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Simultaneous Decoding of Genetic Maps Inside Cells... A Game Changer for Understanding Complex Human Diseases
< (Clockwise from top left) Professor Inkyung Jung (KAIST), Dr. Dongchan Yang (KAIST), Dr. Kyukwang Kim (KAIST), Dr. Yueyuan Xu (Duke University), Dr. Xiaolin Wei (Duke University), Professor Yarui Diao (Duke University) >
The origin of many diseases begins at the cellular level and involves multiple molecular interactions. However, previous methods have struggled to accurately observe changes in individual cells. Analyzing average values across thousands of cells made it challenging to detect the early signals of disease.
Our university's research team has pioneered groundbreaking technology that decodes the genetic blueprint within a cell in 3D, akin to zooming in on Earth using Google Earth. This innovation is poised to transform research into complex diseases such as cancer, dementia, and Parkinson's disease.
KAIST announced on March 4th that Professor Inkyung Jung's research team from the Department of Biological Sciences, in collaboration with Professor Yarui Diao's team at Duke University, has developed scHiCAR (single-cell Hi-C with assay for transposase-accessible chromatin and RNA sequencing). This is the world’s first ultra-high throughput & precise molecular map decoding technology that simultaneously analyzes gene expression (transcriptome), the epigenome, and the 3D genome structure within a single cell.
The key to determining a cell's state lies in how its genes operate. Genes are not simply switches that turn on and off. The destiny of a cell is determined by which genes are actually active (transcriptome), why they are active (epigenome), and within what spatial structure they operate (3D genome structure). Existing technologies required obtaining this information from different cells separately and then matching them afterward, which could lead to the distortion or omission of subtle changes.
The research team introduced ‘Trimodal Multi-omics’ technology, an integrated precision analysis method that concurrently examines these three types of genetic information within a single cell. By incorporating Artificial Intelligence (AI) analysis, they significantly enhanced accuracy and reproducibility, culminating in a unified platform that reads internal cellular genetic information akin to a ‘single 3D map.’
<Ultra-precision Single-cell Molecular Map>
Notably, the team succeeded in lowering the analysis cost to approximately $0.04 (approx. 50 KRW) per cell. Using this, they constructed a high-resolution molecular map of 1.6 million cells in mouse brain tissue. This means it is now possible to precisely identify when, where, and within what structure disease genes are turned on or off at the cellular level.
The research team applied this technology to brain tissue and the muscle regeneration process, revealing distinct gene operation principles across 22 major cell types. Notably, they successfully tracked in real-time how the 3D structure of genes dynamically changes to influence cell fate during muscle stem cell regeneration. This advancement is expected to lay a crucial foundation for developing treatment strategies for aging and incurable diseases.
<Research Result Image (AI-generated)>
Professor Inkyung Jung remarked, ‘This research transcends mere observation of cells; it opens the door to precisely reading and controlling the genomic blueprints within them. It represents a significant turning point in elucidating the developmental mechanisms of complex diseases like Parkinson's and cancer, as well as identifying target points for patient-specific new drugs.’
The study was published on February 19th in the international academic journal Nature Biotechnology (IF=46.9).
Paper Title: Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR
DOI: 10.1038/s41587-026-03013-7
Meanwhile, this research was conducted with support from the Suh Kyungbae Foundation, the Samsung Science and Technology Foundation, and the Basic Research Program and Bio-Medical Technology Development Program of the National Research Foundation of Korea (Ministry of Science and ICT).
2026.03.06 View 1143 -
Unraveling the Secret of Cell Movement
<(From left) Professor Won Do Heo (KAIST), Postdoctoral Researcher Heeyoung Lee (KAIST, First Author), Professor Kwang-Hyun Cho (KAIST), Professor Kapsang Lee (Johns Hopkins University, USA), Dr. Sangkyu Lee (IBS), Dr. Dongsan Kim (LIBD), Dr. Yeaji Seo (Hulux) (Co-First Authors)>
Cell movement is an essential biological process, whether it's cancer cells metastasizing to other parts of the body or immune cells migrating to heal a wound. However, the principle by which cells autonomously determine their direction of movement without external stimuli has remained unknown until now.
Through this research, KAIST and an international joint research team have elucidated the principle by which cells decide their direction and move on their own, offering a crucial clue for identifying the causes of cancer metastasis and immune diseases and establishing new treatment strategies.
KAIST announced on the 10th of November that the research team led by Endowed Chair Professor Won Do Heo of the Department of Biological Sciences, in collaboration with the research team of Endowed Chair Professor Kwang-Hyun Cho of the Department of Bio and Brain Engineering, and Professor Kapsang Lee's research team at Johns Hopkins University in the US, has for the first time in the world identified the 'autonomous driving mechanism' by which cells determine their direction of movement without external signals.
The research team developed a new imaging technique called 'INSPECT (INtracellular Separation of Protein Engineered Condensation Technique)' that allows direct visualization of how proteins interact within living cells. Using this technology, they revealed the principle of the cell's internal program for autonomously deciding its direction of movement.
The team newly analyzed the operation of the key proteins that regulate cell movement, the Rho family proteins (Rac1, Cdc42, RhoA). The results showed that these proteins do not merely divide the front and back of the cell, as previously theorized, but that the cell's decision to move straight or change direction depends on which protein it binds with.
The INSPECT technology artificially implements the phenomenon of 'phase separation,' where proteins, upon binding, naturally form segregated regions that do not mix well. This technique allows for the direct visualization of how proteins actually bind within the cell using a fluorescent signal.
<Figure 1. INSPECT: A technique for visualizing Intracellular Protein-Protein Interactions">
The research team used the proteins ferritin and the fluorescent protein DsRed to make the clusters, or 'condensates,' visible to the eye when proteins bind together like small droplets.
