We have known for years that poor sleep and Alzheimer’s disease travel together. The question is whether they are passengers or drivers of each other. A new study published in Frontiers in Aging Neuroscience adds a molecular layer to that puzzle, identifying two genes, FLOT1 and EEF1D, that may sit at the intersection of sleep loss and neurodegeneration, linked by a little-known type of RNA modification called ac4C.
The analysis, led by Beiyu Zhao and colleagues at the First Affiliated Hospital of Xi’an Jiaotong University in China, combined bulk RNA sequencing, single-cell RNA sequencing, machine learning algorithms, and Mendelian randomization, a statistical technique that uses genetic variants to probe causal relationships. The team drew on multiple public datasets from the GEO database and validated their findings in peripheral blood samples from both Alzheimer’s disease (AD) patients and individuals with sleep deprivation (SD).
What they found
The researchers started by screening for genes that are both differentially expressed in Alzheimer’s disease and associated with N4-acetylcytidine (ac4C), a chemical tag on RNA molecules that influences how stable they are and how efficiently they are translated into protein. From this screen, two genes emerged as consistently overlapping between AD and sleep deprivation: FLOT1 (flotillin-1) and EEF1D (eukaryotic translation elongation factor 1 delta).
FLOT1 encodes a protein that sits in lipid rafts, specialized microdomains on cell membranes, and plays roles in membrane trafficking and signal transmission between neurons. EEF1D is part of the protein synthesis machinery, helping elongate polypeptide chains during translation. Both are involved in fundamental cellular processes, and both appear to be regulated by ac4C modification in ways that may go awry in Alzheimer’s and in chronic sleep disruption.
To strengthen the link, the team used Mendelian randomization, which leverages the random assortment of genes at conception to mimic a natural experiment. The MR analysis supported a causal relationship: genetic variants that influence FLOT1 and EEF1D expression were associated with Alzheimer’s disease risk, suggesting that dysregulation of these genes is not merely correlated with AD but may contribute to it.
Pathway enrichment analyses revealed that the shared genes are involved in the lysosome pathway, chemokine signaling, and leukocyte transendothelial migration, all processes that relate to how cells clear waste, communicate with the immune system, and allow immune cells to cross into the brain. When the researchers looked at immune cell types using single-cell RNA sequencing, they identified myeloid-derived suppressor cells (MDSCs) as the key immune cell population associated with the shared signals. In the Alzheimer’s brain specifically, microglia, CD4+ T cells, CD8+ T cells, and natural killer (NK) cells were the cell types most prominently involved.
Finally, the team validated their key findings by measuring FLOT1 and EEF1D expression in peripheral blood from AD patients and from people with sleep deprivation. The differential expression patterns matched what the computational analyses predicted, lending real-world confidence to the bioinformatics results.
Why it matters
The study sits at the crossroads of two rapidly advancing fields: sleep neuroscience and epitranscriptomics. Epitranscriptomics, the study of chemical modifications to RNA, is where epigenetics was a decade ago: a young, fertile area full of new mechanisms and potential drug targets. ac4C (N4-acetylcytidine) is one of the less-studied marks, but it has been gaining attention for its role in regulating RNA stability and translation efficiency under stress conditions.
If FLOT1 and EEF1D are genuinely causal intermediaries between sleep loss and Alzheimer’s pathology, they could represent entirely new targets for intervention. A drug or lifestyle strategy that normalizes ac4C modification of these genes, or that stabilizes their expression in the face of sleep disruption, might conceivably reduce Alzheimer’s risk in people with chronic poor sleep.
The immune angle is also compelling. MDSCs are typically studied in cancer, where they suppress immune responses. Their emergence as a key cell type in this analysis suggests that sleep deprivation may tilt the brain’s immune environment toward a more permissive state for neurodegenerative processes. The involvement of microglia, the brain’s resident immune cells, and T cells points toward a model in which sleep loss alters RNA modification patterns in immune cells, shifting the balance from protection to inflammation.
For clinicians, the study reinforces a message that bears repeating: sleep is not just about daytime alertness. Chronic sleep deprivation alters gene expression, modifies RNA, and changes immune function in ways that may compound over years. For the growing population of older adults with sleep complaints, understanding those molecular connections could eventually lead to blood tests or other biomarkers that identify those at highest risk.
Limits
This study is a bioinformatics tour de force, but it has important limitations. The core findings come from computational analyses of existing datasets. While the authors validated expression in patient blood samples, the sample sizes for validation were modest, and the sleep deprivation group was defined by questionnaire rather than objective polysomnography. The Mendelian randomization adds causal weight, but MR depends on strong assumptions about genetic instruments that may not always hold.
Perhaps most importantly, the study identifies associations between FLOT1, EEF1D, ac4C modification, and Alzheimer’s disease, but it does not establish the precise mechanism. How exactly does ac4C modification of FLOT1 or EEF1D affect RNA stability or translation in neurons or immune cells? Does the change happen in response to sleep loss, or does it precede it? Those questions will require mechanistic experiments in animal models or cell systems.
The study also did not examine whether sleep improvement, through behavioral interventions or pharmacotherapy, can reverse the ac4C changes or normalize FLOT1 and EEF1D expression. That is the translational question that matters most to patients.
Bottom line
FLOT1 and EEF1D are two ac4C-modified genes that link Alzheimer’s disease and sleep deprivation at the molecular level, with immune mechanisms, particularly involving MDSCs and microglia, as a plausible bridge. The findings open a new epitranscriptomic angle on the well-established sleep-Alzheimer’s connection, but the work is still early. Experimental validation in animal models and clinical studies in humans will be needed before these candidates can be translated into biomarkers or therapies.
Source
Zhao, B., Zhou, R., Liu, P., Li, Q., Yan, Y., Du, J., Zhao, K., Liu, J., Wang, J., & Qu, Q. “FLOT1 and EEF1D: ac4C-related genes bridging Alzheimer’s disease and sleep deprivation.” Frontiers in Aging Neuroscience 18, 1825164 (2026). DOI: 10.3389/fnagi.2026.1825164. PMCID: PMC13323225.