Exploring GPCR-arrestin interfaces with genetically encoded crosslinkers.

ß-arrestins (ßarr1 and ßarr2) are ubiquitous regulators of G protein-coupled receptor (GPCR) signaling. Available data suggest that ß-arrestins dock to different receptors in different ways. However, the structural characterization of GPCR-arrestin complexes is challenging and alternative approaches to study GPCR-arrestin complexes are needed. Here, starting from the finger loop as a major site for the interaction of arrestins with GPCRs, we genetically incorporate non-canonical amino acids for photo- and chemical crosslinking into ßarr1 and ßarr2 and explore binding topologies to GPCRs forming either stable or transient complexes with arrestins: the vasopressin receptor 2 (rhodopsin-like), the corticotropin-releasing factor receptor 1, and the parathyroid hormone receptor 1 (both secretin-like). We show that each receptor leaves a unique footprint on arrestins, whereas the two ß-arrestins yield quite similar crosslinking patterns. Furthermore, we show that the method allows defining the orientation of arrestin with respect to the GPCR. Finally, we provide direct evidence for the formation of arrestin oligomers in the cell.

Designer tRNAs for efficient incorporation of non-canonical amino acids by the pyrrolysine system in mammalian cells.

The pyrrolysyl-tRNA synthetase/tRNAPyl pair is the most versatile and widespread system for the incorporation of non-canonical amino acids (ncAAs) into proteins in mammalian cells. However, low yields of ncAA incorporation severely limit its applicability to relevant biological targets. Here, we generate two tRNAPyl variants that significantly boost the performance of the pyrrolysine system. Compared to the original tRNAPyl, the engineered tRNAs feature a canonical hinge between D- and T-loop, show higher intracellular concentrations and bear partially distinct post-transcriptional modifications. Using the new tRNAs, we demonstrate efficient ncAA incorporation into a G-protein coupled receptor (GPCR) and simultaneous ncAA incorporation at two GPCR sites. Moreover, by incorporating last-generation ncAAs for bioorthogonal chemistry, we achieve GPCR labeling with small organic fluorophores on the live cell and visualize stimulus-induced GPCR internalization. Such a robust system for incorporation of single or multiple ncAAs will facilitate the application of a wide pool of chemical tools for structural and functional studies of challenging biological targets in live mammalian cells.

A validation study of new decision algorithms for interpretation of cancer significance on prostate systematic biopsy.

INTRODUCTION: To test with actual data a new decision algorithm derived by probability modeling of the number of positive cores, for deciding insignificant versus significant prostate cancer, based on prostate volume, Gleason score, tumor length on biopsy cores, and number of positive cores. MATERIALS AND METHODS: A dataset of 59 cancer-involved autopsied prostate glands from patients aged 42 to 92 years with prostate volumes of 22 cc to 95 cc was used. An 18 core-systematic biopsy was performed on the first 47 patients, and saturation biopsy protocol of 36 cores was performed on the remainder. Clinically insignificant prostate cancer was defined on whole-mount prostates as Gleason score < 7, total tumor volume ≤ 0.5 cc. Separate counts of 'significant' versus 'insignificant' prostate cancer by both the model-based decision algorithm and the actual data were obtained. These yielded specificity (SP), sensitivity (SE), and concordance values for evaluation of the efficacy of the decision algorithm. RESULTS: The model-based decision algorithm yielded SP from 83% to 100%, SE from 62% to 100%, and concordance from 78% to 100%. These findings compared favorably with those of currently used study-based algorithms and their individually fitted SP and SE derived from their corresponding studies. CONCLUSIONS: The model-based decision algorithm performed well with this dataset of autopsied prostates for patients with Gleason score 6 or lower, confirming its practical feasibility and its potential to help reduce over- and under-treatment, especially with marginally positive biopsy cases, by taking prostate volume properly into account. However, additional validation studies with other datasets including higher prostate volumes are needed for further calibration and improvement of the model-based decision algorithm.

Probability modeling of the number of positive cores in a prostate cancer biopsy session, with applications.

