Regulation of genome and epigenome plasticity in adaptation and virulence of the human fungal pathogen Cryptococcus neoformans.

The fungus Cryptococcus neoformans is responsible for approximately 200,000 human deaths each year. C.neoformans lives in the environment but possesses a remarkable capacity to adapt to a variety of environments, including different hosts. Upon entering the human respiratory system, C.neoformans is able to adapt to the new conditions and can even evade immune system defences. From the primary infection in the lungs, it spreads to the central nervous system, leading to meningitis. Cryptococcal meningitis is difficult to treat, mortality is high, and therapy is often limited by the efficacy and availability of drugs. Understanding how C. neoformans adapts and survives within the host is crucial for finding new and improved treatments. The success of C.neoformans lies in its adaptability - its ability to change its behaviour (i.e. its 'phenotype') - to survive the harsh conditions within the host. A key strategy enabling adaptability involves "chromatin". Chromatin packages the DNA, which carries the instructions for cells, named "genes". Making "chromatin modifications" alters the packaging, thereby altering how and when the instructions are used and which affects fungal behaviour and ability to adapt. In C.neoformans, removing certain specific chromatin components significantly reduces its ability to cause disease, suggesting that the associated chromatin modifications are involved in adaptation of the fungus to its host. However, we know little about the chromatin changes that normally happen during infection and how they influence the behaviour of the fungus. In this proposal, I will utilise my expertise with C.neoformans chromatin to investigate three key aims: 1) Understanding chromatin changes during infection: I will investigate how chromatin modifications change when the fungus infects a host. Chromatin changes can impact which genes are turned on or off, influencing the ability of the fungus to survive and cause disease. Comparing fungi that can or cannot make these specific chromatin changes will reveal the roles such modifications play in fungal infection. 2) Understanding the role of irreversible chromatin changes: Most chromatin modifications are reversible to allow specific genes to be activated or repressed when necessary. However, my previous work unexpectedly showed that some stably inherited chromatin modifications important for C.neoformans survival in the host are unable to be re-made once removed. The same may be true for several different chromatin modifications, potentially exposing an Achilles' heel for C.neoformans. I will investigate the hypothesis that removing these modifications by treating the fungus with specific drugs will permanently remove such modifications and thereby inhibit the ability of C.neoformans to infect the host. This strategy could provide an alternative route to develop treatments that for fungal infections, that would be less prone to the development of resistance. 3) Explore the role of chromatin modification in evolution of drug resistance: Inside the host, C.neoformans can also change its DNA content or double the amount of specific genes, which can lead to drug resistance. I will investigate how chromatin modifications influence the ability to change DNA content, providing insights into how the fungus adapts to the host and how drug resistance develops. By investigating the underexplored area of chromatin regulation during infection, my research will bring new insights into how C.neoformans adapts to the host environment and causes disease. This knowledge will inform the development of novel antifungal strategies to better combat fungal infections.