The Discovery of Nucleocytosis at the University of Tokyo

Researchers at the Institute of Medical Science (IMSUT), University of Tokyo, have unveiled a groundbreaking cellular process called nucleocytosis, where macrophages—key immune cells—selectively extract nuclear DNA from the nuclei of dying cells. This discovery, published in Nature Communications on February 18, 2026, challenges long-held assumptions about how self-DNA activates the immune system. Unlike traditional mechanisms, nucleocytosis allows direct access to nuclear contents without the nuclear envelope breaking down or the entire cell being engulfed, offering new insights into immune regulation.

Led by Professor Ken J. Ishii and Dr. Hideo Negishi, the team used advanced live-cell imaging to observe this phenomenon in real time. Their work was inspired by efforts to understand antiviral drug mechanisms during the COVID-19 pandemic, highlighting UTokyo's pivotal role in global immunology research.

Background: Self-DNA and the cGAS-STING Pathway

The innate immune system detects self-DNA—DNA from the body's own cells—through the cGAS-STING pathway. Cyclic GMP-AMP synthase (cGAS) binds to cytosolic DNA, producing the second messenger 2'3'-cGAMP, which activates stimulator of interferon genes (STING). This triggers type I interferon (IFN-I) production, mounting protective responses against infections but also risking pathogenic inflammation in autoimmune conditions.

Previously, self-DNA was thought to reach the cytosol mainly via endocytosis into endosomes or during necrosis. However, in controlled cell death like apoptosis, nuclear DNA remains protected. Efferocytosis, the phagocytosis of apoptotic cells by macrophages, clears debris anti-inflammatorily but doesn't explain cytosolic self-DNA sensing. Nucleocytosis bridges this gap, providing a selective extraction route.

How Nucleocytosis Works: Step-by-Step Mechanism

Nucleocytosis begins with lysosomal dysfunction in target cells, caused by proton loss or inhibition of palmitoyl-protein thioesterase 1 (PPT1), a lysosomal enzyme. This leads to calreticulin—a chaperone protein—accumulating in the nucleus.

• Step 1: Dying cell lysosomes malfunction, exposing nuclear calreticulin.
• Step 2: Macrophages detect and access the calreticulin-enriched nucleus.
• Step 3: Nuclear DNA is pulled out selectively into the macrophage cytosol.
• Step 4: Extracted DNA activates cGAS-STING, inducing IFN-I secretion.

Live-cell imaging confirmed this repeatable process, distinct from phagocytosis.

Key Differences from Efferocytosis and Other Processes

Efferocytosis involves macrophages engulfing entire apoptotic cells, promoting resolution and anti-inflammatory cytokines like TGF-β and IL-10. Nucleocytosis is more targeted: only nuclear DNA is extracted, bypassing whole-cell uptake and potentially amplifying pro-inflammatory signals via cGAS-STING.

This selectivity avoids secondary necrosis, where uncleared apoptotic cells release damage-associated molecular patterns (DAMPs), but enables precise immune alerting. Implications extend to non-professional phagocytes too.

For those exploring careers in immunology, research jobs at institutions like UTokyo offer opportunities to delve into such mechanisms.

Experimental Breakthroughs and Methods

The UTokyo team employed fluorescence microscopy, live-cell secretion imaging (LCI-S), and genetic knockouts to validate nucleocytosis. PPT1 inhibition with cationic amphiphilic drugs (CADs) like chloroquine mimicked the trigger, inducing DNA extraction and IFN-I in vitro and in vivo.

Read the full paper for details: Nature Communications DOI. Press release: IMSUT UTokyo.

Implications for Autoimmune Diseases in Japan

Japan faces rising autoimmune burdens: rheumatoid arthritis affects ~1% (~1.2 million), systemic lupus erythematosus (SLE) ~0.3-0.5%. Nucleocytosis explains excessive IFN-I in SLE and Aicardi-Goutières syndrome (AGS), where self-DNA drives pathology.

CADs inhibiting PPT1 could modulate this, repurposing drugs like hydroxychloroquine (used in SLE) for targeted therapy. UTokyo's vaccine expertise positions Japan to lead clinical trials.

Prospective researchers can find higher ed research jobs in Japan's immunology hubs.

Potential in Cancer Immunotherapy

In tumors, dying cancer cells release self-DNA, but impaired efferocytosis limits sensing. Nucleocytosis could enhance cGAS-STING activation, boosting anti-tumor immunity. PPT1 inhibitors may synergize with checkpoint inhibitors like anti-PD-1, as preclinical data shows.

• Increase tumor IFN-I to recruit T cells.
• Overcome immunosuppressive microenvironments.
• Combine with STING agonists for synergy.

Japan's cancer incidence (e.g., 1 million new cases/year) underscores urgency; UTokyo innovations could accelerate clinical research jobs.

Therapeutic Targets: PPT1 and Cationic Amphiphilic Drugs

PPT1, a lysosomal depalmitoylase, is central. Its inhibition by CADs (e.g., chloroquine, amiodarone) triggers nucleocytosis, activating immunity. While CADs treat malaria/Lupus, side effects limit use; selective PPT1 modulators are promising.

Dr. Negishi notes: “This forces us to rethink self-DNA-related diseases.” Prof. Ishii emphasizes drug development potential.

Japan's Immunology Research Landscape

UTokyo's IMSUT exemplifies Japan's prowess: ~$10B annual R&D spend, top global rankings in immunology. Collaborations with RIKEN/RIKEN boost discoveries. Prevalence stats: IgG4-related disease ~8,000 cases; post-COVID autoimmune risks elevated.

Explore opportunities at Japanese universities or professor jobs.

Photo by Szymon Shields on Unsplash

Future Outlook and Actionable Insights

Within 5-10 years, nucleocytosis-targeting drugs could treat IFNopathies. Ongoing trials for STING modulators/CADs analogs. For researchers: Focus on PPT1 KO models, imaging tech. Students: Pursue immunology PhDs; Japan offers scholarships.

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