These ‘master’ proteins protect us from deadly mutations — and could inspire new drugs

Our genomes are full of mutations that have the potential to damage our health or even kill us. Yet most of them rarely cause problems. Why?

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It’s partly thanks to a family of proteins that mask, or ‘buffer’, the ill effects that these mutations would otherwise unleash. This buffering might help to explain why gene variants cause disease in some people but seem to have limited or no impact on others. It could also underlie how some cancer cells and pathogens threaten their hosts and evade drugs. And it enables genetic variation to accumulate in populations, providing a potential resource for future evolution.

Researchers have known for decades that one of the most important factors in mutational buffering is a protein called HSP90 and its family of other HSP proteins. Now, biologists are examining the roles of these proteins in more detail than they ever could before, owing to advances in techniques such as cell screening and genetic editing, as well as the availability of large genomic data sets and extensive health records.

Advances in the past two decades or so have “shifted our view on HSP90 buffering as a theoretical idea to one with immediate and important practical applications, especially in the clinic”, says geneticist Georgios Karras at the University of Texas MD Anderson Cancer Center in Houston. HSP90, for instance, might mediate the risks of breast cancer linked to the BRCA1 gene in some individuals. Some drugs that target buffering proteins are already being developed.

Researchers have long suspected that these proteins might influence the course of evolution, and results from the past several years have strengthened that notion. By ensuring that organisms can thrive despite harbouring risky gene mutations, buffering proteins build up a pool of variation that can be released in the face of environmental stress, triggering the rapid emergence of new adaptations. In this way, says Karras, HSP90 has probably “shaped adaptive evolution of life on Earth”.

Folding assistants

In the 1950s, biologist Conrad Waddington wanted to study how an animal’s environment affected its physical traits. He kept some fruit fly pupae at 40 °C for a few hours — a much higher temperature than the pupae would normally experience. Waddington saw that this heat-shock treatment had induced new wing shapes in some of the resulting flies. By selectively breeding flies with abnormal wings, the mutant phenotypes eventually appeared even without the heat treatment1. They had become genetically fixed. This suggested that the genetic variation underlying these phenotypes was already present in fly populations but was somehow hidden until the heat treatment revealed it.

Waddington’s work puzzled his contemporaries. It didn’t seem to fit with the prevailing view of how genes give rise to inherited traits. Independent work in the following decades identified genes that were switched on by heat exposure; the proteins produced by these genes became known as heat-shock proteins (HSPs).

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Then, in 1998, molecular biologists Suzanne Rutherford and Susan Lindquist, at the time based at the University of Chicago in Illinois, linked the activity of these proteins to the strange effects that Waddington had seen. They bred fruit flies from standard laboratory strains with flies that carried mutations of a gene called Hsp83 (the fly equivalent of HSP90 in humans)2. About 1.7% of the cross-bred strains had developmental defects, including deformed abdomens, no eyes and misshapen legs and wings. Why did a single genetic mutation produce such a wide range of changes?

The researchers concluded that there must be a latent pool of mutations in the normal fly population, and they had found the master switch that unleashed them all. Lindquist thought that the HSP90 protein acts as a “capacitor for morphological evolution”, keeping genetic variation hidden. Turn it off, and all hell can break loose2.

Because organisms can’t be too sensitive to mutations if they are to be viable at all, various forms of buffering are woven into the complex networks formed by genes and their interactions, says genomicist Christine Queitsch at the University of Washington School of Medicine in Seattle. For example, pathways can be reinforced by having a backup if one fails. Buffering can also involve more complex reshuffling of genes’ duties in ways that are still not fully understood: feedback loops, for example, that boost the activity of one gene to compensate for the failures of another.

Since Lindquist’s groundbreaking work, HSP90 and the wider family of HSP proteins have emerged as key components in buffering mechanisms. These heat-defence proteins are found in organisms ranging from bacteria to humans. High temperatures can cause many proteins to denature and lose their functional folded structure. HSP90 is a ‘molecular chaperone’ that helps denatured proteins to refold (see ‘Folding facilitators’). There is a lot of it in cells: it comprises about 1% of the total protein content of human cells.

