Detail publikace

DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double-Strand Break Ionizing Radiation-Induced Foci

VIČAR, T. GUMULEC, J. KOLÁŘ, R. KOPEČNÁ, O. PAGÁČOVÁ, E. FALKOVÁ, I. FALK, M.

Originální název

DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double-Strand Break Ionizing Radiation-Induced Foci

Typ

článek v časopise ve Web of Science, Jimp

Jazyk

angličtina

Originální abstrakt

DNA double-strand breaks (DSBs), marked by ionizing radiation-induced (repair) foci (IRIFs), are the most serious DNA lesions and are dangerous to human health. IRIF quantification based on confocal microscopy represents the most sensitive and gold-standard method in radiation biodosimetry and allows research on DSB induction and repair at the molecular and single-cell levels. In this study, we introduce DeepFoci – a deep learning-based fully automatic method for IRIF counting and morphometric analysis. DeepFoci is designed to work with 3D multichannel data (trained for 53BP1 and γH2AX) and uses U-Net for nucleus segmentation and IRIF detection, together with maximally stable extremal region-based IRIF segmentation. The proposed method was trained and tested on challenging datasets consisting of mixtures of nonirradiated and irradiated cells of different types and IRIF characteristics – permanent cell lines (NHDFs, U-87) and primary cell cultures prepared from tumors and adjacent normal tissues of head and neck cancer patients. The cells were dosed with 0.5–8 Gy γ-rays and fixed at multiple (0–24 h) postirradiation times. Under all circumstances, DeepFoci quantified the number of IRIFs with the highest accuracy among current advanced algorithms. Moreover, while the detection error of DeepFoci remained comparable to the variability between two experienced experts, the software maintained its sensitivity and fidelity across dramatically different IRIF counts per nucleus. In addition, information was extracted on IRIF 3D morphometric features and repair protein colocalization within IRIFs. This approach allowed multiparameter IRIF categorization of single- or multichannel data, thereby refining the analysis of DSB repair processes and classification of patient tumors, with the potential to identify specific cell subclones. The developed software improves IRIF quantification for various practical applications (radiotherapy monitoring, biodosimetry, etc.) and opens the door to advanced DSB focus analysis and, in turn, a better understanding of (radiation-induced) DNA damage and repair.

Klíčová slova

DNA Damage and Repair; Ionizing Radiation-Induced Foci (IRIFs); Biodosimetry; Deep Learning; Convolutional Neural Network; Morphometry; Confocal Microscopy; Image Analysis

Autoři

VIČAR, T.; GUMULEC, J.; KOLÁŘ, R.; KOPEČNÁ, O.; PAGÁČOVÁ, E.; FALKOVÁ, I.; FALK, M.

Vydáno

24. 9. 2021

Nakladatel

Elsevier

ISSN

2001-0370

Periodikum

Computational and Structural Biotechnology Journal

Ročník

19

Číslo

1

Stát

Švédské království

Strany od

1

Strany do

16

Strany počet

16

URL

https://www.sciencedirect.com/science/article/pii/S2001037021004840

Plný text v Digitální knihovně

http://hdl.handle.net/11012/203247

BibTex

@article{BUT173240,
  author="Tomáš {Vičar} and Jaromír {Gumulec} and Radim {Kolář} and Olga {Kopečná} and Eva {Pagáčová} and Iva {Falková} and Martin {Falk}",
  title="DeepFoci: Deep Learning-Based Algorithm for Fast Automatic Analysis of DNA Double-Strand Break Ionizing Radiation-Induced Foci",
  journal="Computational and Structural Biotechnology Journal",
  year="2021",
  volume="19",
  number="1",
  pages="1--16",
  doi="10.1016/j.csbj.2021.11.019",
  issn="2001-0370",
  url="https://www.sciencedirect.com/science/article/pii/S2001037021004840"
}