| Literature DB >> 31492831 |
Gareth Williams1, Ariana Gatt2, Earl Clarke2, Jonathan Corcoran2, Patrick Doherty2, David Chambers2, Clive Ballard3.
Abstract
Alzheimer's disease is a complex disorder encompassing multiple pathological features with associated genetic and molecular culprits. However, target-based therapeutic strategies have so far proved ineffective. The aim of this study is to develop a methodology harnessing the transcriptional changes associated with Alzheimer's disease to develop a high content quantitative disease phenotype that can be used to repurpose existing drugs. Firstly, the Alzheimer's disease gene expression landscape covering severe disease stage, early pathology progression, cognitive decline and animal models of the disease has been defined and used to select a set of 153 drugs tending to oppose disease-associated changes in the context of immortalised human cancer cell lines. The selected compounds have then been assayed in the more biologically relevant setting of iPSC-derived cortical neuron cultures. It is shown that 51 of the drugs drive expression changes consistently opposite to those seen in Alzheimer's disease. It is hoped that the iPSC profiles will serve as a useful resource for drug repositioning within the context of neurodegenerative disease and potentially aid in generating novel multi-targeted therapeutic strategies.Entities:
Mesh:
Year: 2019 PMID: 31492831 PMCID: PMC6731247 DOI: 10.1038/s41398-019-0555-x
Source DB: PubMed Journal: Transl Psychiatry ISSN: 2158-3188 Impact factor: 6.222
The AD sets show varying degrees of overlap
| AD | BRAAKmild | COGI | 5xFAD | 3xTG | |
|---|---|---|---|---|---|
| AD | 11.26 ± 0.45 | −1.81 ± 0.38 | 13.34 ± 1.08 | 3.38 ± 0.33 | 0.05 ± 0.11 |
| BRAAKmild | 4.43 ± 1.00 | −1.03 ± 0.83 | −0.35 ± 0.34 | −0.04 ± 0.20 | |
| COGI | 15.10 ± 3.47 | 3.09 ± 0.70 | 0.26 ± 0.23 | ||
| 5xFAD | 13.23 ± 1.67 | 0.46 ± 0.21 | |||
| 3xTG | −0.06 ± 0.25 |
The overt AD profile set is highly correlated with the cognitive decline profiles. There is a degree of overlap with the 5xFAD profiles but poor agreement with the mild BRAAK and 3xTG animal profiles. The 3xTG profile set is conspicuous for not being internally consistent or having significant overlap with the other AD sets. The numbers in the table correspond to the average Z score across pairs in the sets, excluding correlations of profiles with themselves
Fig. 1The overall comparison between the iPSC profiles and those on the cancer cell lines can be framed as an enrichment analysis for the rank of iPSC queries against CMAP.
For each drug, the correlation between iPSC and CMAP profiles are ranked against the remainder of the CMAP data set profiles. For a good agreement between the profiles, one would expect an enrichment in high rank scores and this is the case for iPSC profiles. The top plot shows the rank distributions in bins of 50 with a clear bias for high rank scores. The bottom plot is the cumulative distribution of ranks contrasted with the non-enriched diagonal. The significance is measured by an MC simulation randomising rank orders and counting the number of times peak deviation from the diagonal exceeds that in the original enrichment
Compounds with iPSC profiles showing anti-correlation with at least two representative AD profiles, referred to as the ADC set
The numbers are the correlation and the associated binomial enrichment score is reflected in the red intensity. The compound descriptions are given and those with reported neuroprotective activity are highlighted in grey
Fig. 2The ADC compounds have relatively high intra-profile correlations.
The correlation Z scores are shown on a heat map with the ADC component split off to highlight the enhanced correlation. The average correlation for intra-ADC profiles is 2.43 as opposed to 0.77 for all other pairs
Fig. 3The gene expression heat map for genes consistently regulated by the ADC set.
Genes were selected based on their having a sum sense change ratio >33%. Specifically, the sum sense change ratio is defined as , where g is the expression change of a gene in the ith profile. The compounds are clustered with the UPGMA algorithm and the corresponding dendrogram shown at left