Controlling the loading of protein nanocages

The work described in this thesis focuses on the use of natural protein building blocks to assemble nanocages. Most common strategies for the loading of different protein nanocages suffer from a lack of numerical control over cargo loading.\ud \ud The aim of this thesis was to create a controllable methodology to selectively load protein nanocages with the cargo of interest. It focuses on two fundamental approaches to optimize the loading: modifying the cargo by genetically engineering and exploring different protein cages.\ud \ud The capsid of the Cowpea Chlorotic Mottle Virus (CCMV) was used as a well-established platform for the design of new cargo loading techniques. Loading could be controlled up to ~20 fluorescent proteins per capsid, however, higher cargo loading ratios led to erroneously formed capsids.\ud \ud A new type of protein nanocage was also explored: the bacterial encapsulins. Overall, the encapsulation of non–natural cargo in encapsulins is highly effective, yet still a very novel approach in which many things remain to be investigated. From this thesis, it is apparent that the best control over protein nanocage loading is achieved in vitro, by purifying the cargo and shell proteins and carefully calculating the mixing ratios

Antibody detection using a FRET-based protein conformational switch

No wash, just go: Classical antibody-detection methods rely on heterogeneous detection schemes that involve multiple, time-consuming binding and washing steps. Here we present a new concept to translate the antigen–antibody interaction directly into a readily detectable fluorescent signal by using a single-chain sensor protein and taking advantage of the unique Y-shaped structure common to all antibodie

Recombinant expression and purification of 'virus-like' bacterial encapsulin protein cages

Ultracentrifugation, particularly the use of sucrose or cesium chloride density gradients, is a highly reliable and efficient technique for the purification of virus-like particles and protein cages. Since virus-like particles and protein cages have a unique size compared to cellular macromolecules and organelles, the rate of migration can be used as a tool for purification. Here we describe a detailed protocol for the purification of recently discovered virus-like assemblies called bacterial encapsulins from Thermotoga maritima and Brevibacterium linens

Detection of DNA methylation markers in urine of cervical cancer patients: a feasibility study

Background and aims: Current cervical screening programs use cervical cytology and is likely to be replaced by primary hrHPV testing in many Western countries. Cytology has a low sensitivity (50-80%), which is largely improved by hrHPV testing. Due to its lower positive predictive value hrHPV testing requires further triage testing. Analysis of DNA methylation of host cell tumor suppressor genes provides promising triage strategy for hrHPV-positive women. Urine collection is expected to increase the uptake of cervical screening programs, and hrHPV testing in urine appears promising. We performed a feasibility study to detect cervical cancer with DNA methylation testing in urine. Methods: Cervical scrapes and urine samples were collected from 29 cervical cancer patient and urine from 24 healthy controls. Extracted DNAs were tested for hrHPV presence and DNA methylation of 6 genes which were previously found to enable cervical (pre)cancer detection in cervical scrapes. Results: A 97% (28/29) concordance was found between hrHPV testing on cervical scrapes and urine samples. DNA methylation levels of all 6 genes were significantly increased in urine samples of cervical cancer patients compared to controls. Receiver operating curve analysis showed a maximum AUC 0.92 (95%CI 0.80-1.0) with 4 out of 6 genes having an AUC>0.86. Moreover, DNA methylation levels in urine were highly correlated to those detected in cervical scrapes of the same patients (Spearmann correlation = 0.83) Conclusions: DNA methylation testing in urine has a high diagnostic accuracy (up to AUC 0.92) to detect cervical cancer, warranting further exploration of methylation markers for use in urine-based cervical cancer screening programs

