title: Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow.
abstract: The microscopic analysis of telomere features provides a wealth of information on the mechanism by which tumor cells maintain their unlimited proliferative potential. Accordingly, the analysis of telomeres in tissue sections of patient tumor samples can be exploited to obtain diagnostic information and to define tumor subgroups. In many instances, however, analysis of the image data is conducted by manual inspection of 2D images at relatively low resolution for only a small part of the sample. As the telomere feature signal distribution is frequently heterogeneous, this approach is prone to a biased selection of the information present in the image and lacks subcellular details. Here we address these issues by using an automated high-resolution imaging and analysis workflow that quantifies individual telomere features on tissue sections for a large number of cells. The approach is particularly suited to assess telomere heterogeneity and low abundant cellular subpopulations with distinct telomere characteristics in a reproducible manner. It comprises the integration of multi-color fluorescence in situ hybridization, immunofluorescence and DNA staining with targeted automated 3D fluorescence microscopy and image analysis. We apply our method to telomeres in glioblastoma and prostate cancer samples, and describe how the imaging data can be used to derive statistically reliable information on telomere length distribution or colocalization with PML nuclear bodies. We anticipate that relating this approach to clinical outcome data will prove to be valuable for pretherapeutic patient stratification.
authors.affiliation: VIROQUANT CellNetworks RNAi Screening Facility and Research Group High-Content Analysis of the Cell (HiCell), Bioquant Center, University of Heidelberg, Germany.
authors.forename: Manuel
authors.initials: M
authors.lastname: Gunkel
authors.affiliation: Research Group Genome Organization & Function, German Cancer Research Center (DKFZ) and Bioquant Center, Germany. Electronic address: i.chung@dkfz.de.
authors.forename: Inn
authors.initials: I
authors.lastname: Chung
authors.affiliation: Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, Bioquant Center and IPMB, University of Heidelberg and German Cancer Research Center (DKFZ), Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wörz
authors.affiliation: Research Group Genome Organization & Function, German Cancer Research Center (DKFZ) and Bioquant Center, Germany.
authors.forename: Katharina I
authors.initials: KI
authors.lastname: Deeg
authors.affiliation: Department of Pathology, University Medical Center Hamburg-Eppendorf, Germany.
authors.forename: Ronald
authors.initials: R
authors.lastname: Simon
authors.affiliation: Department of Pathology, University Medical Center Hamburg-Eppendorf, Germany.
authors.forename: Guido
authors.initials: G
authors.lastname: Sauter
authors.affiliation: Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Germany.
authors.forename: David T W
authors.initials: DTW
authors.lastname: Jones
authors.affiliation: Department of Neuropathology, Heidelberg University Hospital, Germany.
authors.forename: Andrey
authors.initials: A
authors.lastname: Korshunov
authors.affiliation: Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, Bioquant Center and IPMB, University of Heidelberg and German Cancer Research Center (DKFZ), Germany. Electronic address: k.rohr@dkfz.de.
authors.forename: Karl
authors.initials: K
authors.lastname: Rohr
authors.affiliation: VIROQUANT CellNetworks RNAi Screening Facility and Research Group High-Content Analysis of the Cell (HiCell), Bioquant Center, University of Heidelberg, Germany. Electronic address: holger.erfle@bioquant.uni-heidelberg.de.
authors.forename: Holger
authors.initials: H
authors.lastname: Erfle
authors.affiliation: Research Group Genome Organization & Function, German Cancer Research Center (DKFZ) and Bioquant Center, Germany. Electronic address: karsten.rippe@dkfz.de.
authors.forename: Karsten
authors.initials: K
authors.lastname: Rippe
mesh_terms: D001331:Automation; D002648:Child; D005455:Fluorescent Antibody Technique; D005909:Glioblastoma / Q000235:genetics* / Q000473:pathology; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence; D008297:Male; D018613:Microscopy, Confocal; D016612:Paraffin Embedding; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000473:pathology; D016615:Telomere; D057188:Workflow
keywords: Alternative lengthening of telomeres; FFPE tissue; Fluorescence microscopy; Glioblastoma; Image analysis; Prostate cancer