Single-cell transcriptomics enthusiasts have raised the bar again. In a study published in Nature on July 24, scientists led by Li-Huei Tsai and Manolis Kellis at the Massachusetts Institute of Technology in Cambridge analyzed the transcriptomes of 1.3 million cells from six different regions of the human brain. The cells came from 48 people, 26 of whom had died of AD. The regions studied matched those that become inundated with tau tangles as the disease progresses. As you might expect, the findings were varied.

  • The transcriptomics study investigated six brain regions in AD patients and non-AD patients.
  • Reelin-expressing neurons were less abundant in AD.
  • Vulnerable neurons in different brain regions were interconnected.
  • In astrocytes, increased synthesis of polyamines and choline correlated with increased cognitive resilience.

To name a few notable highlights, neurons appeared to have very different transcriptional responses to the disease based on their location in the brain. Neurons that relay signals through Reelin, an extracellular matrix protein that binds to the ApoE receptor, were sparser in the entorhinal cortex and other brain regions of AD patients, suggesting they were vulnerable to the disease. Glial cells responded more consistently across regions, and the researchers identified astrocytes as the only cell type whose gene expression strongly synchronized with cognitive resilience. Specifically, astrocytes increased production of the neuroprotective molecules polyamines and choline. This finding suggests that factors secreted by astrocytes may give neurons more time to heal in the face of increasing AD pathology.

“This study is an important step forward in advancing the field of brain-wide analysis of cell type-specific molecular changes in Alzheimer's disease,” wrote Eitan Kaplan of the Allen Institute for Brain Science in Seattle. “Discoveries like this across many brain regions will be needed to more precisely interpret and treat Alzheimer's disease as a disorder of cell types and circuits.”

This new analysis joins a series of single-cell studies published by these scientists, who have previously used brain samples from the Religious Order Study and Memory and Aging Project (ROS-MAP) cohort to analyze how AD affects gene expression in different cell types (News for October 2023Previous studies have primarily sampled the prefrontal cortex, where neurofibrillary tangles only invade later in the disease process, missing earlier changes in gene expression in other areas, such as the entorhinal cortex. Moreover, cells in one part of the brain may respond differently to a particular pathological challenge than cells in another brain zip code.

To address regional diversity, co-first authors Hansrudy Mathys, Carles Bois, and Leila Akai and their colleagues isolated nuclei from six regions. In Braak stages I-II, the entorhinal cortex is the first to be affected by neurofibrillary tangles. This is followed by the hippocampus and anterior thalamus in Braak stages III-IV, and the angular gyrus, middle temporal cortex, and prefrontal cortex in stages V-VI. Based on the transcriptome, the 1.3 million isolated nuclei represented 76 cell types, including 32 types of excitatory neurons and 23 types of inhibitory neurons. The researchers charted the diversity of transcriptional subtypes of neurons and glia in all six brain regions before looking at disease-related responses.

Kaleidoscope of cellsTranscriptomes of 1.3 million nuclei across 14 major cell types revealed 76 subtypes. [Courtesy of Mathys et al., Nature, 2024.]

With this atlas in hand, the researchers next looked at how AD might change it. First, they looked for vulnerable neurons – neurons that were largely absent in samples from AD patients. Six subtypes of excitatory neurons fit the bill: four in the entorhinal cortex, one in the hippocampus, and one in a neocortical region, at least in people who had neurofibrillary tangles there. Two of the entorhinal cortex subtypes expressed high levels of Reelin, and all six expressed other components of the Reelin signaling pathway. They also detected genes involved in heparin sulfate proteoglycan biosynthesis, a cell surface protein suspected of spreading toxic forms of tau (Holmes et al., 2013).

The scientists found that some of these unlucky neurons in different brain regions appeared to be interconnected. For example, vulnerable pyramidal neurons in the hippocampus made synaptic connections with struggling subtypes in the entorhinal cortex and subiculum. The scientists also identified a loss of inhibitory neuron subtypes in the AD samples, which also expressed high levels of Reelin. This finding is consistent with a report from about 20 years ago of a loss of Reelin-expressing neurons in AD brains (News of August 2005).

Catch the Grim Reaper? In the entorhinal cortex, excitatory neurons expressing Reelin (pink) were fewer in Alzheimer's disease patients (right) compared with controls (left), with the difference being greatest in patients with late-stage Alzheimer's disease (right graph). [Courtesy of Mathys et al., Nature, 2024.]

