Severance+Hospital
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KAIST Develops Virtual Staining Technology for 3D Histopathology
Moving beyond traditional methods of observing thinly sliced and stained cancer tissues, a collaborative international research team led by KAIST has successfully developed a groundbreaking technology. This innovation uses advanced optical techniques combined with an artificial intelligence-based deep learning algorithm to create realistic, virtually stained 3D images of cancer tissue without the need for serial sectioning nor staining. This breakthrough is anticipated to pave the way for next-generation non-invasive pathological diagnosis.
< Photo 1. (From left) Juyeon Park (Ph.D. Candidate, Department of Physics), Professor YongKeun Park (Department of Physics) (Top left) Professor Su-Jin Shin (Gangnam Severance Hospital), Professor Tae Hyun Hwang (Vanderbilt University School of Medicine) >
KAIST (President Kwang Hyung Lee) announced on the 26th that a research team led by Professor YongKeun Park of the Department of Physics, in collaboration with Professor Su-Jin Shin's team at Yonsei University Gangnam Severance Hospital, Professor Tae Hyun Hwang's team at Mayo Clinic, and Tomocube's AI research team, has developed an innovative technology capable of vividly displaying the 3D structure of cancer tissues without separate staining.
For over 200 years, conventional pathology has relied on observing cancer tissues under a microscope, a method that only shows specific cross-sections of the 3D cancer tissue. This has limited the ability to understand the three-dimensional connections and spatial arrangements between cells.
To overcome this, the research team utilized holotomography (HT), an advanced optical technology, to measure the 3D refractive index information of tissues. They then integrated an AI-based deep learning algorithm to successfully generate virtual H&E* images.* H&E (Hematoxylin & Eosin): The most widely used staining method for observing pathological tissues. Hematoxylin stains cell nuclei blue, and eosin stains cytoplasm pink.
The research team quantitatively demonstrated that the images generated by this technology are highly similar to actual stained tissue images. Furthermore, the technology exhibited consistent performance across various organs and tissues, proving its versatility and reliability as a next-generation pathological analysis tool.
< Figure 1. Comparison of conventional 3D tissue pathology procedure and the 3D virtual H&E staining technology proposed in this study. The traditional method requires preparing and staining dozens of tissue slides, while the proposed technology can reduce the number of slides by up to 10 times and quickly generate H&E images without the staining process. >
Moreover, by validating the feasibility of this technology through joint research with hospitals and research institutions in Korea and the United States, utilizing Tomocube's holotomography equipment, the team demonstrated its potential for full-scale adoption in real-world pathological research settings.
Professor YongKeun Park stated, "This research marks a major advancement by transitioning pathological analysis from conventional 2D methods to comprehensive 3D imaging. It will greatly enhance biomedical research and clinical diagnostics, particularly in understanding cancer tumor boundaries and the intricate spatial arrangements of cells within tumor microenvironments."
< Figure 2. Results of AI-based 3D virtual H&E staining and quantitative analysis of pathological tissue. The virtually stained images enabled 3D reconstruction of key pathological features such as cell nuclei and glandular lumens. Based on this, various quantitative indicators, including cell nuclear distribution, volume, and surface area, could be extracted. >
This research, with Juyeon Park, a student of the Integrated Master’s and Ph.D. Program at KAIST, as the first author, was published online in the prestigious journal Nature Communications on May 22.
(Paper title: Revealing 3D microanatomical structures of unlabeled thick cancer tissues using holotomography and virtual H&E staining.
[https://doi.org/10.1038/s41467-025-59820-0]
This study was supported by the Leader Researcher Program of the National Research Foundation of Korea, the Global Industry Technology Cooperation Center Project of the Korea Institute for Advancement of Technology, and the Korea Health Industry Development Institute.
2025.05.26 View 1437 -
Accurate Detection of Low-Level Somatic Mutation in Intractable Epilepsy
KAIST medical scientists have developed an advanced method for perfectly detecting low-level somatic mutation in patients with intractable epilepsy. Their study showed that deep sequencing replicates of major focal epilepsy genes accurately and efficiently identified low-level somatic mutations in intractable epilepsy.
According to the study, their diagnostic method could increase the accuracy up to 100%, unlike the conventional sequencing analysis, which stands at about 30% accuracy. This work was published in Acta Neuropathologica.
Epilepsy is a neurological disorder common in children. Approximately one third of child patients are diagnosed with intractable epilepsy despite adequate anti-epileptic medication treatment.
Somatic mutations in mTOR pathway genes, SLC35A2, and BRAF are the major genetic causes of intractable epilepsies. A clinical trial to target Focal Cortical Dysplasia type II (FCDII), the mTOR inhibitor is underway at Severance Hospital, their collaborator in Seoul, Korea. However, it is difficult to detect such somatic mutations causing intractable epilepsy because their mutational burden is less than 5%, which is similar to the level of sequencing artifacts. In the clinical field, this has remained a standing challenge for the genetic diagnosis of somatic mutations in intractable epilepsy.
Professor Jeong Ho Lee’s team at the Graduate School of Medical Science and Engineering analyzed paired brain and peripheral tissues from 232 intractable epilepsy patients with various brain pathologies at Severance Hospital using deep sequencing and extracted the major focal epilepsy genes.
They narrowed down target genes to eight major focal epilepsy genes, eliminating almost all of the false positive calls using deep targeted sequencing. As a result, the advanced method robustly increased the accuracy and enabled them to detect low-level somatic mutations in unmatched Formalin Fixed Paraffin Embedded (FFPE) brain samples, the most clinically relevant samples.
Professor Lee conducted this study in collaboration with Professor Dong Suk Kim and Hoon-Chul Kang at Severance Hospital of Yonsei University. He said, “This advanced method of genetic analysis will improve overall patient care by providing more comprehensive genetic counseling and informing decisions on alternative treatments.”
Professor Lee has investigated low-level somatic mutations arising in the brain for a decade. He is developing innovative diagnostics and therapeutics for untreatable brain disorders including intractable epilepsy and glioblastoma at a tech-startup called SoVarGen. “All of the technologies we used during the research were transferred to the company. This research gave us very good momentum to reach the next phase of our startup,” he remarked.
The work was supported by grants from the Suh Kyungbae Foundation, a National Research Foundation of Korea grant funded by the Ministry of Science and ICT, the Korean Health Technology R&D Project from the Ministry of Health & Welfare, and the Netherlands Organization for Health Research and Development.
(Figure: Landscape of somatic and germline mutations identified in intractable epilepsy patients. a Signaling pathways for all of the mutated genes identified in this study. Bold: somatic mutation, Regular: germline mutation. b The distribution of variant allelic frequencies (VAFs) of identified somatic mutations. c The detecting rate and types of identified mutations according to histopathology. Yellow: somatic mutations, green: two-hit mutations, grey: germline mutations.)
2019.08.14 View 29691