Prof. Dr. Phillipp Torkler

Professor


Zeitschriftenartikel
  • E. Margolis
  • G. Brown
  • A. Partin
  • B. Carter
  • J. McKiernan
  • R. Tutrone
  • Phillipp Torkler
  • C. Fischer
  • V. Tadigotla
  • M. Noerholm
  • M. Donovan
  • J. Skog
Predicting high-grade prostate cancer at initial biopsy: clinical performance of the ExoDx (EPI) Prostate Intelliscore test in three independent prospective studies

In: Prostate Cancer and Prostatic Diseases

  • 2021

DOI: 10.1038/s41391-021-00456-8

BACKGROUND The ability to discriminate indolent from clinically significant prostate cancer (PC) at the initial biopsy remains a challenge. The ExoDx Prostate (IntelliScore) (EPI) test is a noninvasive liquid biopsy that quantifies three RNA targets in urine exosomes. The EPI test stratifies patients for risk of high-grade prostate cancer (HGPC; ≥ Grade Group 2 [GG] PC) in men ≥ 50 years with equivocal prostate-specific antigen (PSA) (2-10 ng/mL). Here, we present a pooled meta-analysis from three independent prospective-validation studies in men presenting for initial biopsy decision. METHODS Pooled data from two prospective multi-site validation studies and the control arm of a clinical utility study were analyzed. Performance was evaluated using the area under the receiver-operating characteristic curve (AUC), negative predictive value (NPV), positive predictive value (PPV), sensitivity, and specificity for discriminating ≥ GG2 from GG1 and benign pathology. RESULTS The combined cohort (n = 1212) of initial-biopsy subjects had a median age of 63 years and median PSA of 5.2 ng/mL. The EPI AUC (0.70) was superior to PSA (0.56), Prostate Cancer Prevention Trial Risk Calculator (PCPT-RC) (0.62), and The European Randomized Study of Screening for Prostate Cancer (ERSPC) (0.59), (all p-values <0.001) for discriminating GG2 from GG1 and benign histology. The validated cutoff of 15.6 would avoid 23% of all prostate biopsies and 30% of "unnecessary" (benign or Gleason 6/GG1) biopsies, with an NPV of 90%. CONCLUSIONS EPI is a noninvasive, easy-to-use, urine exosome-RNA assay that has been validated across 3 independent prospective multicenter clinical trials with 1212 subjects. The test can discriminate high-grade (≥GG2) from low-grade (GG1) cancer and benign disease. EPI effectively guides the biopsy-decision process independent of PSA and other standard-of-care factors.
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Zeitschriftenartikel
  • R. Tutrone
  • M. Donovan
  • Phillipp Torkler
  • V. Tadigotla
  • T. McLain
  • M. Noerholm
  • J. Skog
  • J. McKiernan
Clinical utility of the exosome based ExoDx Prostate(IntelliScore) EPI test in men presenting for initial Biopsy with a PSA 2-10 ng/mL, vol. 23, pg. 607-614.

In: Prostate Cancer and Prostatic Diseases

  • 2020

DOI: 10.1038/s41391-020-0237-z

BACKGROUND The ExoDx Prostate(IntelliScore) (EPI) test is a non-invasive risk assessment tool for detection of high-grade prostate cancer (HGPC) that informs whether to proceed with prostate biopsy. We sought to assess the impact of EPI on the decision to biopsy in a real-world clinical setting. METHODS We conducted a prospective, randomized, blinded, two-armed clinical utility study that enrolled 1094 patients with 72 urologists from 24 urology practices. Patients were considered for prostate biopsy at enrollment based on standard clinical criteria. All patients had an EPI test; however, patients were randomized into EPI vs. control arms where only the EPI arm received results for their biopsy decision. RESULTS In the EPI arm (N = 458), 93 patients received negative EPI scores of which 63% were recommended to defer biopsy by the urologist and 74% ultimately deferred. In contrast, 87% of patients with positive EPI scores were recommended to undergo biopsy with a 72% compliance rate to the urologist's recommendation. This led to detection of 30% more HGPC compared to the control arm, and we estimate that 49% fewer HGPC were missed due to deferrals compared to standard of care (SOC). Overall, 68% of urologists reported that the EPI test influenced their biopsy decision. The primary reason not to comply with EPI results was rising PSA. CONCLUSION To our knowledge this is the first report on a PC biomarker utility study with a blinded control arm. The study demonstrates that the EPI test influences the overall decision to defer or proceed with a biopsy and improves patient stratification.
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Zeitschriftenartikel
  • J. McKiernan
  • M. Noerholm
  • V. Tadigotla
  • S. Kumar
  • Phillipp Torkler
  • G. Sant
  • J. Alter
  • M. Donovan
  • J. Skog
A urine-based Exosomal gene expression test stratifies risk of high-grade prostate Cancer in men with prior negative prostate biopsy undergoing repeat biopsy, vol. 20