Among men, prostate cancer (CaP) is the most common newly diagnosed cancer and the second leading cause of death from cancer. A major issue of very large scale is avoiding both over-treatment and under-treatment of CaP cases. The central challenge is deciding clinical significance or insignificance when the CaP biopsy results are positive but only marginally so. A related concern is deciding how to increase the number of biopsy cores for larger prostates. As a foundation for improved choice of number of cores and improved interpretation of biopsy results, we develop a probability model for the number of positive cores found in a biopsy, given the total number of cores, the volumes of the tumor nodules, and - very importantly - the prostate volume. Also, three applications are carried out: guidelines for the number of cores as a function of prostate volume, decision rules for insignificant versus significant CaP using number of positive cores, and, using prior distributions on total tumor size, Bayesian posterior probabilities for insignificant CaP and posterior median CaP. The model-based results have generality of application, take prostate volume into account, and provide attractive tradeoffs of specificity versus sensitivity. Copyright © 2015 John Wiley & Sons, Ltd.

Design criteria for synthetic riboswitches acting on transcription.

Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or sequestering of the ribosomal binding site). Due to a modular composition, these elements can be manipulated by combining different aptamers and expression platforms and therefore represent useful tools to regulate gene expression in synthetic biology. Using computationally designed theophylline-dependent riboswitches we show that 2 parameters, terminator hairpin stability and folding traps, have a major impact on the functionality of the designed constructs. These have to be considered very carefully during design phase. Furthermore, a combination of several copies of individual riboswitches leads to a much improved activation ratio between induced and uninduced gene activity and to a linear dose-dependent increase in reporter gene expression. Such serial arrangements of synthetic riboswitches closely resemble their natural counterparts and may form the basis for simple quantitative read out systems for the detection of specific target molecules in the cell.

A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information.

Identification of DNA motifs from ChIP-seq/ChIP-chip [chromatin immunoprecipitation (ChIP)] data is a powerful method for understanding the transcriptional regulatory network. However, most established methods are designed for small sample sizes and are inefficient for ChIP data. Here we propose a new k-mer occurrence model to reflect the fact that functional DNA k-mers often cluster around ChIP peak summits. With this model, we introduced a new measure to discover functional k-mers. Using simulation, we demonstrated that our method is more robust against noises in ChIP data than available methods. A novel word clustering method is also implemented to group similar k-mers into position weight matrices (PWMs). Our method was applied to a diverse set of ChIP experiments to demonstrate its high sensitivity and specificity. Importantly, our method is much faster than several other methods for large sample sizes. Thus, we have developed an efficient and effective motif discovery method for ChIP experiments.

Comparison of two lab-scale protocols for enhanced mRNA-based CAR-T cell generation and functionality.

Process development for transferring lab-scale research workflows to automated manufacturing procedures is critical for chimeric antigen receptor (CAR)-T cell therapies. Therefore, the key factor for cell viability, expansion, modification, and functionality is the optimal combination of medium and T cell activator as well as their regulatory compliance for later manufacturing under Good Manufacturing Practice (GMP). In this study, we compared two protocols for CAR-mRNA-modified T cell generation using our current lab-scale process, analyzed all mentioned parameters, and evaluated the protocols' potential for upscaling and process development of mRNA-based CAR-T cell therapies.

Determination of G-protein-coupled receptor oligomerization by molecular brightness analyses in single cells.

Oligomerization of membrane proteins has received intense research interest because of their importance in cellular signaling and the large pharmacological and clinical potential this offers. Fluorescence imaging methods are emerging as a valid tool to quantify membrane protein oligomerization at high spatial and temporal resolution. Here, we provide a detailed protocol for an image-based method to determine the number and oligomerization state of fluorescently labeled prototypical G-protein-coupled receptors (GPCRs) on the basis of small out-of-equilibrium fluctuations in fluorescence (i.e., molecular brightness) in single cells. The protocol provides a step-by-step procedure that includes instructions for (i) a flexible labeling strategy for the protein of interest (using fluorescent proteins, small self-labeling tags or bio-orthogonal labeling) and the appropriate controls, (ii) performing temporal and spatial brightness image acquisition on a confocal microscope and (iii) analyzing and interpreting the data, excluding clusters and intensity hot-spots commonly observed in receptor distributions. Although specifically tailored for GPCRs, this protocol can be applied to diverse classes of membrane proteins of interest. The complete protocol can be implemented in 1 month.

Quantitative Single-Residue Bioorthogonal Labeling of G Protein-Coupled Receptors in Live Cells.

