selection, performed on a rationally designed dArmRP library. A selection strategy was developed to distinguish the binding difference resulting from a single amino acid mutation in the target peptide. Our reverse-competitor strategy introduced here employs the designated target as a competitor to increase the sensitivity when separating specific from cross-reactive binders that show similar affinities for the target peptide. With this switch in selection focus from affinity to specificity, we found that the enrichment during this specificity sort is indicative of the desired phenotype, regardless of the binder abundance. Hence, deep sequencing of the selection pools allows retrieval of phenotypic hits with only 0.1% abundance in the selectivity sort pool from the next-generation sequencing data alone. In a proof-of-principle study, a binder was created by replacing all corresponding wild-type modules with a newly selected module, yielding a binder with very high affinity for the designated target that has been successfully validated as a detection agent in western blot analysis.

Whole Cell Panning with Phage Display.

Phage display has emerged as one of the leading technologies for the selection of highly specific monoclonal antibodies, offering a number of advantages over traditional methods of antibody generation. While there are various possibilities to conduct phage display (e.g., solution panning, solid-phase panning), whole cell panning is an elegant way to present membrane embedded target antigens in their natural environment and conformation to antibody-bearing phages. Here, a whole cell panning procedure using a Fab-based antibody library including primary cell based screening for selectivity is described.

Comparative laboratory evolution of ordered and disordered enzymes.

Intrinsically disordered proteins are ubiquitous in nature. To assess potential evolutionary advantages and disadvantages of structural disorder under controlled laboratory conditions, we directly compared the evolvability of weakly active ordered and disordered variants of dihydrofolate reductase by genetic selection. The circularly permuted Escherichia coli enzyme, which exists as a molten globule in the absence of ligands, and a well folded deletion mutant of the Bacillus stearothermophilus enzyme served as starting points. Both scaffolds evolved at similar rates and to similar extents, reaching near-native activity after three rounds of mutagenesis and selection. Surprisingly, however, the starting structural properties of the two scaffolds changed only marginally during optimization. Although the ordered and disordered proteins accumulated distinct sets of mutations, the changes introduced likely improved catalytic efficiency indirectly in both cases by bolstering the network of dynamic conformational fluctuations that productively couple into the reaction coordinate.

A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties.

This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds.

HuCAL PLATINUM, a synthetic Fab library optimized for sequence diversity and superior performance in mammalian expression systems.

This article describes the design of HuCAL (human combinatorial antibody library) PLATINUM, an optimized, second-generation, synthetic human Fab antibody library with six trinucleotide-randomized complementarity-determining regions (CDRs). Major improvements regarding the optimized antibody library sequence space were implemented. Sequence space optimization is considered a multistep process that includes the analysis of unproductive antibody sequences in order to, for example, avoid motifs such as potential N-glycosylation sites, which are undesirable in antibody production. Gene optimization has been used to improve expression of the antibody master genes in the library context. As a result, full-length IgGs derived from the library show both significant improvements in expression levels and less undesirable glycosylation sites when compared to the previous HuCAL GOLD library. Additionally, in-depth analysis of sequences from public databases revealed that diversity of CDR-H3 is a function of loop length. Based upon this analysis, the relatively uniform diversification strategy used in the CDR-H3s of the previous HuCAL libraries was changed to a length-dependent design, which replicates the natural amino acid distribution of CDR-H3 in the human repertoire. In a side-by-side comparison of HuCAL GOLD and HuCAL PLATINUM, the new library concept led to isolation of about fourfold more unique sequences and to a higher number of high-affinity antibodies. In the majority of HuCAL PLATINUM projects, 100-300 antibodies each having different CDR-H3s are obtained against each antigen. This increased diversity pool has been shown to significantly benefit functional antibody profiling and screening for superior biophysical properties.

Fiber scaffolds of polysialic acid via electrospinning for peripheral nerve regeneration.

Fiber scaffolds of bioactive polysialic acid have been prepared via electrospinning for peripheral nerve regeneration. The diameter, morphology and alignment of fibers in scaffolds were adjusted by variation of electrospinning parameters, which are decisive for the cell-scaffold interaction. Due to the high water solubility of polysialic acid (poly-alpha-2,8-N-acetylneuraminic acid) a photoactive derivative (poly-alpha-2,8-N-pentenoylneuraminic acid) was used to obtain stable fiber scaffolds in water by photochemical crosslinking. At the optimized fiber scaffolds good cell viability and directed cell proliferation along the fibers was achieved by cell tests with immortalized Schwann cells.

