Analysis of Compositional Bias in a Commercial Phage Display Peptide Library by Next-Generation Sequencing

The principal presumption of phage display biopanning is that the naïve library contains an unbiased repertoire of peptides, and thus, the enriched variants derive from the affinity selection of an entirely random peptide pool. In the current study, we utilized deep sequencing to characterize the widely used Ph.DTM-12 phage display peptide library (New England Biolabs). The next-generation sequencing (NGS) data indicated the presence of stop codons and a high abundance of wild-type clones in the naïve library, which collectively result in a reduced effective size of the library. The analysis of the DNA sequence logo and global and position-specific frequency of amino acids demonstrated significant bias in the nucleotide and amino acid composition of the library inserts. Principal component analysis (PCA) uncovered the existence of four distinct clusters in the naïve library and the investigation of peptide frequency distribution revealed a broad range of unequal abundances for peptides. Taken together, our data provide strong evidence for the notion that the naïve library represents substantial departures from randomness at the nucleotide, amino acid, and peptide levels, though not undergoing any selective pressure for target binding. This non-uniform sequence representation arises from both the M13 phage biology and technical errors of the library construction. Our findings highlight the paramount importance of the qualitative assessment of the naïve phage display libraries prior to biopanning.

Systemic TLR7/8 micelles trigger a novel and potent anti-tumor response by strong recruitment of neutrophils leading to massive tumor cell killing

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Background: Clinical use of TLR7/8 agonists is currently restricted to topical application of Imiquimod for treatment of superficial basal cell carcinoma since systemic administration is prevented due to dose-limiting toxicity. Here, we present a novel micelle-based drug delivery technology containing a lipid-anchored TLR7/8 agonist for intravenous administration. The MBS8 formulation shows good efficacy in mouse cancer models, is well tolerated in rodents and non-human primates and is currently being tested in clinical studies (NCT04855435). Methods: MBS8 was tested in 12 syngeneic mouse cancer models as monotherapy or in combination anti-PD-1 and anti-PD-L1 antibodies. MBS8 was administered IV as slow bolus. Tumors and spleens were analysed using histology, immunohistochemistry, ELISPOT and flow cytometry. Phenotyping of tumor microenvironment was done using flow cytometry and Nanostring analyses. Safety and tolerability were tested in mice, rats and monkeys. Safety-related and PD biomarkers were identified in monkeys using a multiplex MSD technology and validated in whole human blood stimulated with MBS8 ex-vivo. Results: In several syngeneic mouse tumor models, MBS8 led to complete eradication of established tumors. The complete responders showed tumor rejection upon re-challenge. In these mice, a CD8+-dependent tumor-specific immune memory response was evident. Tumors demonstrated a massive tissue necrosis ( > 80%) within 24-48h after the first drug administration and showed massive neutrophil infiltration 6h after dosing. Antigen specific CD8+ T-cells were detected in tumors 24 hours after treatment with increased CD8+:Treg cell ratio and enhanced antigen presentation in tdLN. MBS8 showed both additive and synergistic effect when combined with anti-PD-1 or anti-PD-L1 antibody treatment. Moreover, in tumors being resistant to anti-PD-1 treatment, co-administration of MBS8 reverted sensitivity to anti-PD-1 treatment in a synergistic manner. A panel of cytokines induced by MBS8 upon repeat dose administration in monkeys was identified in plasma as potential biomarkers. Ten of them were further evaluated in whole human blood treated with MBS8 ex vivo. Currently, these cytokines are being used in Phase I clinical studies. Conclusions: MBS8 showed significant anti-cancer activity in multiple in vivo solid tumor models when administered either as monotherapy or in combination with ICIs. MBS8 demonstrated a novel mode of action with neutrophils playing a central role as primary effector cells causing a rapid killing of tumors. Further, adaptive immune response was initiated including generation of tumor specific CD8+ cells and establishment of the immune memory. MBS8 was well tolerated in rodents and cynomolgus monkeys at the dose levels above therapeutic effective doses identified in mice, thus providing a good therapeutic window.