Using this technology, the team analyzed a total of 285 pairs of interactions by combining 15 types of Rho proteins with 19 types of binding proteins, confirming actual binding in 139 pairs. Specifically, they identified that the Cdc42–FMNL protein combination is the core circuit responsible for the cell's 'straight movement,' while the Rac1–ROCK protein combination is responsible for the cell's 'change of direction.'
The research team slightly modified a part of the Rac1 protein (the 37th amino acid), which is crucial for cell direction control, to prevent it from binding well with the 'steering wheel' protein, ROCK. As a result, the cells could not change direction and continued to move in a straight line.
In contrast, in normal cells, Rac1 and ROCK bind well, forming a structure called 'arc stress fiber' at the front of the cell. This fiber enables the cell to make near-perpendicular turns when changing direction.
Furthermore, in an experiment where the environment the cells were attached to was changed, normal cells adjusted their moving speed according to the surrounding environment, but the Rac1F37W cells (cells with a broken 'steering wheel') maintained the same speed regardless of environmental changes. This demonstrates that the Rac–ROCK protein axis subtly controls the cell's ability to recognize and adapt to its surrounding environment.
<Figure 2. Analysis of the Signaling Network through Screening of Protein Interactions that Bind to a Cell Migration-Controlling Protein>
Professor Won Do Heo stated, "This research reveals that cell movement is not a random motion but is precisely controlled by an intrinsic program created by the ensemble of Rho signaling proteins and cell migration-related proteins." He added, "The newly developed INSPECT technology is a powerful tool for visualizing intracellular protein interactions and will be broadly utilized to uncover the molecular mechanisms of various life phenomena and diseases, such as cancer metastasis and neuronal cell migration."
This research, in which Dr. Heeyoung Lee of KAIST, Dr. Sangkyu Lee (currently at IBS), Dr. Yeji Seo (currently at Hulux Co., Ltd.), and Dr. Dongsan Kim (currently at LIBD) participated as co-first authors, was published in Nature Communications on October 31st.
Journal Name: A Rho GTPase-effector ensemble governs cell migration behavior
DOI: https://doi.org/10.1038/s41467-025-64635-0
The research was supported by the Samsung Future Technology Foundation and the National Research Foundation of Korea.
2025.11.10 View 2141 -
KAIST Discovers Role of Huntingtin Protein in Building the Cell Skeleton
<(From Left) Professor Ji-Joon Song, Ph.D candidate Jaesung Kim, Dr. Hyeongju Kim of KAIST’s Department of Biological Sciences>
Huntington’s disease is a rare genetic disorder and a representative neurodegenerative disease, characterized by loss of motor control, cognitive decline, and psychiatric problems. An international research team has discovered that the “huntingtin protein,” the causal protein of Huntington’s disease (whose mutations are the direct cause of the disease), also performs a new function: directly organizing the cytoskeleton, the fine structural framework inside cells. This discovery is expected to contribute not only to understanding the pathogenic mechanism of Huntington’s disease, but also to research on neurodevelopmental disorders such as Alzheimer’s disease and Parkinson’s disease, as well as muscle- or mobility-related diseases such as muscular dystrophy.
KAIST (President Kwang Hyung Lee) announced on September 30 that a research team led by Professor Ji-Joon Song of the Department of Biological Sciences, in collaboration with the Institute of Science and Technology Austria (ISTA), Sorbonne University/Paris Brain Institute, and the Swiss Federal Institute of Technology Lausanne (EPFL), has uncovered—through cryo-electron microscopy (cryo-EM) and cell biology methods—the structural principle by which the huntingtin protein arranges cytoskeletal microfilaments (F-actin) into bundles.
Until now, the huntingtin protein was known only to “use” the cytoskeleton, being involved in vesicle transport or microtubule-based transport. The team, however, demonstrated that huntingtin physically organizes the cytoskeleton itself. This study is considered the first in the world to prove this new role of the huntingtin protein at the molecular level.
The researchers confirmed that huntingtin binds directly to cytoskeletal microfilaments (F-actin), and that pairs of huntingtin proteins bundle the cytoskeleton into arrays at intervals of about 20 nanometers.
Such cytoskeletal bundles play a crucial role in the development of neural connectivity. Indeed, structural development of neurons was found to be impaired in nerve cells deficient in the huntingtin protein.
<Elucidation of the Mechanism of Cytoskeletal Microfilament Bundle Formation by Huntingtin Protein and Its Impact on Neuronal Development>
First author Jaesung Kim, a PhD candidate at KAIST, stated, “This study provides a new perspective for understanding the molecular mechanism of the huntingtin protein, the cause of an incurable disease that has long remained a mystery.”
Professor Ji-Joon Song of KAIST’s Department of Biological Sciences explained, “This achievement not only provides an important clue to understanding the pathogenic mechanism of Huntington’s disease, but is also expected to have a far-reaching impact on research into cytoskeleton-related diseases,” and added that “it opens new avenues for exploring the role of the huntingtin protein in diverse biological phenomena such as cell division, migration, and mechanical signal transduction.”
This research was conducted with Jaesung Kim (PhD candidate, KAIST), Hyeongju Kim (now at Harvard University), Rémi Carpentier (Paris Brain Institute), Mariacristina Capizzi (Paris Brain Institute), and others as co-first authors, and was published on September 19 in Science Advances, a sister journal of Science.
※ Paper title: “Structure of the Huntingtin F-actin complex reveals its role in cytoskeleton organization,” DOI: https://doi.org/10.1126/sciadv.adw4124※ Co-corresponding authors: Ji-Joon Song (KAIST), Florian Schur (ISTA), and Sandrine Humbert (Sorbonne University/Paris Brain Institute).