Polysialic acid immobilized on silanized glass surfaces: a test case for its use as a biomaterial for nerve regeneration.

The immobilization of polysialic acid (polySia) on glass substrates has been investigated with regard to the applicability of this polysaccharide as a novel, biocompatible and bioresorbable material for tissue engineering, especially with regard to its use in nerve regeneration. PolySia, a homopolymer of alpha-2,8-linked sialic acid, is involved in post-translational modification of the neural cell adhesion molecule (NCAM). The degradation of polySia can be controlled which makes it an interesting material for coating and for scaffold construction in tissue engineering. Here, we describe the immobilization of polySia on glass surfaces via an epoxysilane linker. Whereas glass surfaces will not actually be used in nerve regeneration scaffolds, they provide a simple and efficient means for testing various methods for the investigation of immobilized polySia. The modified surfaces were investigated with contact angle measurements and the quantity of immobilized polySia was examined by the thiobarbituric acid assay and a specific polySia-ELISA. The interactions between the polySia-modified surface and immortalized Schwann cells were evaluated via cell adhesion and cell viability assays. The results show that polySia can be immobilized on glass surfaces via the epoxysilane linker and that surface-bound polySia has no toxic effects on Schwann cells. Therefore, as a key substance in the development of vertebrates and as a favourable substrate for the cultivation of Schwann cells, it offers interesting features for the use in nerve guidance tubes for treatment of peripheral nerve injuries.

Synthesis and biological evaluation of a polysialic acid-based hydrogel as enzymatically degradable scaffold material for tissue engineering.

Restorative medicine has a constant need for improved scaffold materials. Degradable biopolymers often suffer from uncontrolled chemical or enzymatic hydrolysis by the host. The need for a second surgery on the other hand is a major drawback for nondegradable scaffold materials. In this paper we report the design and synthesis of a novel polysialic acid-based hydrogel with promising properties. Hydrogel synthesis was optimized and enzymatic degradation was studied using a phage-born endosialidase. After addition of endosialidase, hydrogels readily degraded depending on the amount of initially used cross-linker within 2 to 11 days. This polysialic acid hydrogel is not cytotoxic, completely stable under physiological conditions, and could be evaluated as growth support for PC12 cells. Here, additional coating with collagen I, poly-L-lysine or matrigel is mandatory to improve the properties of the material.

Fab MOR03268 triggers absorption shift of a diagnostic dye via packaging in a solvent-shielded Fab dimer interface.

Molecular interactions between near-IR fluorescent probes and specific antibodies may be exploited to generate novel smart probes for diagnostic imaging. Using a new phage display technology, we developed such antibody Fab fragments with subnanomolar binding affinity for tetrasulfocyanine, a near-IR in vivo imaging agent. Unexpectedly, some Fabs induced redshifts of the dye absorption peak of up to 44 nm. This is the largest shift reported for a biological system so far. Crystal structure determination and absorption spectroscopy in the crystal in combination with microcalorimetry and small-angle X-ray scattering in solution revealed that the redshift is triggered by formation of a Fab dimer, with tetrasulfocyanine being buried in a fully closed protein cavity within the dimer interface. The derived principle of shifting the absorption peak of a symmetric dye via packaging within a Fab dimer interface may be transferred to other diagnostic fluorophores, opening the way towards smart imaging probes that change their wavelength upon interaction with an antibody.

The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies.

