1. Anh Pham
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease

2. Background knowledge
Alzheimer’s disease (AD) is a neurodegenerative disorder caused by the accumulation of amyloid-β plaques and neurofibrillary tangles
Symptoms are usually decrease in neuronal and synaptic activities, and decline in brain function
Several genes have been implicated in AD, but chromatin state alterations during neurodegeneration remain uncharacterized. 
Many genes has been known about AD but chromatin state is not really known so this is what they are testing

3. Causes
Downregulation in the synaptic gene and regulatory regions, and upregulation of immune genes and regulation by ETS family of transcriptional regulators
 increased in enhancers caused AD genetic variant to be enhanced which can lead to AD
Genes diverge during speciation so they have similar ancestor

4. Mouse
Its too difficult to measure epigenetic changes in human so the scientist worked with the hippocampus of CK p25 mouse (AD) and the control is CK littermate mouse.
Measure transcriptional epigenetic changes during early and late stages of neurodegeneration.
 They imitate neurodegeneration in mouse by using Cdk5 activator protein p25 which causes DNA damage. This lead to an increase in amyloid-β levels in the early stages and decreases in neuronal and synaptic activities in the late
Looked at transcription and chromatin state of mouse with AD like neurodegeneration.
Looking at the hippocampus during early and late stage of AD
performed transcriptome analysis by using RNA sequencing to quantify gene expression changes for 13,836 ENSEMBL genes

5. Transcriptome analysis showed 2,815 upregulated genes and 2,310 downregulated genes in the CK- p25 AD mouse model as compared to CK littermate controls
The changes to the genes shows consistency of pathophysiology of AD patients.
When looking at the microglia (immune brain cells) it did show changes to the brain cell
Used reverse transcription followed by quantitative PCR (RT– qPCR) CD11b+ CD45low microglia show specific cell type activations.
The changes seen in the mouse subjects correlates with the same gene expressions in 22 patients with AD
Inflamtion and disfunction in the microglia
Trancriptome analysis uses RNA sequencing
The red shows all the genes that has been upregulated. They got the results by using reverse transcription and pcr

6. Epigenomics analysis ChromHMM
chromatin immunoprecipitation sequencing (ChIP-seq)
How they know using mouse was good because it can line up with human genes
chromatin immunoprecipitation sequencing (ChIP-seq) to profile seven chromatin marks9: histone 3 Lys 4 trimethylation (H3K4me3; associated primarily with active promoters); H3K4me1 (enhancers); H3K27 acetylation (H3K27ac; enhancer/promoter activation); H3K27me3 (Polycomb repression); H3K36me3 and H4K20me1 (transcription); and H3K9me3 (heterochromatin)
DNA analyzes compares DNA protein interaction
Show similarities of Human AD to mouse AD
ChromHMM is software for learning and characterizing chromatin states.
to learn a chromatin state model (Methods and Extended Data Fig. 3a) defined by recurrent combinations of histone modifications, consisting of promoters, enhancers, transcribed, bivalent, repressed, heterochromatin and low-signal states (Extended Data Fig. 3a). We defined 57,840 active promoters using H3K4me3 peaks within promoter chromatin states, and 151,447 active enhancer regions using H3K27ac peaks within enhancer chromatin states 

7. How to know if mouse genes matches with humans?
Using the ChIP-seq and ChromHMM they were able to match orthologous genes of human and mouse
Also matched orthologous noncoding regions
matches for 90% of promoter regions, 84% of enhancers, 74% of Polycomb- repressed regions and 33% of heterochromatin region
Quantification
Using in H3K4me3 (promoter) levels shows 3,667 increased in levels and 5,056 decreased level peaks. These are gene expression changes in early, middle, and late stages of neurodegeneration.
H3K27ac (enhancers) shows 2,456 increased level and 2,154 decreased level
Promotors are more significant
Promotor causes for AD

8. How increased of promoters can be a sign of AD
Increased promoters level bound to macrophages and BV-2 microglial-like cell are implications of AD.
The PU.1 (SPI1 gene) shows an increased in enhancer and expression levels which causes the upregulation of promoter.
PU.1 is part of the ETS family (transcription factor) that is believed to cause neurodegeneration
Only increased-level promoters were bound in macrophages and BV-2 microglial-like cells17,18,19 that are both implicated in AD2

9. The PU.1 (SPI1 gene) shows an increased in enhancer and expression levels which causes the upregulation of promoter.
PU.1 is part of the ETS family (transcription factor) that is believed to cause neurodegeneration
,  figure H

10. Promoters continue.
Decreased enhancers and promoter levels was caused by the binding to CREB and SRF.
They are neuronal activity regulators.
The regulator decrease the enrichment in p300 region while PU.1 increased enrichment
These regulator could be a way to negate the effect of AD neurodegeneration

12. Using Chromatin State to test for AD
Tested 127 human cell tissues
Orthologous regions that shows increased in enhancers level in mouse correlates with immune cell enhancers in human (P < 10−100)
Orthologous regions that shows decreased in enhancers level in mouse correlates with fetal brain tissues enhancer in human (P < 10−8 consistent; P < 10−17 late-stage)
This shows that increase in microglia activation and spread means neurodegeneration is progressing

14. Chromatin State verification
luciferase reporter assay was used to put gene expression in immortalized murine microglial (BV-2) and neuroblastoma (N2a) cell lines.
Used to verify increased enhancers
8 out of 9 showed that the luciferase was able to activate expression.
BIN1 ans ZNF710 was active in both microglial and neuroblastoma cells while the other six one showed in BV-2 cell.
This tells us that increased in enhancers level is a sign of AD

16. CD14 role in AD
To clarify that enhancer plays a role in AD. Enhancer CD4+ T cells and CD14+monocytes was enriched.
The SNPs of these enhancers was then studied using Genome wide association studies.
Concluded that the enrichment of AD associated variant such as CD14+ suggest AD conditions is caused by immune function while the decreased in neuronal plasticity is affected by age, diet , physical activity (non genetic)

17. Conclusion
AD is mostly associated with immune genes but enhancers and promoter also plays a role in the progression of AD
Ways to alleviate AD
Using CRISPR or Cas9 to edit out genes associated with AD
Editing out transcription factor PU.1, PU.1 motif, or PU.1 binding sites can help relieve AD
Have better diet and perform more physical activities to stop the decreases in neural plasticity.

18. References
Gjoneska, Elizabeta, et al. “Conserved Epigenomic Signals in Mice and Humans Reveal Immune Basis of Alzheimer's Disease.” Nature News, Nature Publishing Group, 18 Feb. 2015,