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Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

By July 27, 2020 No Comments


CARTANA In Situ Sequencing (CARTANA ISS) technology provides unique spatial gene expression information through simultaneous detection of hundreds of genes at single-cell resolution and within the morphological context.

In a recent study by Chen et al. (2020) on the effect of amyloid-β plaques’ formation on Alzheimer’s disease progress, the use of CARTANA ISS technology provided novel insight at the single-cell level and helped creating a detailed picture of the induced transcriptional responses of different brain cells with spatial context. This work offers more conclusive evidence on the role of amyloid-β plaques in the neurodegenerative process.


Established scientific techniques have given us extensive understanding of the cellular physiology and pathology of Alzheimer’s disease (AD). However, the exact role of amyloid-β plaques in the neurodegenerative process remains unclear. In addition, most studies have focused on the response of microglia towards amyloid-β plaque formation and less is known about other brain cells such as neurons, astrocytes or oligodendrocytes (Figure 1) 2, 3, 4, 5. Given the fact that amyloid lowering therapies show little effects in improving memory, this gap is particularly relevant to provide insight.

Therefo re, there is a need to implement new technologies to broaden the knowledge of molecular mechanisms and processes involved in the development of AD. The use of these new technologies can potentially also lead to more efficient diagnostics and treatment strategies.

Amyloid-β plaques and their role in Alzheimer’s disease

Amyloid-β peptides are fragments of a transmembrane protein called amyloid precursor protein (APP). Amyloid-β peptides are formed at the plasma membrane by proteolysis and are usually released into the extracellular space and degraded. In AD brains, these fragments aggregate into big clusters called amyloid-β plaques, which are mainly found in hippocampus, amygdala, entorhinal cortex and basal forebrain. Amyloid-β plaques have a negative impact on memory, learning and emotional behaviour. It has been proven that the presence of amyloid-β plaques results in synapses number reduction and neuronal damage6,7.

Figure 1. Illustration of multicellular pathway induced by amyloid-β plaque in AD brain.


In Situ 2D-RNAseq via Spatial Transcriptomics – Multicellular gene co-expressing networks around the amyloid plaque

Extensive Spatial Transcriptomics (ST)8 analysis of coronal brain sections from a knock-in AD mouse model, showed expression changes of 57 Plaque-Induced Genes (PIGs) in several cell types. However, ST can only provide spatial resolution of spots at 100 μm in diameter, which is not sufficient to capture the cellular response in the plaque niches that are normally 10-100 μm in diameter.

CARTANA In Situ Sequencing – single cell information of the response network

In order to independently evaluate which cell types contributed to the PIG response, CARTANA ISS technology9,10 was used on mouse and post-mortem human brain sections, respectively. The ISS assay was designed to simultaneously target 84 mouse and 222 human genes, including PIGs and cell type specific markers (Figure 2 and 3).

Figure 2. CARTANA ISS shows differences between wild type and knock-in AD mouse model and provided PIGs location at single-cell resolution.

Figure 3. Detection of 222 genes in post-mortem human brain using CARTANA ISS.

Results obtained with CARTANA ISS validated those by ST and complemented the study by providing single-cell resolved transcriptional profiles of the plaque reactive network. These results revealed strong and coordinated plaque responses mainly in microglia and astrocytes (Figure 4).

Figure 4. A. Illustration of the classification of the genes into 5 concentric rings around the plaques. B. Cellular distribution based on rings was revealed with CARTANA ISS.


Chen et al. (2020) have identified a network of gradually co-expressed genes in response to increasing amyloid stress in different brain cell types. This response was observed for the first time at single-cell resolution and within intact tissue samples, demonstrating the power of CARTANA ISS technology in both mouse and human samples. Such a thorough exploration enabled by novel in situ analysis technologies helps to understand the exact role of amyloid plaques in the development and progression of Alzheimer’s disease.


1. Chen, W.T. et al. (2020). Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease. Cell. 182, 1-16.
2. Keren-Shaul, H. et al. (2017). A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease. Cell. 169(7), 1276–1290.
3. Krasemann, S. et al. (2017). The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases. Immunity. 47(3), 566–581.
4. Sala Frigerio, C. et al. (2019). The Major Risk Factors for Alzheimer’s Disease: Age, Sex, and Genes Modulate the Microglia Response to Aβ Plaques. Cell Reports. 27(4), 1293–1306.e6.
5. Srinivasan, K. et al. (2020). Alzheimer’s Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation. Cell Reports 31, 107843.
6. Karran, E., Mercken, M. and De Strooper, B. (2011). The amyloid cascade hypothesis for Alzheimer’s disease: an appraisal for the development of therapeutics. Nat Rev Drug Discov. 10(9), 698–712.
7. Strooper, B. De and Karran, E. (2016). The Cellular Phase of Alzheimer’s Disease. Cell. 64(4), 603–615.
8. Ståhl, P. L. et al. (2016). Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 353(6294), 78–82.
9. Ke, R. et al. (2013). In situ sequencing for RNA analysis in preserved tissue and cells. Nature Methods. 10(9), 857–860.
10. Qian, X. et al. (2019). Probabilistic cell typing enables fine mapping of closely related cell types in situ. Nat Methods 17, 101–106.


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