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von Auw N, Serfling R, Kitte R, Hilger N, Zhang C, Gebhardt C, Duenkel A, Franz P, Koehl U, Fricke S, Tretbar US. Comparison of two lab-scale protocols for enhanced mRNA-based CAR-T cell generation and functionality. Sci Rep 2023; 13:18160. [PMID: 37875523 PMCID: PMC10598065 DOI: 10.1038/s41598-023-45197-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/17/2023] [Indexed: 10/26/2023] Open
Abstract
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.
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Affiliation(s)
- Nadine von Auw
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
| | - Robert Serfling
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
| | - Reni Kitte
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
| | - Nadja Hilger
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
| | | | - Clara Gebhardt
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
| | - Anna Duenkel
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
| | - Paul Franz
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
| | - Ulrike Koehl
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
- Medical Faculty, Institute for Clinical Immunology, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany
| | - Stephan Fricke
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Leipzig, Germany
| | - U Sandy Tretbar
- Department for Cell and Gene Therapy Development, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Perlickstr. 1, 04103, Leipzig, Germany.
- Fraunhofer Cluster of Excellence Immune-Mediated Diseases CIMD, Leipzig, Germany.
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Işbilir A, Serfling R, Möller J, Thomas R, De Faveri C, Zabel U, Scarselli M, Beck-Sickinger AG, Bock A, Coin I, Lohse MJ, Annibale P. Determination of G-protein-coupled receptor oligomerization by molecular brightness analyses in single cells. Nat Protoc 2021; 16:1419-1451. [PMID: 33514946 DOI: 10.1038/s41596-020-00458-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
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.
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Affiliation(s)
- Ali Işbilir
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Jan Möller
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Romy Thomas
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Chiara De Faveri
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Ulrike Zabel
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Marco Scarselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Andreas Bock
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Martin J Lohse
- Max Delbrück Center for Molecular Medicine, Berlin, Germany. .,Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany. .,ISAR Bioscience Institute, Munich, Germany.
| | - Paolo Annibale
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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Böttke T, Ernicke S, Serfling R, Ihling C, Burda E, Gurevich VV, Sinz A, Coin I. Exploring GPCR-arrestin interfaces with genetically encoded crosslinkers. EMBO Rep 2020; 21:e50437. [PMID: 32929862 PMCID: PMC7645262 DOI: 10.15252/embr.202050437] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 12/18/2022] Open
Abstract
β‐arrestins (βarr1 and βarr2) are ubiquitous regulators of G protein‐coupled receptor (GPCR) signaling. Available data suggest that β‐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 βarr1 and βarr2 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 β‐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.
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Affiliation(s)
- Thore Böttke
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Stefan Ernicke
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Christian Ihling
- Institute of Pharmacy, Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Edyta Burda
- Institute of Pharmacy, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | | | - Andrea Sinz
- Institute of Pharmacy, Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
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Serfling R, Seidel L, Bock A, Lohse MJ, Annibale P, Coin I. Quantitative Single-Residue Bioorthogonal Labeling of G Protein-Coupled Receptors in Live Cells. ACS Chem Biol 2019; 14:1141-1149. [PMID: 31074969 DOI: 10.1021/acschembio.8b01115] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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 β2-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.
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Affiliation(s)
- Robert Serfling
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
| | - Lisa Seidel
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
| | - Andreas Bock
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Martin J. Lohse
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Paolo Annibale
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Irene Coin
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstr. 34, 04103 Leipzig, Germany
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Serfling R, Lorenz C, Etzel M, Schicht G, Böttke T, Mörl M, Coin I. Designer tRNAs for efficient incorporation of non-canonical amino acids by the pyrrolysine system in mammalian cells. Nucleic Acids Res 2019; 46:1-10. [PMID: 29177436 PMCID: PMC5758916 DOI: 10.1093/nar/gkx1156] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/09/2017] [Indexed: 11/12/2022] Open
Abstract
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.
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Affiliation(s)
- Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Christian Lorenz
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Maja Etzel
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Gerda Schicht
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Thore Böttke
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Mario Mörl
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Brüderstraße 34, 04103 Leipzig, Germany
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Serfling R, Seidel L, Böttke T, Coin I. Optimizing the Genetic Incorporation of Chemical Probes into GPCRs for Photo-crosslinking Mapping and Bioorthogonal Chemistry in Live Mammalian Cells. J Vis Exp 2018. [PMID: 29683449 DOI: 10.3791/57069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
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.
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Affiliation(s)
- Robert Serfling
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Lisa Seidel
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Thore Böttke
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig
| | - Irene Coin
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig;
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Ogola GO, Delongchamps N, Serfling R. A validation study of new decision algorithms for interpretation of cancer significance on prostate systematic biopsy. Can J Urol 2017; 24:8721-8727. [PMID: 28436358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
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.