This research was supported by the Ministry of Health and Welfare’s Global Research Collaboration Program (Korea–Switzerland Biohealth International Joint Research) and the Korea–Austria Cooperation Program.
2025.09.30 View 3268 -
KAIST team links early life epigenetic memory to adult brain inflammation
<(From left) Professor Won-Suk Chung, Ph.D. Ph.D candidate Hyeonji Park Dr. Seongwan Park, Professor Inkyung Jung>
Why do some people remain healthy through childhood yet become more vulnerable to brain disorders such as dementia later in life? A KAIST (President Kwang Hyung Lee) -led team has uncovered a key part of the answer: a developmental ‘switch’ in astrocytes—the brain’s most abundant support cells that shapes how strongly the brain’s immune system reacts in adulthood. The study identifies a gene, NR3C1 (encoding the glucocorticoid receptor), as a master regulator of this switch and shows how early-life epigenetic ‘memory’ can predispose the adult brain to excessive inflammation.
The work was carried out by a joint team led by Professor Inkyung Jung (Department of Biological Sciences, KAIST) and Associate Director Won-Suk Chung (Center for Vascular Research, Institute for Basic Science; Professor, KAIST Biological Sciences). Using mouse models, the researchers mapped gene-regulatory programs across multiple stages of astrocyte development and found that NR3C1 acts during a brief early-postnatal window to enforce long-term immune restraint.
<The schematic illustrates how the NR3C1 gene (glucocorticoid receptor) suppresses the immune response of astrocytes. In normal (control) astrocytes, NR3C1 binds to specific regulatory regions of DNA (nGRE) to inhibit the expression of immune-related genes, thereby maintaining brain homeostasis even under immune stimulation. In contrast, in NR3C1-deficient astrocytes (KO), this suppression is lost, leading to excessive activation of inflammation-related genes such as Gfap, Il6st, Stat2, and Cxcl10. As a result, in an autoimmune encephalomyelitis (EAE) model, pronounced neuroinflammation and clinical symptoms (paralysis and severe debilitation) are observed>
To build this map, the team combined state-of-the-art 3D epigenome profiling with RNA sequencing and chromatin accessibility analyses, capturing how DNA folds and which regulatory elements contact target genes. They identified 55 stage-specific transcription factors that guide astrocyte maturation; among them, NR3C1 emerged as the critical ‘switch’ in early life. Notably, deleting NR3C1 in astrocytes did not disrupt normal development. However, when the adult mice were challenged with an autoimmune model of multiple sclerosis, animals lacking astrocytic NR3C1 mounted exaggerated inflammatory responses and developed more severe disease.
Mechanistically, the study shows that early loss of NR3C1 epigenetically primes immune genes - keeping their regulatory elements open and ready - so that later in life these genes respond too strongly to inflammatory cues. In effect, NR3C1 serves as an early ‘brake’ that prevents over-activation of astrocyte immune programs in adulthood.
“This is the first demonstration that astrocyte immune functions are governed by epigenetic memory,” said Professor Won-Suk Chung. “Our findings offer new clues to the origins of degenerative brain disorders, including Alzheimer’s disease.”
“We reveal a temporal regulatory window in astrocyte development that can set the stage for disease vulnerability in adulthood,” added Professor Inkyung Jung. “Understanding the 3D genome logic behind these programs could open paths to therapies for immune-related brain disorders such as multiple sclerosis.”
<The figure shows the three-dimensional genome structure of astrocytes at specific gene loci, illustrating how NR3C1 regulates their expression. In normal cells, NR3C1 binds to DNA and maintains the chromatin in a closed state, thereby preventing unnecessary activation between distal regulatory elements (enhancers) and gene promoters. In contrast, when NR3C1 is absent, the chromatin becomes open, creating a state in which enhancers and genes can be more easily activated. As a result, genes such as Mxi1 are overexpressed, triggering inflammatory responses. This clearly demonstrates that NR3C1 plays an essential role in maintaining immune homeostasis by stabilizing three-dimensional gene regulatory mechanisms.>
The results of this study were published online on September 22 in the international journal Nature Communications (IF 15.7), with Dr. Seongwan Park and PhD student Hyeonji Park of KAIST’s Department of Biological Sciences as co-first authors.
※ Paper title: “NR3C1-mediated epigenetic regulation suppresses astrocytic immune responses in mice,” DOI: https://www.nature.com/articles/s41467-025-64088-5
In addition, on September 17, the journal published a commentary article introducing this research: https://www.nature.com/articles/s41467-025-64102-w
This research was supported by the Suh Kyungbae Science Foundation, the Ministry of Health and Welfare, the Ministry of Science and ICT, and IBS.
Glossary - Epigenetic priming: preparing genes for rapid future activation by altering chromatin without changing DNA sequence
2025.09.25 View 3836 -
“Why are we depressed?” KAIST is identifying the cause of depression and uncovering clues for treatment
Major depressive disorder (MDD) is one of the most common psychiatric illnesses worldwide, but its molecular causes* have still not been clearly identified. A domestic research team has discovered that depression may not simply be caused by neuronal damage, but can also arise from the dysregulation of specific neural signaling pathways. In particular, they identified the molecular reason why elderly patients with depression do not respond to conventional antidepressants. This study suggests the possibility of therapeutic approaches using optogenetic technology to regulate neural signaling, and it provides clues for the development of new treatment strategies targeting the protein ‘Numb’ protein for elderly patients with depression.
*Molecular causes: explanations for the origin of a disease at the level of molecules, proteins, or genes in the brain.