This article describes the generation of the Human Combinatorial Antibody Library HuCAL GOLD. HuCAL GOLD is a synthetic human Fab library based on the HuCAL concept with all six complementarity-determining regions (CDRs) diversified according to the sequence and length variability of naturally rearranged human antibodies. The human antibody repertoire was analyzed in-depth, and individual CDR libraries were designed and generated for each CDR and each antibody family. Trinucleotide mixtures were used to synthesize the CDR libraries in order to ensure a high quality within HuCAL GOLD, and a beta-lactamase selection system was employed to eliminate frame-shifted clones after successive cloning of the CDR libraries. With these methods, a large, high-quality library with more than 10 billion functional Fab fragments was achieved. By using CysDisplay, the antibody fragments are displayed on the tip of the phage via a disulfide bridge between the phage coat protein pIII and the heavy chain of the antibody fragment. Efficient elution of specific phages is possible by adding reducing agents. HuCAL GOLD was challenged with a variety of different antigens and proved to be a reliable source of high-affinity human antibodies with best affinities in the picomolar range, thus functioning as an excellent source of antibodies for research, diagnostic, and therapeutic applications. Furthermore, the data presented in this article demonstrate that CysDisplay is a robust and broadly applicable display technology even for high-throughput applications.

A study on polysialic acid as a biomaterial for cell culture applications.

Polysialic acid (PSA) was investigated for its applicability as coating material for mammalian cell cultivation. PSA is involved in post-translational modification of the vertebrate neural cell adhesion molecule (NCAM). It is biocompatible and degradation-controlled. Thus, it becomes interesting for use as a coating and scaffold material for tissue engineering applications, especially for peripheral nerve regeneration. As a preliminary study of the use of PSA as scaffold material it was tested in its soluble form as coating material. The cytotoxicity was investigated and compared to another polysaccharide beta-glucan, to widely used coating substances (collagen I, poly-L-lysine, hyaluronic acid) and uncoated tissue culture plastic material. The interactions between the modified cell culture surface and the cells were investigated using a model liver cell line Hep-G2 and a neurobiological cell line PC-12. The PSA coating itself was analyzed by immunoanalysis. Viability of the cells was investigated by the MTT assay. The number and distribution of adhered cells were studied by cell nuclei staining. Furthermore, the differentiation status of the PC-12 cells was monitored, as well as glucose and lactate levels in the cell culture medium from the Hep-G2 cells. Comparable viability and similar numbers of attached cells were observed. Growth in cell clusters was observed for PSA, beta-glucan, and hyaluronic acid coated materials. In general, the results indicate that PSA is comparable to other well-established coating materials (e.g. collagen I, hyaluronic acid, and poly-L-lysine). Moreover, as a key substance in vertebrate development it offers interesting features for nerve regeneration, especially as an insoluble, modified scaffold material.

Collagen biomaterial doped with colominic acid for cell culture applications with regard to peripheral nerve repair.

Colominic acid (CA) is a homopolymer of sialic acid residues and is solely composed of polymerised units of alpha-2,8-linked N-acetylneuraminic acid. CA is a specific derivative of polysialic acid (PSA), produced as the capsular polysaccharide of Escherichia coli K1 derived molecule of PSA. PSA in vivo plays a significant role in synaptic plasticity and neural development. The use of collagen materials doped with defined CA is presented for the cultivation of various cell lines relevant for possible applications in Tissue Engineering. First, the release behaviour under culture conditions of the collagen-based (C-CA) materials was investigated by thiobarbituric acid assay. Additionally, the established cell lines, PC-12 and immortalised Schwann cells (ISC), used for neurobiological and neurochemical studies and the model liver cell line Hep-G2 as indicator for biocompatibility testing, were cultured on the C-CA matrix. Cell proliferation (MTT-test) and cell adhesion (DAPI-staining) of the cell lines on the matrices were observed. Likewise, gene expression of the marker genes thyrosine hydroxylase for the PC-12 cells, and albumin, transferrin and CYP3A4 for the Hep-G2 cells was evaluated via RT-PCR. The results indicate that CA integration in established biomaterial constructs enhances cell proliferation and offers promising features as conduits additive in regarding peripheral nerve regeneration.

Crystallization and molecular-replacement solution of a diagnostic fluorescent dye in complex with a specific Fab fragment.

