BATF Regulates T Regulatory Cell Functional Specification and Fitness of Triglyceride Metabolism in Restraining Allergic Responses

Preserving appropriate function and metabolism in regulatory T (Treg) cells is crucial for controlling immune tolerance and inflammatory responses. Yet how Treg cells coordinate cellular metabolic programs to support their functional specification remains elusive. In this study, we report that BATF couples the TH2-suppressive function and triglyceride (TG) metabolism in Treg cells for controlling allergic airway inflammation and IgE responses. Mice with Treg-specific ablation of BATF developed an inflammatory disorder characterized by TH2-type dominant responses and were predisposed to house dust mite-induced airway inflammation. Loss of BATF enabled Treg cells to acquire TH2 cell-like characteristics. Moreover, BATF-deficient Treg cells displayed elevated levels of cellular TGs, and repressing or elevating TGs, respectively, restored or exacerbated their defects. Mechanistically, TCR/CD28 costimulation enhanced expression and function of BATF, which sustained IRF4 activity to preserve Treg cell functionality. Thus, our studies reveal that BATF links Treg cell functional specification and fitness of cellular TGs to control allergic responses, and suggest that therapeutic targeting of TG metabolism could be used for the treatment of allergic disease

Harnessing Chromatin 3D interactions to Understand Ancestry‐Specific Alzheimer Disease (AD) risk

Background Ancestry‐specific Alzheimer Disease (AD) genetic risk is well recognized. Chromatin 3D interaction map in AD‐relevant cells with different ancestries is lacking but needed to understand the genetic/epigenetic basis for AD in diverse populations. We have shown that the local ancestry (LA) block (∼2Mb in size) surrounding APOE confers differential genetic risk for APOE ε4 carriers in Non‐Hispanic Whites (NHW) and African Americans (AA). Recently, we reported that NHW APOE ε4 carriers have a higher APOE ε4 expression and higher number of astrocytes compared to their AA counterparts in the frontal cortex. We therefore sought to characterize chromatin 3D interactions in astrocytes within different APOE LA. Method Induced pluripotent stem cells (iPSCs) with African or European LA block (N=2 individuals for each) were differentiated into astrocytes. Chromatin Hi‐C libraries were constructed with 4‐cutter enzyme and sequenced targeting 500 million pair‐end reads per library. Spatial genome structure was examined at compartment, topological associated domain (TAD), and loop levels. To better define enhancer‐promoter interaction (EPI), high‐resolution contact matrices were built using the HiCorr and DeepLoop algorithms. Result Each library generated over 250 million uniquely mapped, non‐redundant reads for Hi‐C analysis. Compartment and TAD had limited variability among samples (correlation co‐efficiency = 0.62∼0.90 for compartment, 0.84∼0.94 for TAD). Chromatin loop, which usually represents EPI, displays higher variability among samples (correlation co‐efficiency = 0.38∼0.75). In the 5kb‐contact‐matrix analysis, a chromatin interactive event involving APOE was detected, which is supported by Capture‐C data. The higher‐resolution 500bp‐contact‐matrix analysis revealed multiple better‐defined interactions within the event. Of particular interest, an interaction between the 5’end of TOMM40 and CLPTM1 (about 100 kb apart from each other) surrounding APOE is only observed on European but not African LA background. Conclusion Chromatin loop displays more inter‐individual variations compared to other spatial genome structures and therefore is more informative in elucidating the epigenetic basis for inter‐ancestry differences in gene expression regulation. While identifying chromatin loop from Hi‐C data at higher resolution is challenging, it has the potential to delimitate EPI and offers insights on the ancestry‐specific AD genetic risk by providing functional mechanisms underlying AD‐associated genetic variants

ATAC-seq on iPSC derived astrocytes to assess chromatin accessibility differences between African and European local ancestry

Local ancestry (LA) surrounding the APOE4 allele is associated with an increased risk for Alzheimer Disease (AD) in European (EU) LA compared to African (AF) LA. We recently demonstrated that APOE4 has significantly higher expression in astrocytes in brain from EU compared to AF APOE4 LA carriers, but the specific molecular mechanism leading to this difference is not known. We investigated whether evaluating chromatin accessibility and gene expression profiles of inducible pluripotent stem cell (iPSC) derived astrocytes in the LA region in both AF and EU LA could lead us to identify potential regulatory factors affecting chromatin remodeling and expression of APOE. We assayed for Transposase Accessible Chromatin (ATAC-seq), and RNA-seq in three iPSC derived astrocytes from two AF LA and one EU LA individuals with AD. We processed the ATAC-seq data with the ENCODE ATAC-seq pipeline and called peaks using MACS2. An average of 692 peaks were detected in the LA region with no statistical difference between EU and AF LA. Interestingly, an African APOE4 homozygote LA astrocyte line with high APOE expression had an exclusive ATAC peak at the APOE promoter. Amongst the transcription factors (TFs) suggested to bind this differentially accessible peak in APOE are HNF4A and TEAD4. Both TFs had significantly increased expression in this astrocyte line compared to the other lines. Additionally, differential accessibility in this line include peaks in an intragenic enhancer of PVRL2 and the promoter of CBLC, both shown to be bound by HNF4A and both overexpressed in this cell line and one in the promoter of CYP2S1 with TEAD4 binding, which was also overexpressed. This study is one of the first studies to compare chromatin accessibility in AF and EU ancestries. It also represents initial efforts to investigate potential mechanisms and factors, using iPSC-derived cell lines, that could contribute to the differential expression we have previously reported in APOE4 between AF and EU LA brains. Our data suggest that elevated astrocytic expression of APOE4 is associated with rs