A protocol for urine collection and storage prior to DNA methylation analysis

Background: Urine poses an attractive non-invasive means for obtaining liquid biopsies for oncological diagnostics. Especially molecular analysis on urinary DNA is a rapid growing field. However, optimal and practical storage conditions that result in preservation of urinary DNA, and in particular hypermethylated DNA (hmDNA), are yet to be determined. Aim: To determine the most optimal and practical conditions for urine storage that result in adequate preservation of DNA for hmDNA analysis. Methods: DNA yield for use in methylation analysis was determined by quantitative methylation specific PCR (qMSP) targeting the ACTB and RASSF1A genes on bisulfite modified DNA. First, DNA yield (ACTB qMSP) was determined in a pilot study on urine samples of healthy volunteers using two preservatives (Ethylenediaminetetraacetic acid (EDTA) and Urine Conditioning Buffer, Zymo Research) at four different temperatures (room temperature (RT), 4°C, -20°C, -80°C) for four time periods (1, 2, 7, 28 days). Next, hmDNA levels (RASSF1A qMSP) in stored urine samples of patients suffering from bladder cancer (n = 10) or non-small cell lung cancer (NSCLC; n = 10) were measured at day 0 and 7 upon storage with and without the addition of 40mM EDTA and/or 20 μl/ml Penicillin Streptomycin (PenStrep) at RT and 4°C. Results: In the pilot study, DNA for methylation analysis was only maintained at RT upon addition of preserving agents. In urine stored at 4°C for a period of 7 days or more, the addition of either preserving agent yielded a slightly better preservation of DNA. When urine was stored at -20 °C or -80 °C for up to 28 days, DNA was retained irrespective of the addition of preserving agents. In bladder cancer and NSCLC samples stored at RT loss of DNA was significantly less if EDTA was added compared to no preserving agents (p0.99). Upon storage at 4°C, no difference in DNA preservation was found after the addition of preserving agents (p = 0.18). The preservation of methylated DNA (RASSF1A) was strongly correlated to that of unmethylated DNA (ACTB) in most cases, except when PCR values became inaccurate. Conclusions: Addition of EDTA offers an inexpensive preserving agent for urine storage at RT up to seven days allowing for reliable hmDNA analysis. To avoid bacterial overgrowth PenStrep can be added without negatively affecting DNA preservation

Assembly and Mechanical Properties of the Cargo-Free and Cargo-Loaded Bacterial Nanocompartment Encapsulin

Prokaryotes mostly lack membranous compartments that are typical of eukaryotic cells, but instead, they have various protein-based organelles. These include bacterial microcompartments like the carboxysome and the virus-like nanocompartment encapsulin. Encapsulins have an adaptable mechanism for enzyme packaging, which makes it an attractive platform to carry a foreign protein cargo. Here we investigate the assembly pathways and mechanical properties of the cargo-free and cargo-loaded nanocompartments, using a combination of native mass spectrometry, atomic force microscopy and multiscale computational molecular modeling. We show that encapsulin dimers assemble into rigid single-enzyme bacterial containers. Moreover, we demonstrate that cargo encapsulation has a mechanical impact on the shell. The structural similarity of encapsulins to virus capsids is reflected in their mechanical properties. With these robust mechanical properties encapsulins provide a suitable platform for the development of nanotechnological applications

Cervical cancer detection by DNA methylation analysis in urine

Urine samples provide a potential alternative to physician-taken or self-collected cervical samples for cervical screening. Screening by primary hrHPV testing requires additional risk assessment (so-called triage) of hrHPV-positive women. Molecular markers, such as DNA methylation, have proven most valuable for triage when applied to cervical specimens. This study was set out to compare hrHPV and DNA methylation results in paired urine and cervical scrapes, and to evaluate the feasibility of DNA methylation analysis in urine to detect cervical cancer. Urine samples (n = 41; native and sediment) and paired cervical scrapes (n = 38) from cervical cancer patients, and urine from 44 female controls, were tested for hrHPV and 6 methylation markers. Results on native urine and sediment were highly comparable. A strong agreement was found between hrHPV testing on urine and scrapes (kappa = 0.79). Also, methylation levels in urine were moderately to strongly correlated to those detected in scrapes (r = 0.508-0.717). All markers were significantly increased in urine from cervical cancer patients compared to controls and showed a good discriminatory power for cervical cancer (AUC = 0.744-0.887). Our results show a good agreement of urine-based molecular analysis with reference cervical samples, and suggest that urine-based DNA methylation testing may provide a promising strategy for cervical cancer detectio