Most studies of gene-expression changes in Alzheimer’s brain analyze tissue samples containing a mix of different cell types. This makes it impossible to definitively figure out the contribution of specific cells. In the November 25 Nature Neuroscience, researchers led by Jose Polo at Monash University in Clayton, Australia, and Enrico Petretto and Owen Rackham at Duke-National University of Singapore Medical School now present cell-type-specific gene-expression data from the entorhinal cortices of late-stage AD and control brains. The researchers sequenced RNA from 13,214 cells representing six types: neurons, astrocytes, oligodendrocytes, oligodendrocyte progenitor cells (OPCs), endothelial cells, and microglia. They found distinct gene-expression differences between AD and controls, not only in each cell type, but also in subtypes. In addition, they identified transcription factors that may control suites of differentially expressed genes. “Taken together, these observations will allow us to better understand how AD progresses and, as a result, find new ways to tackle this debilitating disease,” the authors wrote to Alzforum. The data are available to researchers on a searchable web interface.
- Single-cell RNA-Seq offers a glimpse of how different cell types change in AD brain.
- Data largely agree with prior studies, add new details about transcriptional control.
- In AD astrocytes, lysosomal TFEB regulates 10 AD-associated genes.
“This study provides direct evidence of significant gene-expression changes in all major cell types in AD,” noted Jeremy Miller at the Allen Institute for Brain Science in Seattle (full comment below).
Previously, researchers led by Bin Zhang at Mount Sinai Medical School, New York, and Valur Emilsson at the University of Iceland, Kopavogur, used bulk transcriptomic analysis of cortical samples from 376 AD patients and 173 controls to pinpoint immune genes as the network most altered in AD. At the time, these researchers could not parse out cell-specific changes (Zhang et al., 2013). Earlier this year, Li-Huei Tsai and Manolis Kellis and colleagues at the Massachusetts Institute of Technology reported single-cell RNA-Seq data from the prefrontal cortices of 24 AD patients and 24 controls, opening a more granular view. They found that microglia, astrocytes, and oligodendrocytes harbored the majority of the differentially expressed genes (May 2019 news).
Polo and colleagues focused on a different brain region, the entorhinal cortex, one of the first areas to lose neurons in Alzheimer’s disease. First authors Alexandra Grubman, Gabriel Chew, and John Ouyang isolated nuclei from the postmortem brains of six AD patients at Braak stage VI and six controls, who had died at an average age of 78. In total, they obtained 7,432 oligodendrocytes, 2,171 astrocytes, 1,078 OPCs, 656 neurons, 449 microglia, and 98 endothelial cells, as well as 1,330 cells that could not be clearly sorted into one of these categories. Analysis of expression profiles further subdivided each cell type. Altogether, the authors delineated six oligodendrocyte subtypes, eight astrocyte, four OPC, six neuronal, five microglial, and two endothelial subtypes. For all cells except neurons, these subtypes segregated cleanly into either AD or control brain. For example, two astrocyte subtypes were found only in AD brain, the remaining six only in controls.
The changes in AD varied by subtype. Excitatory neurons turned down synaptic transmission genes, while inhibitory neurons dialed back genes involved in ion transport and memory. Oligodendrocytes boosted genes responsible for myelination, perhaps as a compensatory response to myelin loss in AD, the authors speculated. As expected, astrocytes, microglia, and endothelial cells turned up inflammatory genes. At the same time, microglia dampened genes involved in homeostasis, cell adhesion, and lipid metabolism, in agreement with other studies (Sep 2017 news; Aug 2019 news). Some expression changes were common to multiple cell types. Glial cell types in general turned down cell-death pathways, perhaps to protect damaged cells, the authors noted. And most of the cells that remained in these late-stage AD brain samples had ramped up pathways for dealing with misfolded proteins and cellular stress.
The authors paid particular attention to the expression of about 1,000 genes that have been implicated as AD risk or protective factors by GWAS with a p value of 9 x 10-6 or better. In some cases, they found the gene was expressed in only a single cell type in both AD and control brain. For example, the endocytosis gene RIN3 and the vasoconstrictor TBXAS1 were expressed only in microglia, a new finding. In other cases, the authors found AD differential expression in only one cell type; for example, MS4A6A expression in AD increased only in microglia.