Whether and how Reelin signaling determines the fates of these different neuronal subtypes is unclear, Kellis said. Recent studies suggest that Reelin signaling is a good thing. Mutations that increase the gene's function may also protect against dementia in carriers of autosomal dominant mutations in presenilin 1 (News for May 2023How Reelin's apparent neuroprotective role relates to the loss of neurons that express it remains to be explored, Tsai told AlzForum. Perhaps the loss of Reelin-expressing cells occurs early and could itself contribute to Alzheimer's progression, she noted. Previous work in mouse models suggests that loss of Reelin makes synapses highly sensitive to even low levels of Aβ aggregates (News for July 2015).

How region-specific was the transcriptional response to AD? For neurons, this was significantly so, whereas glial cells showed more consistent disease-associated transcription across regions. The disease signature of astrocytes overlapped considerably across all regions sampled, as did oligodendrocytes.

Microglia showed largely overlapping responses within subcortical regions, but these cells expressed both broad and region-specific signatures: for example, microglia in all regions enhanced clathrin-based endocytosis and suppressed viral response genes, but only in the entorhinal cortex and hippocampus enhanced MHC II expression, and only in the entorhinal cortex and prefrontal cortex promoted glycolysis.

Several AD risk genes identified in GWAS were increased or decreased in microglial cells and other cell types in a region-specific manner, for example, the lipid transporter ABCA7 was enriched in the thalamus in AD, and the complement receptor CR1 was enriched in the neocortex.

Some ROS-MAP participants died cognitively intact, but autopsies revealed massive Aβ plaques and tau tangles. What preserved their memories? To answer this question, the researchers turned to the larger ROS-MAP cohort, which included snRNA-Seq data from a single region of 427 brains: the prefrontal cortex. Surprisingly, astrocyte subtypes were the only cell population that tracked with cognitive resilience. These cells expressed a set of genes associated with antioxidant activity, including HMGN2, NQO1, GPX3, and ODC1.

The latter encodes a rate-limiting enzyme in the synthesis of polyamines. These nitrogen-rich molecules, especially spermidine, promote autophagy and are associated with improved cognitive performance (News for May 2021; News for May 2021).

Daniel Lee of the University of Kentucky, Lexington, who studies the relationship between polyamines and tau deposition, called the new data intriguing. He noted that the so-called polyamine stress response is a highly regulated and complex pathway that can be activated by tau pathology and a variety of other disorders. “Under certain conditions, astrocyte activation of PSR may appear to be beneficial under the chronic burden of overall AD pathology,” he wrote. “However, it will be interesting to know how protein expression, polyamines themselves, and their end-product metabolites function in astrocytes or as a whole,” he added. He thinks that a deeper understanding of the downstream biology of this pathway could point the way to therapeutics.

Choline biosynthesis emerged as another resilience-related pathway in astrocytes. Genes required for choline synthesis were increased, while genes involved in degradation were decreased. Choline helps produce the neurotransmitter acetylcholine, which is decreased in AD. As phosphatidylcholine, choline forms a major component of lipid membranes. Tsai and Kellis recently reported that choline supplementation corrects lipid imbalances caused by AD risk variants in the ABCA7 gene (Meidel et al., 2024The synthetic pathways of choline and polyamines are intertwined.

“Whether these pathways are a cause or effect of cognitive resilience is unclear. Tsai noted that the findings are consistent with the idea that astrocytes may produce large amounts of neuroprotective compounds that could slow the cognitive decline caused by progressive Alzheimer's pathology.”

Kellis and Tsai believe their findings will inspire hypotheses and further research, and the data will be published in an interactive Website“We've only just scratched the surface of these datasets,” Kellis said. “We hope others will use this to make further discoveries.” —Jessica Shugart

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  2. Can the brain recover from early cell losses in Alzheimer's?
  3. Reelin mutant protects against dementia in Colombian siblings
  4. Reelin in Aβ damage?
  5. Can polyamines improve your life?
  6. Polyamines – what is their role in neurodegeneration?

Citation

  1. Holmes BB, DeVos SL, Kfoury N, Lee M, Jacks R, Yanamandla K, Ouija MO, Brodsky FM, Maratha J, Bagchi DP, Kotzbauer PT, Miller TM, Papy-Garcia D, Diamond MI..
    Heparan sulfate proteoglycans mediate the internalization and proliferation of certain proteolytic seeds..
    Proceedings of the National Academy of Sciences. 2013 August 13;110(33):E3138-47. Epub 2013 7 29
    Publisher.
  2. von Meidel D, Wright S, Bonner JM, Staab C, Spitalelli A, Liu L, Pao PC, Yu CJ, Scannail AN, Li M, Bois CA, Matisse H, Leclerc G, Menchaca GS, Welch G, Graziosi A, Leary N, Samaan G, Kellis M, Tsai LH.
    Single-cell atlas of ABCA7 loss-of-function reveals impaired neuronal respiration due to choline-dependent lipid imbalance.
    BioRxivJune 28, 2024;
    Publisher.

External citations

  1. Website