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Affiliation(s)
- Gerald O Ogola
- Center for Clinical Effectiveness, Office of the Chief Quality Officer, Baylor Scott and White Health, Dallas, Texas, USA
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Abstract
With the aim of providing greater flexibility in developing and applying shot noise models, this paper studies shot noise on cluster point processes with both pointwise and cluster marks. For example, in financial modelling, responses to events in the financial market may occur in clusters, with random amplitudes including a ‘cluster component’ reflecting a degree of commonness among responses within a cluster. For such shot noise models, general formulae for the characteristic functional are developed and specialized to the case of Neyman-Scott clustering with cluster marks. For several general forms of response function, long range dependence of the corresponding equilibrium shot noise models is investigated. It is shown, for example, that long range dependence holds when the ‘structure component’ of the response function decays slowly enough, or when the response function has a finite random duration with a heavy tailed distribution.
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Abstract
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.
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Affiliation(s)
- Manja Wachsmuth
- a University of Leipzig ; Institute for Biochemistry ; Leipzig , Germany
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Serfling R, Ogola G. Probability modeling of the number of positive cores in a prostate cancer biopsy session, with applications. Stat Med 2015; 35:424-54. [PMID: 26337506 DOI: 10.1002/sim.6636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 08/02/2015] [Accepted: 08/10/2015] [Indexed: 11/11/2022]
Abstract
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.
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Affiliation(s)
- Robert Serfling
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, 75080, TX, U.S.A
| | - Gerald Ogola
- Center for Clinical Effectiveness, Office of the Chief Quality Officer, Baylor Scott and White Health, 8080 N. Central Expressway, Suite 500, Dallas, 75206, TX, U.S.A
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Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ. A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Res 2012; 40:e50. [PMID: 22228832 PMCID: PMC3326300 DOI: 10.1093/nar/gkr1135] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
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.
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Affiliation(s)
- Xiaotu Ma
- Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, 800 W. Campbell Road, Richardson, TX 75080, USA
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Dang X, Serfling R. A numerical study of multiple imputation methods using nonparametric multivariate outlier identifiers and depth-based performance criteria with clinical laboratory data. J STAT COMPUT SIM 2011. [DOI: 10.1080/00949650903437842] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Serfling R. Equivariance and invariance properties of multivariate quantile and related functions, and the role of standardisation. J Nonparametr Stat 2010. [DOI: 10.1080/10485250903431710] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Brunner E, Puri M, Serfling R. Editorial for the special issue on ‘Papers inspired by the Workshop “Nonparametric Statistics: Refined, Redefined, and Renewed”’. J Nonparametr Stat 2010. [DOI: 10.1080/10485251003773944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Zhou W, Serfling R. Multivariate spatial U-quantiles: A Bahadur–Kiefer representation, a Theil–Sen estimator for multiple regression, and a robust dispersion estimator. J Stat Plan Inference 2008. [DOI: 10.1016/j.jspi.2007.05.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Affiliation(s)
- Robert Serfling
- Department of Mathematical Sciences, University of Texas at Dallas
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Serfling R, Shulman M, Thompson GL, Xiao Z, Benaim E, Roehrborn CG, Rittmaster R. Quantifying the Impact of Prostate Volumes, Number of Biopsy Cores and 5α-Reductase Inhibitor Therapy on the Probability of Prostate Cancer Detection Using Mathematical Modeling. J Urol 2007; 177:2352-6. [PMID: 17509357 DOI: 10.1016/j.juro.2007.01.116] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Indexed: 11/24/2022]
Abstract
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.
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Affiliation(s)
- Robert Serfling
- Department of Mathematical Sciences, University of Texas at Dallas, Richardson, TX 75083, USA.
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Leitner P, Serfling R. [The value of psychopharmacotherapy in the treatment of borderline personality disorder]. Psychiatr Prax 1993; 20:207-10. [PMID: 7906044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The interest in the psychopharmacological treatment of the borderline personality disorder (BPS) has been steadily increased in the last years. There isn't, however, any investigation, which has proved the existence of a specific "Anti-Borderline-Drug" yet. There are, however, identifiable drug-responsive syndromes. The description by Coccaro and Karoussi (1991) of a syndrome of affective instability (abnormalities in the brain's adrenergic and cholinergic systems, respond to carbamazepine and lithium), transient psychotic phenomena (abnormalities in the central dopaminergic systems, respond to low-dose neuroleptics) and impulsive, aggressive behaviour (abnormalities in the central serotonergic systems, respond to serotonergic agents) seems to be very promising in this regard.
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Affiliation(s)
- P Leitner
- Klinikum Berlin-Buch, Psychiatrische Klinik, Berlin
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Janssen P, Serfling R, Veraverbeke N. Asymptotic Normality for a General Class of Statistical Functions and Applications to Measures of Spread. Ann Stat 1984. [DOI: 10.1214/aos/1176346797] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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