KAIST (President Kwang Hyung Lee) announced on the 19th of August that a research team led by Distinguished Professor Won Do Heo of the Department of Biological Sciences at KAIST, in collaboration with forensic pathologist Minju Lee of the National Forensic Service (Director Bong Woo Lee) and Professor Seokhwi Kim of the Department of Pathology at Ajou University Medical Center (Director Sangwook Han), identified a new molecular mechanism for depression through RNA sequencing and the immunohistochemical analysis of brain tissue from patients who had committed suicide. Furthermore, they demonstrated in animal models that antidepressant effects can be restored by regulating the signaling pathway that induces neural recovery using optogenetic technology.
The research team focused on the hippocampus, the brain region responsible for memory and emotion, and in particular on the dentate gyrus (DG). The DG is the entry point of information into the hippocampus, playing a role in new memory formation, neurogenesis, and emotional regulation, and is closely linked with depression.
Using two representative mouse models for depression (the corticosterone stress model and the chronic unpredictable stress model), the team found that stress induced a striking increase in the signaling receptor FGFR1 (Fibroblast Growth Factor Receptor 1) in the DG. FGFR1 receives growth factor (FGF) signals and transmits growth and differentiation commands within cells.
Subsequently, using conditional knockout (cKO) mice in which the FGFR1 gene was deleted, the researchers revealed that the absence of FGFR1 made mice more vulnerable to stress and led them to exhibit depressive symptoms more quickly. This indicates that FGFR1 plays a critical role in proper neural regulation and stress resistance.
The team then developed an ‘optoFGFR1 system’ using optogenetics, enabling FGFR1 —essential for stress resistance—to be activated by light. They observed that activating FGFR1 in depression mouse models lacking FGFR1 restored antidepressant effects. In other words, they experimentally demonstrated that the activation of FGFR1 signaling alone could improve depressive behavior.
Surprisingly, however, in aged depression mouse models, the activation of FGFR1 signaling through the optoFGFR1 system did not yield antidepressant effects. Investigating further, the researchers found that in the aged brains, a protein called ‘Numb’ was excessively expressed and interfered with FGFR1 signaling.
Indeed, analysis of postmortem human brain tissue also showed the specific overexpression of Numb protein only in elderly patients with depression. When the researchers suppressed Numb using a gene regulatory tool (shRNA) while simultaneously activating FGFR1 signaling in mouse models, neurogenesis and behavior—previously unrecoverable—returned to normal even in aged depression models. This shows that the Numb protein acts as a “blocker” of FGFR1 signaling and is a key factor preventing the hippocampus from executing antidepressant mechanisms.
Distinguished Professor Won Do Heo of KAIST said, “This study is meaningful in that it revealed that depression may not only result from simple neuronal damage, but can also arise from the dysregulation of specific neural signaling pathways. In particular, we identified the molecular reason why antidepressants are less effective in elderly patients, and we expect this to provide a clue for the development of new therapeutic strategies targeting the Numb protein.”
He added, “Moreover, this interdisciplinary study, which combined KAIST’s expertise in neuroscience with the National Forensic Service’s forensic brain analysis technologies, is expected to serve as a bridge between basic research on psychiatric disorders and clinical applications.”
This study, led by first author Jongpil Shin, a PhD student in the Department of Biological Sciences at KAIST, was published on August 15, 2025, in the international journal Experimental & Molecular Medicine.
Paper title: “Dysregulation of FGFR1 signaling in the hippocampus facilitates depressive disorder”
DOI: https://doi.org/10.1038/s12276-025-01519-9
This research was supported by the Ministry of Science and ICT’s National Research Foundation of Korea through the ASTRA program and the Bio-Medical Technology Development project.
2025.08.19 View 3746 -
KAIST Identifies Key to Slowing Aging via RNA Regulation... Unlocks Mechanism for Longevity
As aging progresses, the quality of DNA and proteins inside cells declines, known to be the cause of various degenerative diseases. However, the connection between aging and RNA has remained largely unexplored. Now, a Korean research team has discovered that a ribosome-associated quality control factor—PELOTA, a protein essential for eliminating abnormal mRNA—plays a central role in slowing aging and promoting longevity. This breakthrough is expected to provide a new direction for future therapeutic strategies targeting human aging and neurodegenerative diseases.
KAIST (President Kwang Hyung Lee) announced that a joint research team—led by Professor Seung-Jae V. Lee of the Department of Biological Sciences at KAIST and the Research Center for RNA-mediated Healthy Longevity, Professor Jinsoo Seo of Yonsei University (President Dong-Sup Yoon), and Professor Kwang-Pyo Lee of the Korea Research Institute of Bioscience and Biotechnology (KRIBB, President Suk Yoon Kwon) under the National Research Council of Science & Technology (NST, Chairman Yeung-Shik Kim—has discovered that the protein ‘PELOTA*’, which plays a key role in ribosome-associated quality control, regulates the pace of aging.
*PELOTA: A key protein in maintaining cellular translational homeostasis, responsible for detecting and resolving errors during mRNA translation by ribosomes.
Until now, RNA—particularly mRNA—has generally been regarded as a transient intermediary in protein synthesis. Its instability made it difficult to study quantitatively or track over time, leaving its physiological and functional roles relatively understudied compared to DNA.
Using C. elegans (a nematode widely used in aging research due to its short lifespan), the researchers first discovered that the ribosome-associated quality control factor PELOTA is essential for longevity. In particular, when PELOTA was overexpressed in normal nematodes, their lifespan was extended, suggesting that ribosome-associated quality control mechanisms involved in removing abnormal mRNA are necessary for promoting longevity.
The study also revealed that the ribosome-associated quality control system simultaneously regulates both the mTOR signaling pathway—which senses nutrient status or growth signals to control cell growth, protein synthesis, and autophagy, and plays a key role in aging and energy metabolism—and the autophagy pathway, the cellular cleanup and recycling system through which cells break down and reuse unnecessary or damaged components.