In: BMC Urology

  • 2020

DOI: 10.1186/s12894-020-00712-4

BACKGROUND Initial prostate biopsy often fails to identify prostate cancer resulting in patient anxiety, especially when clinical features such as prostate specific antigen (PSA) remain elevated, leading to the need for repeat biopsies. Prostate biomarker tests, such as the ExoDx™ Prostate (IntelliScore), or EPI test, have been shown to provide individualized risk assessment of clinically significant prostate cancer at initial biopsy; however, the performance in the repeat biopsy setting is not well established. METHODS As part of a previous prospective clinical validation study evaluating the performance of the EPI test, we collected first-catch, non-DRE urine samples across 22 sites from men with at least one prior negative biopsy scheduled to undergo a repeat prostate biopsy to rule out prostate cancer. All men were 50 years or older with a PSA 2-10 ng/mL. Exosomal mRNA was extracted and expression of three genomic markers, PCA3, ERG and SPDEF was measured. The resulting EPI score was correlated with biopsy results. RESULTS 229 men with a prior negative biopsy underwent repeat biopsies. ExoDx Prostate demonstrated good performance ruling out high-grade (Grade group 2, GG2, or higher) prostate cancer (HGPCa) using the previously validated 15.6 cut point in the initial biopsy setting. The EPI test yielded an NPV of 92% independent of other clinical features and would have avoided 26% of unnecessary biopsies while missing only five patients with HGPCa (2.1%). Furthermore, the EPI test provided additional information at a cut-point of 20 and 29.6 with an NPV of 94%, potentially delaying 35 and 61% of unnecessary biopsies, respectively. AUC curves and Net Health Benefit Analyses demonstrated superior performance of ExoDx Prostate over PSA and clinical only risk calculators, i.e. ERSPC. CONCLUSIONS The EPI test provided good performance using the 15.6 cut-point for ruling out HGPCa / GG2 or higher in men undergoing a repeat prostate biopsy with a PSA of 2-10 ng/ml. Furthermore, the test utilizes gene expression data independent of clinical features to predict the likelihood of HGPCa / GG2 on a subsequent needle biopsy.
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Zeitschriftenartikel
  • J. McKiernan
  • M. Donovan
  • E. Margolis
  • A. Partin
  • Ballentine Carter
  • G. Brown
  • Phillipp Torkler
  • M. Noerholm
  • J. Skog
  • N. Shore
  • G. Andriole
  • I. Thompson
  • P. Carroll
A Prospective Adaptive Utility Trial to Validate Performance of a Novel Urine Exosome Gene Expression Assay to Predict High-grade Prostate Cancer in Patients with Prostate-specific Antigen 2-10ng/ml at Initial Biopsy, vol. 74, pg. 731-738.