Tetrasulfocyanine (TSC) has been described as a fluorescent probe for tumour imaging. The complex of TSC and the Fab antibody fragment MOR03268 has been crystallized in three different crystal forms. MOR03268 was identified from the HuCAL GOLD library and further optimized to bind TSC with high affinity (Kd = 0.6 nM). For two of the three crystal forms (forms 1 and 2), data sets could be collected to 2.8 and 2.85 A resolution, respectively. Form 1 belongs to space group I222, with unit-cell parameters a = 72, b = 99, c = 154 A. Form 2 belongs to space group P4(3)2(1)2, with unit-cell parameters a = b = 77, c = 379 A. Form 3 only diffracted to 8 A and was not analyzed further. Molecular-replacement solutions for forms 1 and 2 were found and rebuilding and refinement is in progress. Form 1 contains one Fab molecule per asymmetric unit, while form 2 harbours two. Judging from the green colour of the crystals, both forms contain the Fab molecule bound to the green TSC dye and in both the hydrolysis-sensitive dye molecule is protected from degradation for several weeks to months. The structures should reveal the molecular basis of the high-affinity recognition of TSC by the Fab molecule MOR03268.

Fast and efficient screening system for new biomaterials in tissue engineering: a model for peripheral nerve regeneration.

The use of three-dimensional biodegradable matrices is one major issue in tissue engineering. Numerous materials, fabrication techniques, and modifications have been used and tested in different areas of tissue engineering recently. But nevertheless, technology is far from being optimized and optimal constructs with bioidentical and mechanical properties have not been described in the literature so far. Hence, there is great demand of new suitable biomaterials for tissue engineering applications. In this study, a fast and efficient screening system for initial testing of biomaterials for cell culture application was developed. The set up for the screening system and the decision criteria applied for the determination of suitability of new materials are presented. Hep-G2 and PC-12 cells were seeded onto different matrices and cultured over a period of 2 weeks. The viability of the cells was monitored via the MTT assay. Cell spreading was investigated by DAPI-staining of cell nuclei. Furthermore, the adhesion of the cells on the different matrices was examined by counting the number of attached cells. With these general assays a classification of materials is possible with regard to their suitability. Optimal cell models must be chosen for the defined applications and at least two cell lines are necessary for a differentiating interpretation.

Application of collagen matrices for cartilage tissue engineering.

Articular cartilage shows little capacity for self-repair once it has been damaged. The aim of this study was to investigate different collagen matrices regarding their applicability for cartilage tissue engineering. The matrices consist of collagen I and small amounts of elastine, were crosslinked with carbodiimide or glucose. Primary chondrocytes were seeded onto these different collagen matrices and cultured with or without differentiation medium. The viability of the cells was monitored via MTT test. The arrangement of the cells onto the scaffold was investigated by histological staining. Furthermore, extracellular matrix synthesis was studied by immunohistological staining, especially the expression of the typical chondrogenic marker collagen II. Moreover gene expression for collagen type II was analysed by RT-PCR. The chondrocytes showed high viability on all matrices used. The results for the histological staining revealed a three-dimensional arrangement of the chondrocytes in the collagen matrices. Moreover, the matrices also supported chondrogenic differentiation. On the matrix MATRIDERM 2 mm the synthesis of collagen II was stimulated without adding any differentiation supplements to the cell culture medium, as observed by immunohistological staining and by gene expression analysis of collagen II.

Size and composition of T-cell receptor delta (TCRD) junctional sequences are not predictive of the sensitivity of clonospecific oligonucleotides designed for detection of minimal residual disease in acute lymphoblastic leukemia.

We characterized 168 junctional regions of T-cell receptor delta (TCRD) rearrangements from 116 children with acute lymphoblastic leukemia (ALL) (101 with precursor B-cell ALL, 15 with T-cell ALL). Application of 101 allele-specific oligonucleotide (ASO) probes representing 85 Vdelta2Ddelta3, 10 Ddelta2Ddelta3, 3 Vdelta1Jdelta1, 1 Vdelta3Jdelta1, and 2 Ddelta2Jdelta1 junctions for the detection of minimal residual disease (MRD) revealed detection levels of 10(-4) to 10(-6) leukemia cells in the vast majority of cases (93 of 101). Of interest was that neither the N, D, P (nontemplated, diversity, palindromic) content and length of the junctional regions nor the number of nucleotides deleted from the flanking V, D, or J (variable, diversity, joining) elements correlated with the sensitivity of ASO probes. These data indicated that in ALL TCRD rearrangements can serve as suitable tools for the detection of MRD irrespective of the specific composition of the junctional region.