When PELOTA was deficient, the mTOR pathway became abnormally activated, and autophagy was suppressed—accelerating aging. Conversely, activation of PELOTA inhibited mTOR and induced autophagy, thereby maintaining cellular homeostasis and extending lifespan.
Notably, this mechanism was found to be conserved in both mice and humans. The study also showed that the loss of PELOTA could contribute to muscle aging and Alzheimer’s disease, suggesting its relevance to age-related disorders.
These findings indicate that the study of PELOTA and ribosome-associated quality control could play an important role in developing therapeutic strategies for human aging and neurodegenerative diseases.
Professor Seung-Jae V. Lee of KAIST, who led the research, stated, “While the connection between quality control and aging has been well established at the DNA and protein levels, molecular evidence showing that RNA quality control also functionally contributes to lifespan regulation has been very limited.” He emphasized that the “study provides strong evidence that the removal of abnormal RNA is a central axis in the aging regulatory network.”
The study was published on August 5th in the prestigious journal PNAS (Proceedings of the National Academy of Sciences), with Dr. Jongsun Lee and Dr. Eun Ji Kim of KAIST, Dr. Bora Lee of KRIBB, and Dr. Hyein Lee of Yonsei University as co-first authors.
※ Title: Pelota-mediated ribosome-associated quality control counteracts aging and age-associated pathologies across species ※ DOI: https://doi.org/10.1073/pnas.2505217122
This research was supported by the Global Leader Research Project of the National Research Foundation of Korea.
2025.08.18 View 4886 -
KAIST Reveals Placental Inflammation as the Cause of Allergies such as Pediatric Asthma
<(From left)Professor Heung-kyu Lee from the Department of Biological Sciences, Dr.Myeong Seung Kwon from the Graduate School of Medical Science>
It is already well-known that when a mother experiences inflammation during pregnancy, her child is more likely to develop allergic diseases. Recently, a KAIST research team became the first in the world to discover that inflammation within the placenta affects the fetus's immune system, leading to the child exhibiting excessive allergic reactions after birth. This study presents a new possibility for the early prediction and prevention of allergic diseases such as pediatric asthma.
KAIST (President Kwang Hyung Lee) announced on the 4th of August that a research team led by Professor Heung-kyu Lee from the Department of Biological Sciences found that inflammation occurring during pregnancy affects the fetus's stress response regulation system through the placenta. As a result, the survival and memory differentiation of T cells (key cells in the adaptive immune system) increase, which can lead to stronger allergic reactions in the child after birth.
The research team proved this through experiments on mice that had excessive inflammation induced during pregnancy. First, they injected the toxin component 'LPS (lipopolysaccharide),' a substance known to be a representative material that induces an inflammatory response in the immune system, into the mice to cause an inflammatory response in their bodies, which also caused inflammation in the placenta.
It was confirmed that the placental tissue, due to the inflammatory response, increased a signaling substance called 'Tumor Necrosis Factor-alpha (TNF-α),' and this substance activated immune cells called 'neutrophils*', causing inflammatory damage to the placenta. *Neutrophils: The most abundant type of white blood cells in our bodies (40-75%), playing an important role in innate immunity and killing invading bacteria and fungi.
This damage modulated postnatal offspring stress response, leading to a large secretion of stress hormone (glucocorticoid). As a result, the offspring's T cells, which are responsible for immune memory, survived longer and had stronger memory functions.
In particular, the memory T cells created through this process caused excessive allergic reactions when repeatedly exposed to antigens after birth. Specifically, when house dust mite 'allergens' were exposed to the airways of mice, a strong eosinophilic inflammatory response and excessive immune activation were observed, with an increase in immune cells important for allergy and asthma reactions.
Professor Heung Kyu Lee stated, "This study is the first in the world to identify how a mother's inflammatory response during pregnancy affects the fetus's allergic immune system through the placenta." He added, "This will be an important scientific basis for developing biomarkers for early prediction and establishing prevention strategies for pediatric allergic diseases."
The first author of this study is Dr. Myeong Seung Kwon from the KAIST Graduate School of Medical Science (currently a clinical fellow of gynecological oncology at Konyang University Hospital's Department of Obstetrics and Gynecology), and the research results were published in the authoritative journal in the field of mucosal immunology, 'Mucosal Immunology,' on July 1st. ※ Paper Title: Placental inflammation-driven T cell memory formation promotes allergic responses in offspring via endogenous glucocorticoids ※ DOI: https://doi.org/10.1016/j.mucimm.2025.06.006
This research was conducted as part of the Basic Science Research Program and the Bio-Medical Technology Development Program supported by the Ministry of Science and ICT and the National Research Foundation of Korea.
2025.08.03 View 2690 -
KAIST Team Develops Optogenetic Platform for Spatiotemporal Control of Protein and mRNA Storage and Release
<Dr. Chaeyeon Lee, Professor Won Do Heo from Department of Biological Sciences>
A KAIST research team led by Professor Won Do Heo (Department of Biological Sciences) has developed an optogenetic platform, RELISR (REversible LIght-induced Store and Release), that enables precise spatiotemporal control over the storage and release of proteins and mRNAs in living cells and animals.
Traditional optogenetic condensate systems have been limited by their reliance on non-specific multivalent interactions, which can lead to unintended sequestration or release of endogenous molecules. RELISR overcomes these limitations by employing highly specific protein–protein (nanobody–antigen) and protein–RNA (MCP–MS2) interactions, enabling the selective and reversible compartmentalization of target proteins or mRNAs within engineered, membrane-less condensates.
In the dark, RELISR stably sequesters target molecules within condensates, physically isolating them from the cellular environment. Upon blue light stimulation, the condensates rapidly dissolve, releasing the stored proteins or mRNAs, which immediately regain their cellular functions or translational competency. This allows for reversible and rapid modulation of molecular activities in response to optical cues.