Unravelling Heterogeneities in Complement and Antibody Opsonization of Individual Liposomes as a Function of Surface Architecture

Coating nanoparticles with poly(ethylene glycol) (PEG) is widely used to achieve long-circulating properties after infusion. While PEG reduces binding of opsonins to the particle surface, immunogenic anti-PEG side-effects show that PEGylated nanoparticles are not truly "stealth" to surface active proteins. A major obstacle for understanding the complex interplay between opsonins and nanoparticles is the averaging effects of the bulk assays that are typically applied to study protein adsorption to nanoparticles. Here, a microscopy-based method for directly quantifying opsonization at the single nanoparticle level is presented. Various surface coatings are investigated on liposomes, including PEG, and show that opsonization by both antibodies and complement C3b is highly dependent on the surface chemistry. It is further demonstrated that this opsonization is heterogeneous, with opsonized and non-opsonized liposomes co-existing in the same ensemble. Surface coatings modify the percentage of opsonized liposomes and/or opsonin surface density on the liposomes, with strikingly different patterns for antibodies and complement. Thus, this assay provides mechanistic details about opsonization at the single nanoparticle level previously inaccessible to established bulk assays.

Matrix effect in tumor lysates - Does it affect your cytokine ELISA and multiplex analyses?

Quantification of cytokines in cancerous tissue is important for understanding basic tumor biology and for deciphering anti-cancer mechanisms in drug development. Cytokine measurements on protein-level are often done by immunoassays such as enzyme-linked immunosorbent assay (ELISAs) and multiplex assays. However, immunoassays are prone to interference due to the presence of perturbing factors. The sum of these factors is known as the matrix effect, which results in a deviation of the measured cytokine concentration from the actual concentration. In this study, we demonstrated that matrix effects are present in tumor lysates from 11 different syngeneic murine tumors and that it can greatly affect cytokine measurements in ELISAs and multiplex assays. Dilution of tumor lysates and careful selection of lysis buffer components may decrease matrix effects. However, matrix effects are still present, and care should be taken when analyzing cytokine measurements of tumor lysates.

Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition

Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields.

Comparison of two commercial broad-range PCR and sequencing assays for identification of bacteria in culture-negative clinical samples

BACKGROUND

Culturing has long been the gold standard for detecting aetiologic agents in bacterial infections. In some cases, however, culturing fails to detect the infection. To further investigate culture-negative samples, amplification and subsequent sequencing of the 16S rRNA gene is often applied. The aim of the present study was to compare the current method used at our Department of Clinical Microbiology, based on the MicroSeq ID system (Applied Biosystems, USA) with the Universal Microbe Detection (UMD) SelectNA kit (Molzym, Germany).

METHODS

76 culture-negative samples were first processed with the MicroSeq ID analysis, where total DNA was extracted and the 16S gene amplified and sequenced with the MicroSeq ID system. Samples were subsequently processed with the UMD SelectNA analysis, where human DNA was removed during the DNA extraction procedure and the 16S gene amplified in a real-time PCR and sequenced.

RESULTS

22 of 76 samples (28.9%) were positive for bacteria with the UMD SelectNA, which was significantly more (p = 0.0055) than the MicroSeq ID where 11 of 76 samples (14.5%) were positive. The UMD SelectNA assay identified more relevant bacterial pathogens than the MicroSeq ID analysis (p = 0.0233), but also found a number of species that were considered contaminations.

CONCLUSIONS

The UMD SelectNA assay was valuable for the identification of pathogens in culture-negative samples; however, due to the sensitive nature of the assay, extreme care is suggested in order to avoid false positives.

Maxillary Sinus Impaction of a Core Carrier Causing Sustained Apical Periodontitis, Sinusitis, and Nasal Stenosis: A 3-year Follow-up

INTRODUCTION

The aim was to present a case report of a full-length extrusion of an obturator's core carrier into the maxillary sinus, causing clinical symptoms from the nose region with differential diagnostics aspects, which, in turn, led to several surgical treatments of the nostrils before diagnosis and correct endodontic retreatment of a maxillary right first molar. A 36-year-old man presented in 2012 with complaints from the right nostril region. Medical treatment with antibiotics and surgical procedures because of nasal stenosis resulted only in partial improvement. Five years earlier, a root canal treatment was performed on the maxillary right first molar. Intraoral radiographs revealed 10-mm overfilling of root filling material into the maxillary sinus from the palatal root of tooth #3.

METHODS

Before surgical removal of the excess root filling material, orthograde revision was performed. Cone-beam computed tomographic imaging was used to localize the position of the root filling material, which protruded through the maxillary sinus and reached the inferior nasal wall.

RESULTS

Surgical removal from the palatal aspect revealed that the root filling material was a core carrier of an obturator. Scanning electron microscopy and transmission electron microscopy showed evidence of microbial biofilm on the core carrier as well as remnants of sinus mucosa. At the long-term follow-ups, the tooth had healed apically, and symptoms of nasal stenosis were markedly reduced.

CONCLUSIONS

This case report represents a challenging differential diagnostic topic urging the importance of a medical and dental interdisciplinary dialogue. The use of cone-beam computed tomographic imaging was crucial for the surgical retreatment.