Expression of some AD risk genes varied by cell type. ApoE went up in microglia and down in astrocytes, oligodendrocytes, and OPCs. BIN1 went up in one astrocyte subtype and down in one neuronal one. Curiously, the authors found no change in microglial BIN1 expression, even though recent studies have placed the AD risk variant for this gene in a microglia-specific enhancer (Nov 2019 news).
The authors also identified coordinated changes in multiple genes controlled by single transcription factors. This analysis suggested key genes that may drive a cell’s transition to an AD state. For example, the transcription factor AEBP1, which goes up with amyloid plaque burden, likely directs many of the expression changes in astrocytes (Hokama et al., 2013; Shijo et al., 2016). HIF3A, which inhibits hypoxia-induced genes, seemed to be responsible for some neuronal transitions. The lysosomal master transcription factor TFEB rises in AD astrocytes, where it controls expression of 10 loci that associated with AD in GWAS—BIN1, CLDN11, POLN, STK32B, EDIL3, AKAP12, HECW1, WDR5, LEMD2, and DLC1.
“The link to TFEB is really interesting, and speaks to the role of lysosome dysfunction in AD,” Fenghua Hu at Cornell University in Ithaca, New York, wrote to Alzforum.
Despite the wealth of data, the study’s findings are limited by the small sample size, the authors acknowledge. Many more samples will be needed to parse out how age, disease stage, and individual genetic variation affect gene expression. Curiously, the specific genes identified as changing in AD in this study showed little overlap with those found by Tsai and Kellis. For example, among 182 differentially expressed microglial genes in this data set, only 11 also turned up in the earlier study. Numbers were similar for the other cell types. Nonetheless, the two data sets do broadly agree on which processes are up- or downregulated in specific cell types.—Madolyn Bowman Rogers
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- Cell-Specific Enhancer Atlas Centers AD Risk in Microglia. Again.
- Zhang B, Gaiteri C, Bodea LG, Wang Z, McElwee J, Podtelezhnikov AA, Zhang C, Xie T, Tran L, Dobrin R, Fluder E, Clurman B, Melquist S, Narayanan M, Suver C, Shah H, Mahajan M, Gillis T, Mysore J, MacDonald ME, Lamb JR, Bennett DA, Molony C, Stone DJ, Gudnason V, Myers AJ, Schadt EE, Neumann H, Zhu J, Emilsson V. Integrated systems approach identifies genetic nodes and networks in late-onset Alzheimer's disease. Cell. 2013 Apr 25;153(3):707-20. PubMed.
- Hokama M, Oka S, Leon J, Ninomiya T, Honda H, Sasaki K, Iwaki T, Ohara T, Sasaki T, Laferla FM, Kiyohara Y, Nakabeppu Y. Altered Expression of Diabetes-Related Genes in Alzheimer's Disease Brains: The Hisayama Study. Cereb Cortex. 2013 Apr 17; PubMed.
- Shijo M, Honda H, Suzuki SO, Hamasaki H, Hokama M, Abolhassani N, Nakabeppu Y, Ninomiya T, Kitazono T, Iwaki T. Association of adipocyte enhancer-binding protein 1 with Alzheimer's disease pathology in human hippocampi. Brain Pathol. 2016 Dec 20; PubMed.
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- AD Genetic Risk Tied to Changes in Microglial Gene Expression
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- Expression, Expression, Expression—Time to Get on Board with eQTLs
- Rogue Gene Networks Track with Neurodegeneration Across Diseases
- Microglia Reveal Formidable Complexity, Deep Culpability in AD
- Grubman A, Chew G, Ouyang JF, Sun G, Choo XY, McLean C, Simmons RK, Buckberry S, Vargas-Landin DB, Poppe D, Pflueger J, Lister R, Rackham OJ, Petretto E, Polo JM. A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation. Nat Neurosci. 2019 Dec;22(12):2087-2097. PubMed.