< Figure 1. Overview of the Artificial Condensate System (RELISR). The artificial condensate system, RELISR, includes "Protein-RELISR" for storing proteins and "mRNA-RELISR" for storing mRNA. These artificial condensates can be disassembled by blue light irradiation and reassembled in a dark state>
The research team demonstrated that RELISR enables temporal and spatial regulation of protein activity and mRNA translation in various cell types, including cultured neurons and mouse liver tissue. Comparative studies showed that RELISR provides more robust and reversible control of translation than previous systems based on spatial translocation.
While previous optogenetic systems such as LARIAT (Lee et al., Nature Methods, 2014) and mRNA-LARIAT (Kim et al., Nat. Cell Biol., 2019) enabled the selective sequestration of proteins or mRNAs into membrane-less condensates in response to light, they were primarily limited to the trapping phase. The RELISR platform introduced in this study establishes a new paradigm by enabling both the targeted storage of proteins and mRNAs and their rapid, light-triggered release. This approach allows researchers to not only confine molecular function on demand, but also to restore activity with precise temporal control.
< Figure 2. Cell shape change using the artificial condensate system (RELISR). A target protein, Vav2, which contributes to cell shape, was stored within the artificial condensate and then released after light irradiation. This release activated the target protein Vav2, causing a change in cell shape. It was confirmed that the storage, release, and activation of various proteins were effectively achieved>
Professor Heo stated, “RELISR is a versatile optogenetic tool that enables the precise control of protein and mRNA function at defined times and locations in living systems. We anticipate this platform will be broadly applicable for studies of cell signaling, neural circuits, and therapeutic development. Furthermore, the combination of RELISR with genome editing or tissue-targeted delivery could further expand its utility for molecular medicine.”
< Figure 3. Expression of a target mRNA using the artificial condensate system (RELISR) in mice. The genetic material for the artificial condensate system, RELISR, was injected into a living mouse. Using this system, a target mRNA was stored within the mouse's liver. Upon light irradiation, the mRNA was released, which induced the translation of a luminescent protein>
This research was conducted by first author Dr. Chaeyeon Lee, under the supervision of Professor Heo, with contributions from Dr. Daseuli Yu (co-corresponding author) and Professor YongKeun Park (co-corresponding author, Department of Physics), whose group performed quantitative imaging analyses of biophysical changes induced by RELISR in cells.
The findings were published in Nature Communications (July 7, 2025; DOI: 10.1038/s41467-025-61322-y). This work was supported by the Samsung Future Technology Foundation and the National Research Foundation of Korea.
2025.07.23 View 4333 -
KAIST Develops Novel Candidiasis Treatment Overcoming Side Effects and Resistance
<(From left) Ph. D Candidate Ju Yeon Chung, Prof.Hyun Jung Chung, Ph.D candidate Seungju Yang, Ph.D candidate Ayoung Park, Dr. Yoon-Kyoung Hong from Asan Medical Center, Prof. Yong Pil Chong, Dr. Eunhee Jeon>
Candida, a type of fungus, which can spread throughout the body via the bloodstream, leading to organ damage and sepsis. Recently, the incidence of candidiasis has surged due to the increase in immunosuppressive therapies, medical implants, and transplantation. Korean researchers have successfully developed a next-generation treatment that, unlike existing antifungals, selectively acts only on Candida, achieving both high therapeutic efficacy and low side effects simultaneously.
KAIST (President Kwang Hyung Lee) announced on the 8th that a research team led by Professor Hyun-Jung Chung of the Department of Biological Sciences, in collaboration with Professor Yong Pil Jeong's team at Asan Medical Center, developed a gene-based nanotherapy (FTNx) that simultaneously inhibits two key enzymes in the Candida cell wall.
Current antifungal drugs for Candida have low target selectivity, which can affect human cells. Furthermore, their therapeutic efficacy is gradually decreasing due to the emergence of new resistant strains. Especially for immunocompromised patients, the infection progresses rapidly and has a poor prognosis, making the development of new treatments to overcome the limitations of existing therapies urgent.
The developed treatment can be administered systemically, and by combining gene suppression technology with nanomaterial technology, it effectively overcomes the structural limitations of existing compound-based drugs and successfully achieves selective treatment against only Candida.
The research team created a gold nanoparticle-based complex loaded with short DNA fragments called antisense oligonucleotides (ASO), which simultaneously target two crucial enzymes—β-1,3-glucan synthase (FKS1) and chitin synthase (CHS3)—important for forming the cell wall of the Candida fungus.
By applying a surface coating technology that binds to a specific glycolipid structure (a structure combining sugar and fat) on the Candida cell wall, a targeted delivery device was implemented. This successfully achieved a precise targeting effect, ensuring the complex is not delivered to human cells at all but acts selectively only on Candida.
<Figure 1: Overview of antifungal therapy design and experimental approach>
This complex, after entering Candida cells, cleaves the mRNA produced by the FKS1 and CHS3 genes, thereby inhibiting translation and simultaneously blocking the synthesis of cell wall components β-1,3-glucan and chitin. As a result, the
Candida cell wall loses its structural stability and collapses, suppressing bacterial survival and proliferation.
In fact, experiments using a systemic candidiasis model in mice confirmed the therapeutic effect: a significant reduction in
Candida count in the organs, normalization of immune responses, and a notable increase in survival rates were observed in the treated group.
Professor Hyun-Jung Chung, who led the research, stated, "This study presents a method to overcome the issues of human toxicity and drug resistance spread with existing treatments, marking an important turning point by demonstrating the applicability of gene therapy for systemic infections". She added, "We plan to continue research on optimizing administration methods and verifying toxicity for future clinical application."