HSP90 helps to fold a wide range of ‘client’ proteins, many of which sit at the heart of important processes. These include hormone receptors, transcription factors and cell-signalling molecules. It’s now clear that HSP90 isn’t just helping to protect against heat shock — it is also keeping its client proteins functional under normal conditions in the face of mutations that might otherwise impair their folding.

But there are limits to how much stress HSP90 can cope with. It can be overpowered by demand in times of stress, and unable to contain genetic variation. That’s not necessarily a bad thing, because some genetic variants might confer advantages in some organisms — phenotypes that can help a population to deal with the stress. These variants might then become dominant in the population through selection.

HSP90 is not alone. Work in the past few years has identified several more relevant genes outside the HSP family. In 2024, Kevin Verstrepen, a geneticist at the VIB-KU Leuven Center for Microbiology in Belgium, and his co-workers used a high-throughput technique to identify buffer genes in the yeast Saccharomyces cerevisiae3. They took around 5,000 strains, each with a different gene deleted, and then used ultraviolet light to induce more mutations at random. If the deleted gene was involved in buffering, you would expect to see more variation in growth or other characteristics when the cells are exposed to UV.

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The study identified a handful of genes with strong effects of this sort, all of which are involved in protein folding (similar to HSP90) or in organizing chromatin, the DNA–protein complex that forms chromosomes. But Verstrepen says that what constitutes a buffering gene is up for debate: many, if not most, genes interact with others. “There is no clear definition of the magnitude of genetic interactions that a gene must have before we call it a buffer gene”, says Verstrepen. “It is a bit of an arbitrary cut-off.”

Buffering in disease

HSP90 remains the poster child of the field, however. That, says Queitsch, is because it is so sensitive to stresses — it plays an important part linking an organism’s biology to its environment — and because its client proteins have such important roles in shaping phenotypes. If there are problems with HSP90, defective gene variants or random mutations that occur constantly in our cells, especially when we are exposed to stresses such as UV light, alcohol and cigarette smoke, can emerge in ways that might be problematic. “If someone lacks a buffer gene, or has a buffer gene with lower activity, that person may be more susceptible to the effects of new, random or already present mutations,” says Verstrepen.

This is why buffering is becoming a focus of biomedical research. In 2017, Karras was a postdoc in Lindquist’s lab when the team first identified a role for two buffering proteins, HSP90 and HSP70, in human health4. (Lindquist was a co-author of the paper but had died from cancer the year before.) The researchers looked at the buffering of FANC proteins, which are involved in repairing damaged DNA. Mutations in the genes that code for these proteins are associated with the rare disease Fanconi anaemia, which can lead to developmental complications as well as a predisposition to cancer. Karras and his colleagues found that HSP90 buffers some variants of one such gene, called FANCA (the role of HSP70 is more complex).

They also tested the effects of compromising HSP90 in cells. When subjected to temperatures of 39–40 °C (in the range that might be experienced by someone with a fever), the cells became more vulnerable to DNA damage caused by chemical compounds. The researchers determined that the HSP90 reservoir is exhausted by the demands created by the heat stress, so that it can no longer mask FANCA mutations.

One implication of the work, says Karras, is that the effects of particular disease-linked gene variants could depend on environmental stressors such as temperature, which can alter the degree of buffering. The researchers have yet to study this possibility.

If environmental stress can indeed affect disease risk from gene variants, it would complicate efforts to estimate such risk from genetic analysis alone. What’s more, the clinical implications of a mutation are also muddied by complex interactions with other genes, making it even harder to establish how much a given variant impacts someone’s risk of disease — its ‘penetrance’.

Although Fanconi anaemia is a rare condition, the same considerations should apply to more common genetic disease variants. Karras has been investigating the buffering effects of HSP90 on the BRCA1 gene. Similar to the FANCA gene, BRCA1 is involved in genome maintenance, and HSP90 stabilizes mutant variants and helps them to perform their functions. This lowers the chances of developing cancer early in life for people who carry these variants5. The age-related cancer risk seems to depend on the extent to which the BRCA1 proteins bind to HSP70 and HSP906. Compromise HSP90, and the problems associated with those variants are revealed — although the extent to which this is happening in BRCA1-associated cancers isn’t yet known, says Karras.