Cellular SOS: CRISPR Technique Reveals How Cell’s ‘Power Plants’ Activate Emergency Response

The integrated stress response (ISR) is a well-studied biological circuit that behaves like a disaster response center: it takes control when something in the cell goes awry. When the ISR receives a distress signal, it responds by reallocating cellular resources. Run-of-the-mill cellular functions are shut off so that valuable resources can be used to fuel the cell’s emergency response circuits. Scientists knew that damage to mitochondria, tiny energy-producing compartments found in virtually all nonbacterial cells, could activate the ISR. They just didn’t know what the mitochondria-to-ISR distress signal looked like.

But now, as reported in a paper published March 4, 2020, in the journal Nature, UC San Francisco researchers have finally identified the circuit responsible for conveying stress signals from inside mitochondria to the ISR, a discovery that may have important implications for treating the many debilitating diseases associated with mitochondrial stress.

“Mitochondrial dysfunction is a key hallmark of neurodegeneration, heart failure and other age-related diseases. We believe the findings in this paper will have important consequences for understanding and eventually treating these conditions,” said Martin Kampmann, PhD, associate professor in UCSF’s Institute for Neurodegenerative Diseases, a CZ Biohub Investigator, and senior author of the new study.

Often referred to as the powerhouse of the cell, mitochondria are responsible for taking the calories that we ingest and converting them into the energy that fuels almost every biochemical process that keeps us, and virtually all other complex organisms, alive.

But when mitochondria experience stress, they can stop functioning normally. This not only results in the loss of the cell’s primary energy supply, it can also cause mitochondria to leak and release dangerous reactive oxygen species that can seriously damage the rest of the cell. When the damage reaches a tipping point, mitochondria can even activate proteins that initiate apoptosis, a complex biochemical process that causes cells to self-destruct. In an effort to minimize lasting damage and make any necessary repairs, mitochondria need a way tell the ISR that something’s gone wrong.

To determine how mitochondria relay this signal, Kampmann and his team used CRISPRi – a version of the CRISPR gene-targeting technology that shuts off a gene without altering its sequence – to scour the entire human genome for genes that, when shut off, prevent the ISR from being activated in situations in which mitochondria are stressed.

These CRISPRi screens revealed three genes, only one of which was previously known to be associated with the ISR, whose protein products form a three-step signaling pathway that relays SOS messages from inside the mitochondria to the cytosol – the fluid that fills cells and surrounds structures like the nucleus and mitochondria – where it triggers the ISR.

In the first step of the process, mitochondrial stress activates OMA1, a protein-cleaving enzyme that’s attached to mitochondria’s inner membrane. Once activated, OMA1 cleaves a nearby protein called DELE1, cutting the cord that anchors DELE1 to the inner mitochondrial membrane. DELE1 then makes its way into the cytosol via a transport mechanism that scientists are still trying to pin down.

“We were very surprised to find that DELE1 leaves the mitochondria and accumulates in the cytosol. There are very few examples of proteins that leave mitochondria,” said Kampmann.

Regardless of how it gets there, once in the cytosol, DELE1 encounters HRI, the third protein in the newly discovered pathway and the only one that was previously known to participate in ISR activation. DELE1 attaches itself to HRI, which activates HRI and allows it to make a chemical modification to a protein called eIF2α.

Modifying eIF2α has two important consequences. First, it shuts off most protein production, basically bringing every cellular process to a standstill except for the cell’s stress response. Second, it activates a protein called ATF4 which ramps up the production of stress response proteins.

Though the ISR evolved to protect cells, it can actually harm cells in situations of prolonged stress. For example, some genes activated by ATF4 promote apoptosis, so under prolonged stress, the ISR can end up killing the cells it’s trying to save.

But with the mitochondria-to-ISR signaling pathway finally identified, the study’s authors say that it offers an attractive new target for future therapies, especially in cases where the stress response, and not the stress that triggered it, causes most of the damage. 

“Not everything the ISR does is good for cells,” said Kampmann. “Context affects whether it’s beneficial or harmful. In cases where the ISR is maladaptive, inhibiting it could prove beneficial.”

The Walter Lab at UCSF has already developed a drug called ISRIB, which blocks the ISR and prevents it from becoming a maladaptive response. ISRIB has proven effective in restoring cognitive function following traumatic brain injury as well as preventing deafness and radiation poisoning, all of which can result from a hyperactive ISR. Kampmann is now eager to explore how ISRIB might prove useful in the context of mitochondrial stress.

However, Kampmann is especially interested in the new pathway because it offers an attractive target for diseases, including heart failure and neurodegeneration, where mitochondrial stress in particular has been implicated. “We now have a pathway that could be a target for therapies that specifically block the ISR downstream of the mitochondria, but not other ISR-activating pathways. This is very exciting in the context of mitochondrial disease.”

Authors: Additional authors are Xiaoyan Guo, Giovanni Aviles, Yi Liu, Ruilin Tian, Yu-Hsiu T. Lin, Arun P. Wiita and M. Almira Correia of UCSF; Bret A. Unger and Ke Xu of UC Berkeley. All authors except Liu, Lin, Wiita and Correia are Chan Zuckerberg Biohub affiliates.

Funding: This work was supported by the National Institutes of Health grants GM119139, DK26506, GM44037, OD022552, the Beckman Young Investigator Program, a Larry L. Hillblom Foundation Postdoctoral Fellowship, the Chan Zuckerberg Biohub, and NIH Shared Instrumentation Grant 1S10OD010786-01.

Disclosures: The authors declare no competing interests.

The University of California, San Francisco (UCSF) is exclusively focused on the health sciences and is dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. UCSF Health, which serves as UCSF’s primary academic medical center, includes top-ranked specialty hospitals and other clinical programs, and has affiliations throughout the Bay Area.