This research involved Ju Yeon Chung and Yoon-Kyoung Hong as co-first authors , and was published in the international journal 'Nature Communications' on July 1st.
Paper Title: Effective treatment of systemic candidiasis by synergistic targeting of cell wall synthesis
DOI: 10.1038/s41467-025-60684-7
This research was supported by the Ministry of Health and Welfare and the National Research Foundation of Korea.
2025.07.08 View 3929 -
KAIST Enhances Immunotherapy for Difficult-to-Treat Brain Tumors with Gut Microbiota
< Photo 1.(From left) Prof. Heung Kyu Lee, Department of Biological Sciences,
and Dr. Hyeon Cheol Kim>
Advanced treatments, known as immunotherapies that activate T cells—our body's immune cells—to eliminate cancer cells, have shown limited efficacy as standalone therapies for glioblastoma, the most lethal form of brain tumor. This is due to their minimal response to glioblastoma and high resistance to treatment.
Now, a KAIST research team has now demonstrated a new therapeutic strategy that can enhance the efficacy of immunotherapy for brain tumors by utilizing gut microbes and their metabolites. This also opens up possibilities for developing microbiome-based immunotherapy supplements in the future.
KAIST (President Kwang Hyung Lee) announced on July 1 that a research team led by Professor Heung Kyu Lee of the Department of Biological Sciences discovered and demonstrated a method to significantly improve the efficiency of glioblastoma immunotherapy by focusing on changes in the gut microbial ecosystem.
The research team noted that as glioblastoma progresses, the concentration of ‘tryptophan’, an important amino acid in the gut, sharply decreases, leading to changes in the gut microbial ecosystem. They discovered that by supplementing tryptophan to restore microbial diversity, specific beneficial strains activate CD8 T cells (a type of immune cell) and induce their infiltration into tumor tissues. Through a mouse model of glioblastoma, the research team confirmed that tryptophan supplementation enhanced the response of cancer-attacking T cells (especially CD8 T cells), leading to their increased migration to tumor sites such as lymph nodes and the brain.
In this process, they also revealed that ‘Duncaniella dubosii’, a beneficial commensal bacterium present in the gut, plays a crucial role. This bacterium helped T cells effectively redistribute within the body, and survival rates significantly improved when used in combination with immunotherapy (anti-PD-1).
Furthermore, it was demonstrated that even when this commensal bacterium was administered alone to germ-free mice (mice without any commensal microbes), the survival rate for glioblastoma increased. This is because the bacterium utilizes tryptophan to regulate the gut environment, and the metabolites produced in this process strengthen the ability of CD8 T cells to attack cancer cells.
Professor Heung Kyu Lee explained, "This research is a meaningful achievement, showing that even in intractable brain tumors where immune checkpoint inhibitors had no effect, a combined strategy utilizing gut microbes can significantly enhance treatment response."
Dr. Hyeon Cheol Kim of KAIST (currently a postdoctoral researcher at the Institute for Biological Sciences) participated as the first author. The research findings were published online in Cell Reports, an international journal in the life sciences, on June 26.
This research was conducted as part of the Basic Research Program and Bio & Medical Technology Development Program supported by the Ministry of Science and ICT and the National Research Foundation of Korea.
※Paper Title: Gut microbiota dysbiosis induced by brain tumor modulates the efficacy of immunotherapy
※DOI: https://doi.org/10.1016/j.celrep.2025.115825
2025.07.02 View 7470 -
KAIST develops technology for selective RNA modification in living cells and animals
· A team led by Professor Won Do Heo from the Department of Biological Sciences, KAIST, has developed a pioneering technology that selectively acetylates specific RNA molecules in living cells and tissues.
· The platform uses RNA-targeting CRISPR tools in combination with RNA-modifying enzymes to chemically modify only the intended RNA.
· The method opens new possibilities for gene therapy by enabling precise control of disease-related RNA without affecting the rest of the transcriptome.
< Photo 1. (From left) Professor Won Do Heo and Jihwan Yu, a Ph.D. Candidate of the Department of Biological Sciences >
CRISPR-Cas13, a powerful RNA-targeting technology is gaining increasing attention as a next-generation gene therapy platform due to its precision and reduced side effects. Utilizing this system, researchers at KAIST have now developed the world’s first technology capable of selectively acetylating (chemically modifying) specific RNA molecules among countless transcripts within living cells. This breakthrough enables precise, programmable control of RNA function and is expected to open new avenues in RNA-based therapeutic development.
KAIST (President Kwang Hyung Lee) announced that a research team led by Professor Won Do Heo in the Department of Biological Sciences has recently developed a groundbreaking technology capable of selectively acetylating specific RNA molecules within the human body using the CRISPR-Cas13 system—an RNA-targeting platform gaining increasing attention in the fields of gene regulation and RNA-based therapeutics.
RNA molecules can undergo chemical modifications—the addition of specific chemical groups—which alter their function and behavior without changing the underlying nucleotide sequence. However, some of these modifications, a critical layer of post-transcriptional gene regulation, remain poorly understood. Among them, N4-acetylcytidine (ac4C) has been particularly enigmatic, with ongoing debate about its existence and function in human messenger RNA (mRNA), the RNA that encodes proteins.
To address this gap, the KAIST research team developed a targeted RNA acetylation system, named dCas13-eNAT10. This platform combines a catalytically inactive Cas13 enzyme (dCas13) that guides the system to specific RNA targets, with a hyperactive variant of the NAT10 enzyme (eNAT10), which performs RNA acetylation. This approach enables precise acetylation of only the desired RNA molecules among the vast pool of transcripts within the cell.
