Using Persistent Homology as a New Approach for Super-Resolution Localization Microscopy Data Analysis and Classification of γH2AX Foci/Clusters

• Published in: International journal of molecular sciences Vol. 19; no. 8; p. 2263
• Main Authors: Hofmann, Andreas, Krufczik, Matthias, Heermann, Dieter W, Hausmann, Michael
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 02.08.2018; MDPI
• Subjects: Cell Line; Chromatin; Data processing; Deoxyribonucleic acid; DNA; DNA Breaks, Double-Stranded; DNA damage; DNA double strand breaks; DNA Repair; Double-strand break repair; Fluorescence; foci/cluster classification relative to heterochromatin; Genomes; Heterochromatin; Heterochromatin - chemistry; Heterochromatin - genetics; Histones - analysis; Histones - genetics; Homologous recombination; Homologous recombination repair; Homology; Humans; Ionizing radiation; Linear energy transfer (LET); Localization; Microscopy; Microscopy, Fluorescence - methods; Multigene Family; Non-homologous end joining; Nuclei (cytology); Parameterization; persistent homology; Phosphorylation; Proteins; Radiation damage; Repair; Similarity; similarity measure; single-molecule localization microscopy; Spatial distribution; Topology; γH2AX formation; similarity measure; foci/cluster classification relative to heterochromatin; topology; γH2AX formation; persistent homology; DNA double strand breaks; single-molecule localization microscopy
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms19082263

DNA double strand breaks (DSB) are the most severe damages in chromatin induced by ionizing radiation. In response to such environmentally determined stress situations, cells have developed repair mechanisms. Although many investigations have contributed to a detailed understanding of repair processes, e.g., homologous recombination repair or non-homologous end-joining, the question is not sufficiently answered, how a cell decides to apply a certain repair process at a certain damage site, since all different repair pathways could simultaneously occur in the same cell nucleus. One of the first processes after DSB induction is phosphorylation of the histone variant H2AX to γH2AX in the given surroundings of the damaged locus. Since the spatial organization of chromatin is not random, it may be conclusive that the spatial organization of γH2AX foci is also not random, and rather, contributes to accessibility of special repair proteins to the damaged site, and thus, to the following repair pathway at this given site. The aim of this article is to demonstrate a new approach to analyze repair foci by their topology in order to obtain a cell independent method of categorization. During the last decade, novel super-resolution fluorescence light microscopic techniques have enabled new insights into genome structure and spatial organization on the nano-scale in the order of 10 nm. One of these techniques is single molecule localization microscopy (SMLM) with which the spatial coordinates of single fluorescence molecules can precisely be determined and density and distance distributions can be calculated. This method is an appropriate tool to quantify complex changes of chromatin and to describe repair foci on the single molecule level. Based on the pointillist information obtained by SMLM from specifically labeled heterochromatin and γH2AX foci reflecting the chromatin morphology and repair foci topology, we have developed a new analytical methodology of foci or foci cluster characterization, respectively, by means of persistence homology. This method allows, for the first time, a cell independent comparison of two point distributions (here the point distributions of two γH2AX clusters) with each other of a selected ensample and to give a mathematical measure of their similarity. In order to demonstrate the feasibility of this approach, cells were irradiated by low LET (linear energy transfer) radiation with different doses and the heterochromatin and γH2AX foci were fluorescently labeled by antibodies for SMLM. By means of our new analysis method, we were able to show that the topology of clusters of γH2AX foci can be categorized depending on the distance to heterochromatin. This method opens up new possibilities to categorize spatial organization of point patterns by parameterization of topological similarity.