In: European Urology

  • 2018

DOI: 10.1016/j.eururo.2018.08.019

BACKGROUND Discriminating indolent from clinically significant prostate cancer (PCa) in the initial biopsy setting remains an important issue. Prospectively evaluated diagnostic assays are necessary to ensure efficacy and clinical adoption. OBJECTIVE Performance and utility assessment of ExoDx Prostate (IntelliScore) (EPI) urine exosome gene expression assay versus standard clinical parameters for discriminating Grade Group (GG) ≥2 PCa from GG1 PCa and benign disease on initial biopsy. DESIGN, SETTING, AND PARTICIPANTS A two-phase adaptive clinical utility study (NCT03031418) comparing EPI results with biopsy outcomes in men, with age ≥50 yr and prostate-specific antigen (PSA) 2-10ng/ml, scheduled for initial prostate biopsy. After EPI performance assessment during phase I, a clinical implementation document (ie, CarePath) was developed for utilizing the EPI test in phase II, where the biopsy decision is uncertain. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Performance evaluation of the EPI test in patients enrolled in phase I and publication of a consensus CarePath for phase II. RESULTS AND LIMITATIONS In a total of 503 patients, with median age of 64 yr, median PSA 5.4ng/ml, 14% African American, 70% Caucasian, 53% positive biopsy rate (22% GG1, 17% GG2, and 15% ≥ GG3), EPI was superior to an optimized model of standard clinical parameters with an area under the curve (AUC) 0.70 versus 0.62, respectively, comparable with previously published results (n=519 patients, EPI AUC 0.71). Validated cut-point 15.6 would avoid 26% of unnecessary prostate biopsies and 20% of total biopsies, with negative predictive value (NPV) 89% and missing 7% of ≥GG2 PCa. Alternative cut-point 20 would avoid 40% of unnecessary biopsies and 31% of total biopsies, with NPV 89% and missing 11% of ≥GG2 PCa. The clinical investigators reached consensus recommending use of the 15.6 cut-point for phase II. Outcome of the decision impact cohort in phase II will be reported separately. CONCLUSIONS EPI is a noninvasive, easy-to-use, gene expression urine assay, which has now been successfully validated in over 1000 patients across two prospective validation trials to stratify risk of ≥GG2 from GG1 cancer and benign disease. The test improves identification of patients with higher grade disease and would reduce the total number of unnecessary biopsies. PATIENT SUMMARY It is challenging to predict which men are likely to have high-grade prostate cancer (PCa) at initial biopsy with prostate-specific antigen 2-10ng/ml. This study further demonstrates that the ExoDx Prostate (IntelliScore) test can predict ≥GG2 PCa at initial biopsy and defer unnecessary biopsies better than existing risk calculator's and standard clinical data.
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Zeitschriftenartikel
  • C. Baejen
  • J. Andreani
  • Phillipp Torkler
  • S. Battaglia
  • B. Schwalb
  • M. Lidschreiber
  • K. Maier
  • A. Boltendahl
  • P. Rus
  • S. Esslinger
  • J. Söding
  • P. Cramer
Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes, vol. 66, pg. 38-49.

In: Molecular Cell

  • 2017

DOI: 10.1016/j.molcel.2017.02.009

At the end of protein-coding genes, RNA polymerase (Pol) II undergoes a concerted transition that involves 3'-processing of the pre-mRNA and transcription termination. Here, we present a genome-wide analysis of the 3'-transition in budding yeast. We find that the 3'-transition globally requires the Pol II elongation factor Spt5 and factors involved in the recognition of the polyadenylation (pA) site and in endonucleolytic RNA cleavage. Pol II release from DNA occurs in a narrow termination window downstream of the pA site and requires the "torpedo" exonuclease Rat1 (XRN2 in human). The Rat1-interacting factor Rai1 contributes to RNA degradation downstream of the pA site. Defects in the 3'-transition can result in increased transcription at downstream genes.
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Zeitschriftenartikel
  • S. Battaglia
  • M. Lidschreiber
  • C. Baejen
  • Phillipp Torkler
  • S. Vos
  • P. Cramer
RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases, vol. 6

In: eLife

  • 2017

DOI: 10.7554/eLife.25637

For transcription through chromatin, RNA polymerase (Pol) II associates with elongation factors (EFs). Here we show that many EFs crosslink to RNA emerging from transcribing Pol II in the yeast Saccharomyces cerevisiae. Most EFs crosslink preferentially to mRNAs, rather than unstable non-coding RNAs. RNA contributes to chromatin association of many EFs, including the Pol II serine 2 kinases Ctk1 and Bur1 and the histone H3 methyltransferases Set1 and Set2. The Ctk1 kinase complex binds RNA in vitro, consistent with direct EF-RNA interaction. Set1 recruitment to genes in vivo depends on its RNA recognition motifs (RRMs). These results strongly suggest that nascent RNA contributes to EF recruitment to transcribing Pol II. We propose that EF-RNA interactions facilitate assembly of the elongation complex on transcribed genes when RNA emerges from Pol II, and that loss of EF-RNA interactions upon RNA cleavage at the polyadenylation site triggers disassembly of the elongation complex.
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Zeitschriftenartikel
  • C. Baejen
  • Phillipp Torkler
  • S. Gressel
  • K. Essig
  • J. Söding
  • P. Cramer
Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition, vol. 55, pg. 745-57.