< Figure 1. Development of hyperactive variant eNAT10 through NAT10 protein engineering. By engineering the NAT10 protein, which performs RNA acetylation in human cells, based on its domain and structure, eNAT10 was developed, showing approximately a 3-fold increase in RNA acetylation activity compared to the wild-type enzyme. >
Using this system, the researchers demonstrated that guide RNAs could direct the dCas13-eNAT10 complex to acetylate specific RNA targets, and acetylation significantly increased protein expression from the modified mRNA. Moreover, the study revealed, for the first time, that RNA acetylation plays a role in intracellular RNA localization, facilitating the export of RNA from the nucleus to the cytoplasm—a critical step in gene expression regulation.
To validate its therapeutic potential, the team successfully delivered the targeted RNA acetylation system into the livers of live mice using adeno-associated virus (AAV), a commonly used gene therapy vector. This marks the first demonstration of in vivo RNA modification, extending the applicability of RNA chemical modification tools from cell culture models to living organisms.
< Figure 2. Acetylation of various RNA in cells using dCas13-eNAT10 fusion protein. Utilizing the CRISPR-Cas13 system, which can precisely target specific RNA through guide RNA, a dCas13-eNAT10 fusion protein was created, demonstrating its ability to specifically acetylate various endogenous RNA at different locations within cells. >
Professor Won Do Heo, who previously developed COVID-19 treatment technology using RNA gene scissors and technology to activate RNA gene scissors with light, stated, "Existing RNA chemical modification research faced difficulties in controlling specificity, temporality, and spatiality. However, this new technology allows selective acetylation of desired RNA, opening the door for accurate and detailed research into the functions of RNA acetylation." He added, "The RNA chemical modification technology developed in this study can be widely used as an RNA-based therapeutic agent and a tool for regulating RNA functions in living organisms in the future."
< Figure 3. In vivo delivery of targeted RNA acetylation system. The targeted RNA acetylation system was encoded in an AAV vector, commonly used in gene therapy, and delivered intravenously to adult mice, showing that target RNA in liver tissue was specifically acetylated according to the guide RNA. >
This research, with Ph.D. candidate Jihwan Yu from the Department of Biological Sciences at KAIST as the first author, was published in the journal Nature Chemical Biology on June 2, 2025. (Title: Programmable RNA acetylation with CRISPR-Cas13, Impact factor: 12.9, DOI: https://doi.org/10.1038/s41589-025-01922-3)
This research was supported by the Samsung Future Technology Foundation and the Bio & Medical Technology Development Program of the National Research Foundation of Korea.
2025.06.10 View 6737 -
A 10-Month Journey of Tiny Flaps Completed: A Special Family Returns to KAIST Duck Pond
On the morning of June 9, 2025, gentle activity stirred early around the KAIST campus duck pond. It was the day a special family of ducks—and two goslings—were to be released back into the pond after spending a month in a temporary shelter. One by one, the ducklings cautiously emerged from their box, waddling toward the water's edge and scanning their surroundings, followed closely by their mother.
< The landscape manager from the KAIST Facilities Team releases the ducks and goslings. >
The mother duck, once a rescued loner who couldn’t integrate with the flock, returned triumphantly as the head of a new family—caring for both ducklings and goslings. Students and faculty looked on quietly, welcoming them back and reflecting on their remarkable 10-month journey.
The story began in July 2024, as a student filed a report of spotting two ducklings wandering near the pond without a mother. Based on their soft down, flat beaks, and lack of fear around humans, it was presumed they had been abandoned. Professor Won Do Heo of the Department of Biological Sciences—affectionately known as the “Goose Dad”—and the KAIST Facilities Team quickly stepped in to rescue them. After about a month of care, the ducklings were released back into the pond.
< On June 9, the day of the release, KAIST President Kwang-Hyung Lee (left), the former “Goose Dad,” and Professor Won Do Heo (right), the current “Goose Dad,” watched the flock as they freely wobbled about. >
At first, the ducklings seemed to adapt, but they started distancing themselves from the established goose flock. One eventually disappeared, and the remaining duckling was found injured by the pond during winter. Although KAIST typically avoids making human interference in the natural ecosystem, an exception was made to save the young duck’s life. It was put under the care of Professor Heo and the Facilities Team to regain its health within a month.
In the spring, the healed duck began laying eggs. Professor Heo supported the process by adjusting its diet, avoiding further intervention. On Children’s Day, May 5, the duck’s eggs hatched. The once-isolated duck had become a mother. Ten days later, on May 15, four goslings also hatched from the resident goose flock. With new life flourishing, the pond was more vibrant than ever.
< Rescued baby goslings near the pond, alongside the duck family that took them in. The mother duck—once a vulnerable duckling herself—had grown strong enough to care for others in need. >
But just days later, the mother goose disappeared, and two goslings—still unable to swim—were found shivering by the pond. Dahyeon Byeon, a student from Seoul National University who came for a visit on that day, reported this upon sighting, prompting another rescue. The vulnerable goslings were brought to the shelter to stay with the duck family.
Initially, the interspecies cohabitation was uneasy. But the mother duck did not reject the goslings. Slowly, they began to eat and sleep together, forming a new kind of family. After a month, they were released together into the pond—and to everyone’s surprise, the existing goose flock accepted both the goslings and the duck family.
< A peaceful moment for the duck family. The baby goslings naturally followed the mother duck. >
It took ten months for this family to return. From abandonment and injury to healing, birth, and unexpected bonds, this was more than a story of survival. It was a journey of transformation. The duck family’s ten-month saga is a quiet miracle—written in small moments of crisis, care, and connection—and a lasting memory on the KAIST campus.
< The resident goose flock at KAIST’s pond naturally accepted the returning duck and goslings as part of their group. >
2025.06.10 View 6745