The Backstory
A paradigm shift in Alzheimer's research
For 30 years, research focused on amyloid plaques. Genetics changed everything.
- Amyloid plaques as primary cause
- Drugs targeting plaques
- 99% clinical trial failure rate
- Neurons as central actors
- Genetic risk in immune cells
- Microglia as central actors
- IRF1 as the master switch
- Enhancers as drug targets
How the pieces connect — click any node to learn more
The amyloid hypothesis
For three decades, Alzheimer's research focused on amyloid plaques — dark, sticky protein deposits that accumulate between neurons. The assumption: clear the plaques, cure the disease.
But drug after drug failed. Over 99% of clinical trials targeting amyloid have not worked. Something was missing from the picture.
Enter the gardeners
The brain has its own immune system — microglia. Like gardeners, they patrol the tissue, pruning dead synapses, clearing debris, and keeping the environment healthy.
In a healthy brain, microglia are branched and watchful, constantly sampling their surroundings and engulfing waste.
When gardeners become soldiers
In Alzheimer's disease, microglia undergo a dramatic transformation. They retract their branches, swell into an amoeboid shape, and switch on an aggressive inflammatory programme.
This is the Disease-Associated Microglia (DAM) state — and it's driven by changes in which genes are switched on.
Inside the nucleus: genetic switches
Genes don't switch on randomly. Hidden in your DNA are regulatory sequences called enhancers — stretches that don't code for proteins, but act as volume knobs for nearby genes.
Enhancers are the molecular switches that control the DAM transformation. They are also the sites where most Alzheimer's genetic risk concentrates.
IRF1: the finger on the switch
A protein called IRF1 binds directly to these microglial enhancers — acting as the master regulator that flips the switch from healthy gardener to disease-driving soldier.
Map where IRF1 binds across the entire genome, and you have a roadmap to new Alzheimer's treatments.
The genetic map of risk
To find genes that cause Alzheimer's, scientists scan the entire human genome across hundreds of thousands of people — comparing those with the disease to those without. Each peak on this chart marks a location where a genetic variant consistently appears more often in people with Alzheimer's.
The tallest spike? APOE on chromosome 19 — the most powerful known genetic risk factor for late-onset Alzheimer's.
But what do these genes do?
Researchers identified 29 risk loci across the genome — positions where variants reliably raise or lower your chance of developing Alzheimer's. The question is: what cell type do they act in?
Highlighted in orange are the loci whose nearest genes are known to be highly expressed in microglia — the brain's resident immune cells.
The pattern is unmistakable
Genes like TREM2, INPP5D, CD33, MEF2C, and MS4A are all predominantly active in microglia — not neurons, not astrocytes. The immune cells of the brain are not bystanders. They are the central actors in Alzheimer's risk.
Your brain has an immune system
Most people know the brain is made of neurons — the cells that fire electrical signals and form memories. But the brain also contains five other major cell types, each playing a different role.
Hover over any cell type to learn what it does.
Microglia: the sentinels
Microglia make up roughly 10–15% of all brain cells. They are the brain's dedicated immune cells — constantly patrolling for damage, clearing debris, and shaping synaptic connections.
When the brain is healthy, microglia exist in a quiet, watchful state. In Alzheimer's disease, they transform into something quite different.
The "disease-associated" transformation
In brains with Alzheimer's, microglia undergo a dramatic shift into a Disease-Associated Microglia (DAM) state. They change which genes they switch on — ramping up inflammation and dramatically altering how they interact with amyloid plaques and tau tangles.
This transformation is driven by changes in gene regulation — specifically, the activation of genetic "switches" called enhancers.
The smoking gun: only microglia change
A landmark reanalysis of single-nucleus RNA-sequencing data — examining over 80,000 individual brain cells from Alzheimer's patients and healthy controls — found something extraordinary.
Using rigorous statistical methods, just 26 genes were reliably different between AD and control brains. And 25 of 26 were in microglia.
Earlier studies got it wrong
Earlier analyses of the same data reported 23,923 genes as changed in Alzheimer's — across all cell types. This was a statistical artefact called pseudoreplication.
When the data is analysed properly, the signal almost entirely disappears — except in microglia. The noise was masking the truth.
Convergent evidence from genetics
Independently, a method called EWCE (Expression-Weighted Cell Type Enrichment) asked: across all known Alzheimer's risk genes, which cell type expresses them most?
The answer was unambiguous. AD risk genes are expressed 4.1 standard deviations above chance in microglia. No other cell type comes close.
Genetics confirms the same answer
Independently of the RNA data, a method called EWCE (Expression-Weighted Cell Type Enrichment) asked: across all known Alzheimer's risk genes from GWAS, which brain cell type expresses them the most?
The answer is clear. Look at the eight brain cell types ranked by their enrichment score.
The microglial signal is overwhelming
Microglia score ζ = 4.1 standard deviations above chance (p < 0.00001). Every other cell type is below 0.4 — barely above random.
This is not a subtle clue. Two completely independent lines of evidence — RNA expression and genetics — point directly at the same cell type.
We know microglia are the answer.
But how do they get activated?