In: Molecular Cell

  • 2014

DOI: 10.1016/j.molcel.2014.08.005

Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the synthesis, splicing, and 3' processing of pre-mRNA, and the assembly of mature mRNPs for nuclear export. We mapped 23 mRNP biogenesis factors onto the yeast transcriptome, providing 10(4)-10(6) high-confidence RNA interaction sites per factor. The data reveal how mRNP biogenesis factors recognize pre-mRNA elements in vivo. They define conserved interactions between splicing factors and pre-mRNA introns, including the recognition of intron-exon junctions and the branchpoint. They also identify a unified arrangement of 3' processing factors at pre-mRNA polyadenylation (pA) sites in yeast and human, which results from an A-U sequence bias at pA sites. Global data analysis indicates that 3' processing factors have roles in splicing and RNA surveillance, and that they couple mRNP biogenesis events to restrict nuclear export to mature mRNPs.
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Zeitschriftenartikel
  • D. Schulz
  • B. Schwalb
  • A. Kiesel
  • C. Baejen
  • Phillipp Torkler
  • J. Gagneur
  • J. Soeding
  • P. Cramer
Transcriptome surveillance by selective termination of noncoding RNA synthesis, vol. 155, pg. 1075-87.

In: Cell

  • 2013

DOI: 10.1016/j.cell.2013.10.024

Pervasive transcription of eukaryotic genomes stems to a large extent from bidirectional promoters that synthesize mRNA and divergent noncoding RNA (ncRNA). Here, we show that ncRNA transcription in the yeast S. cerevisiae is globally restricted by early termination that relies on the essential RNA-binding factor Nrd1. Depletion of Nrd1 from the nucleus results in 1,526 Nrd1-unterminated transcripts (NUTs) that originate from nucleosome-depleted regions (NDRs) and can deregulate mRNA synthesis by antisense repression and transcription interference. Transcriptome-wide Nrd1-binding maps reveal divergent NUTs at most promoters and antisense NUTs in most 3' regions of genes. Nrd1 and its partner Nab3 preferentially bind RNA motifs that are depleted in mRNAs and enriched in ncRNAs and some mRNAs whose synthesis is controlled by transcription attenuation. These results define a global mechanism for transcriptome surveillance that selectively terminates ncRNA synthesis to provide promoter directionality and to suppress antisense transcription.
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Zeitschriftenartikel
  • P. Smialowski
  • G. Doose
  • Phillipp Torkler
  • S. Kaufmann
  • D. Frishman
PROSO II--a new method for protein solubility prediction, vol. 279, pg. 2192-200.

In: The FEBS Journal

  • 2012

DOI: 10.1111/j.1742-4658.2012.08603.x

Many fields of science and industry depend on efficient production of active protein using heterologous expression in Escherichia coli. The solubility of proteins upon expression is dependent on their amino acid sequence. Prediction of solubility from sequence is therefore highly valuable. We present a novel machine-learning-based model called PROSO II which makes use of new classification methods and growth in experimental data to improve coverage and accuracy of solubility predictions. The classification algorithm is organized as a two-layered structure in which the output of a primary Parzen window model for sequence similarity and a logistic regression classifier of amino acid k-mer composition serve as input for a second-level logistic regression classifier. Compared with previously published research our model is trained on five times more data than used by any other method before (82 000 proteins). When tested on a separate holdout set not used at any point of method development our server attained the best results in comparison with other currently available methods: accuracy 75.4%, Matthew's correlation coefficient 0.39, sensitivity 0.731, specificity 0.759, gain (soluble) 2.263. In summary, due to utilization of cutting edge machine learning technologies combined with the largest currently available experimental data set the PROSO II server constitutes a substantial improvement in protein solubility predictions. PROSO II is available at http://mips.helmholtz-muenchen.de/prosoII.
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Zeitschriftenartikel
  • B. Zacher
  • Phillipp Torkler
  • A. Tresch
Analysis of Affymetrix ChIP-chip data using starr and R/Bioconductor, vol. 2011

In: Cold Spring Harbor Protocols

  • 2011

DOI: 10.1101/pdb.top110

This article provides a flexible workflow for the analysis of chromatin immunoprecipitation data (ChIP-chip) that covers issues from quality control, probe sequence remapping, data preprocessing/normalization, visualization, and high-level analysis like peak finding. It emphasizes the peculiarities of single-color Affymetrix arrays, but it is flexible enough to be also amenable to other array platforms. The article is accompanied by extensive code implementing each of the analysis steps.
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