High-end microscopy studies of G protein-coupled receptors (GPCRs) require installing onto the receptors bright and photostable dyes. Labeling must occur in quantitative yields, to allow stoichiometric data analysis, and in a minimally invasive fashion, to avoid perturbing GPCR function. We demonstrate here that the genetic incorporation of trans-cyclooct-2-ene lysine (TCO*) allows achieving quantitative single-residue labeling of the extracellular loops of the ß2-adrenergic and the muscarinic M2 class A GPCRs, as well as of the corticotropin releasing factor class B GPCR. Labeling occurs within a few minutes by reaction with dye-tetrazine conjugates on the surface of live cells and preserves the functionality of the receptors. To precisely quantify the labeling yields, we devise a method based on fluorescence fluctuation microscopy that extracts the number of labeling sites at the single-cell level. Further, we show that single-residue labeling is better suited for studies of GPCR diffusion than fluorescent-protein tags, since the latter can affect the mobility of the receptor. Finally, by performing dual-color competitive labeling on a single TCO* site, we devise a method to estimate the oligomerization state of a GPCR without the need for a biological monomeric reference, which facilitates the application of fluorescence methods to oligomerization studies. As TCO* and the dye-tetrazines used in this study are commercially available and the described microscopy techniques can be performed on a commercial microscope, we expect our approach to be widely applicable to fluorescence microscopy studies of membrane proteins in general.

Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells.

The genetic incorporation of non-canonical amino acids (ncAAs) via amber stop codon suppression is a powerful technique to install artificial probes and reactive moieties onto proteins directly in the live cell. Each ncAA is incorporated by a dedicated orthogonal suppressor-tRNA/amino-acyl-tRNA-synthetase (AARS) pair that is imported into the host organism. The incorporation efficiency of different ncAAs can greatly differ, and be unsatisfactory in some cases. Orthogonal pairs can be improved by manipulating either the AARS or the tRNA. However, directed evolution of tRNA or AARS using large libraries and dead/alive selection methods are not feasible in mammalian cells. Here, a facile and robust fluorescence-based assay to evaluate the efficiency of orthogonal pairs in mammalian cells is presented. The assay allows screening tens to hundreds of AARS/tRNA variants with a moderate effort and within a reasonable time. Use of this assay to generate new tRNAs that significantly improve the efficiency of the pyrrolysine orthogonal system is described, along with the application of ncAAs to the study of G-protein coupled receptors (GPCRs), which are challenging objects for ncAA mutagenesis. First, by systematically incorporating a photo-crosslinking ncAA throughout the extracellular surface of a receptor, binding sites of different ligands on the intact receptor are mapped directly in the live cell. Second, by incorporating last-generation ncAAs into a GPCR, ultrafast catalyst-free receptor labeling with a fluorescent dye is demonstrated, which exploits bioorthogonal strain-promoted inverse Diels Alder cycloaddition (SPIEDAC) on the live cell. As ncAAs can be generally applied to any protein independently on its size, the method is of general interest for a number of applications. In addition, ncAA incorporation does not require any special equipment and is easily performed in standard biochemistry labs.

Quantifying the impact of prostate volumes, number of biopsy cores and 5alpha-reductase inhibitor therapy on the probability of prostate cancer detection using mathematical modeling.

PURPOSE: Previous studies demonstrated a negative correlation between prostate volume and biopsy yield. By decreasing prostate volume 5alpha-reductase inhibitors may enhance cancer detection, which may explain the greater detection of high grade tumors in the finasteride arm of the Prostate Cancer Prevention Trial. MATERIALS AND METHODS: A mathematical model was constructed to analyze the effects of prostate and tumor volumes, and biopsy core number on cancer detection. The effects of the volume reduction observed with finasteride in the Prostate Cancer Prevention Trial were also modeled, as was the potential reduction in tumor volume needed to explain the observed difference in prostate cancer detection. The model was also applied to the Reduction by Dutasteride of Prostate Cancer Events study. RESULTS: A higher number of biopsies are required to ensure a detection probability of 0.90 or greater in larger glands or with smaller tumors. In the Prostate Cancer Prevention Trial for a tumor volume of 1 cc a 17% increase in the detection rate in the finasteride arm would be predicted if there was no change in tumor volume, likewise the rate would be 11% to 17% for the dutasteride arm of the Reduction by Dutasteride of Prostate Cancer Events study. The calculated reduction in tumor volume needed to explain the difference in cancer detection between the finasteride and placebo arms of the Prostate Cancer Prevention Trial would be 51% to 66%. CONCLUSIONS: This model provides guidance on the optimal number of biopsy cores that accord with an earlier model. These findings also suggest that, if there were no reduction in tumor volume, 5alpha-reductase inhibitor therapy could lead to excess cancer detection, including high grade tumors.