The evidence is overwhelming: Alzheimer's risk concentrates in microglia. But simply knowing which cell matters isn't enough to find treatments. We need to understand the molecular machinery — what flips the switch that transforms a healthy microglial cell into a disease-driving one.
The genetic switch
Scattered across the genome are regulatory regions called enhancers — stretches of DNA that don't code for proteins, but instead control when and how much of nearby genes get made. In microglia, these enhancers are the molecular switches that control the transition to the DAM state.
The key protein: IRF1
A protein called IRF1 (Interferon Regulatory Factor 1) appears to be the "finger" that flips these enhancer switches — binding to microglial DNA and activating the disease-associated gene programme. IRF1 is a master transcription factor for immune activation.
The problem
Standard laboratory tools — antibodies — cannot reliably track IRF1 in the genome. Existing commercial antibodies fail quality control in ChIP-seq experiments, making it impossible to map exactly where IRF1 binds in microglial DNA. We are flying blind.
A molecular flag
on the genetic switch
The solution is to bypass the antibody problem entirely — by tagging IRF1 directly in living cells with a small molecular "flag" that we know can be tracked. This PhD project uses two cutting-edge technologies to do exactly that.
Prime Editing
A next-generation form of CRISPR — more precise than standard gene editing, with no DNA double-strand breaks. We use it to insert a small DNA sequence (an "epitope tag") directly into the IRF1 gene itself, in living human cells. Every copy of IRF1 the cell makes will now carry the flag.
CETCh-seq
Once IRF1 carries its flag, we use an antibody against the flag (not IRF1 itself) to pull down every piece of DNA it touches — a technique called ChIP-seq. This gives us a genome-wide map of every location where IRF1 binds, in healthy microglia and in the disease state.
Drug Targets
By overlapping IRF1's binding sites with the 29 known Alzheimer's risk loci from GWAS, we can identify which microglial enhancers are causally relevant to human disease — and which represent viable targets for new treatments.
Four steps to a treatment
This PhD project unfolds over 3.5 years across four interlocking aims. Here is where we are right now.
Proving the Tool Works
Before using our molecular flag in brain cells, we first prove it works in a simpler system — a colorectal cancer cell line called HCT116 that's easy to grow and manipulate in the lab.
Moving to Brain Cells
Once validated, we transfer the approach into microglial model systems: mouse BV2 cells and human iPSC-derived microglia (iMG), which closely mimic real brain immune cells.
Mapping the Disease Switch
We run genome-wide ChIP-seq with our anti-FLAG antibody to map every location where IRF1 (and its partner IRF8) bind in healthy vs. disease-associated microglia. This is the first complete map of its kind.
Finding Drug Targets
The final step links our binding maps to human genetics — using statistical methods to identify which microglial enhancers are causally responsible for Alzheimer's risk, pinpointing potential drug targets.
The first genetic map of
Alzheimer's immune switches
For the first time, this research will produce a genome-wide atlas of where IRF1 acts in microglia — in health, in activation, and in the disease state. Overlaid with human GWAS data, this atlas will transform how we identify drug targets for Alzheimer's disease.
Every molecular "flag" placed, every binding site mapped, brings us one step closer to understanding — and ultimately treating — the most devastating neurodegenerative disease of our time.
Research conducted at the Skene Lab · Supported by Alzheimer's Research UK · Data from Murphy et al. 2023 (eLife), Jansen et al. 2019 (Nature Genetics), Skene & Grant 2016 (Frontiers in Neuroscience)
The evidence, summarised
Four independent lines of evidence converge on the same answer.
Both GWAS genetics and single-cell RNA-sequencing independently point to microglia as the central cell type in Alzheimer's risk. This convergence across completely separate methods is not a coincidence.
IRF1 is a master transcription factor for immune activation. It binds microglial enhancers and drives the transition to the disease-associated state — making it a prime candidate for therapeutic intervention.
Existing commercial antibodies against IRF1 fail quality control in ChIP-seq experiments. This means we currently have no way to map where IRF1 binds in the genome. The field is flying blind.
By using Prime Editing to tag IRF1 directly in living cells, then pulling down every piece of DNA it touches (CETCh-seq), this PhD project will produce the first genome-wide atlas of IRF1 binding in microglia.
Why it matters
Neurons are the cells that die in Alzheimer's — but that doesn't mean they're the cause. Genetics tells us where risk originates. The 29 variants most strongly linked to Alzheimer's are almost all active in microglia, not neurons. Targeting the cause (microglial dysfunction) is more promising than treating the consequence (neuronal death).
IRF1 is a known master regulator of immune cell activation, with a well-established role in the interferon signalling pathway. Single-cell studies show it is one of the most differentially expressed transcription factors in disease-associated microglia. Critically, its binding sites overlap with known Alzheimer's risk loci — suggesting a direct causal link between IRF1 activity and human genetic risk.
A genome-wide map of where IRF1 binds tells us exactly which enhancers it controls. When those enhancers overlap with Alzheimer's risk variants from GWAS, they become validated drug targets — locations where a small molecule or gene therapy could modulate IRF1 activity and potentially slow the disease. This is the same logic that has led to successful drugs in cancer and autoimmune disease.