Relation Between Faulty DNA Disposal System and Inflammation

The path from mitochondrial stress to leaking endosomes to immune system initiation in mouse cells is outlined by Salk scientists, providing new therapeutic targets to potentially reduce inflammation in aging and disease.

Relation Between Faulty DNA Disposal System and Inflammation
From left: Gerald Shadel, Laura Newman, and Uri Manor. Image Credit: Salk Institute

The power-producing mitochondria found in every human cell have their mtDNA, a distinct set of genetic instructions that is distinct from the nuclear DNA of the cell and is used by the mitochondria to produce life-giving energy. Both mitochondrial and cellular health are maintained when mtDNA stays inside mitochondria, where it belongs. However, when mtDNA leaves the mitochondria, it can trigger an inflammatory immune response.

Researchers from Salk and associates at UC San Diego have now uncovered a novel mechanism that can be used to extract mtDNA that isn't working properly from inside to outside of mitochondria. In this scenario, the mtDNA is recognized as foreign DNA and triggers a cellular mechanism that typically induces inflammation to eliminate pathogens, such as viruses, from the cell.

Published in Nature Cell Biology, on February 8th, 2023, the findings provide a wealth of new targets for therapeutics aimed at blocking the inflammatory pathway and reducing inflammation associated with aging and diseases such as rheumatoid arthritis and lupus.

We knew that mtDNA was escaping mitochondria, but how was still unclear. Using imaging and cell biology approaches, we’re able to trace the steps of the pathway for moving mtDNA out of the mitochondria, which we can now try to target with therapeutic interventions to hopefully prevent the resulting inflammation.”

Gerald Shadel, Senior and Co-corresponding Author and Director, San Diego-Nathan Shock Center of Excellence

Shadel is also a Basic Biology of Aging and holder of the Audrey Geisel Chair in Biomedical Science at Salk.

Human cells use something called the innate immune system as one of their defense mechanisms against injury and infection. The body’s natural defense against viruses is the innate immune response, but it can also react to substances the body produces that vaguely resemble infections, such as misplaced mtDNA. This reaction can cause long-term inflammation, ageing, and human diseases.

Researchers have been trying to figure out how mtDNA exits mitochondria and sets off the innate immune response, but the pathways that have been previously identified did not fit the particular mtDNA stress scenarios that the Salk team was looking into. In order to learn more about the location and timing of the malfunctions in those mitochondria, scientists resorted to highly advanced imaging techniques.

We had a huge breakthrough when we saw that mtDNA was inside of a mysterious membrane structure once it left mitochondria - after assembling all of the puzzle pieces, we realized that structure was an endosome. That discovery eventually led us to the realization that the mtDNA was being disposed of and, in the process, some of it was leaking out.”

Laura Newman, Study First Author and Assistant Professor, University of Virginia

The researchers found that the accumulation of mtDNA-containing protein masses known as nucleoids inside of mitochondria was the result of a process that started with a malfunction in mtDNA replication. When the cell detects this malfunction, it starts to eliminate the replication-inhibiting nucleoids by moving them to endosomes, a group of organelles that sort and send biological material for eventual removal.

When the endosome becomes overburdened with these nucleoids, it bursts, causing the mtDNA to become unbound within the cell. Similar to how it flags a virus's DNA, the cell interprets the mtDNA as foreign DNA and triggers the DNA-sensing cGAS-STING pathway, which results in inflammation.

Using our cutting-edge imaging tools for probing mitochondria dynamics and mtDNA release, we have discovered an entirely novel release mechanism for mtDNA. There are so many follow-up questions we cannot wait to ask, like how other interactions between organelles control innate immune pathways, how different cell types release mtDNA, and how we can target this new pathway to reduce inflammation during disease and aging.”

Uri Manor, Study Co-Corresponding Author and Assistant Professor, University of California, San Diego

To better understand this intricate mtDNA-disposal and immune-activation pathway, the researchers plan to map out the biological conditions that must exist for the pathway to begin—such as defective mtDNA replication and viral infection—as well as any potential negative consequences on human health. Additionally, they see a chance for novel therapeutic approaches that target this pathway as a new cellular target to lower inflammation.

The Scripps Research Institute's Danielle Grotjahn and Michaela Medina, the University of Victoria in Canada’s Marie-Ève Tremblay, Joshua Chevez of UC San Diego, Ian Lemersal of the La Jolla Institute for Immunology, and Salk's Sammy Weiser Novak, Gladys Rojas, Nimesha Tadepalle, Cara Schiavon, Christina Towers, Matthew Donnelly, Sagnika Ghosh, Sienna Rocha, and Ricardo Rodriguez-Enriquez are among the other authors.

The National Institutes of Health, the Waitt Foundation, the Yale University School of Medicine Center for Cellular and Molecular Imaging, an Allen-AHA Initiative in Brain Health and Cognitive Impairment award, a National Science FoundationNeuroNex Award, the Chan-Zuckerberg Initiative Imaging Scientist Award, the LIFE Foundation, a George E. Hewitt Foundationfor Medical Research Postdoctoral Fellowship, Paul F. Glenn Foundationfor Medical Research Postdoctoral Fellowship, Salk Pioneer Fund Postdoctoral Scholar Award, the Waitt Foundation, and the LIFE Foundation Grant 39965 from the John R. Evans Leaders Fund funded the study.

Source:
Journal reference:

Newman, L. E., et.al (2024) Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal. Nature Cell Biology. doi.org/10.1038/s41556-023-01343-1

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