Green, P. H. R. | Search bioRxiv

bioRxiv2022

Toward a Cell Culture Model of Portal Axis Lipid Handling

The health risks posed by excessive visceral white adipose tissue (WAT) may arise from exposure to deleterious intestinal factors in transit through the portal system. These may include an altered bile acid (BA) pool - particularly with respect to 12-hydroxylated BA (12-HBA), which we have previously demonstrated are closely associated with insulin resistance. However, given the complexity of the enterohepatic milieu, we have worked to develop a co-culture system that allows for controlled study of the interactions between human induced pluripotent stem cell (hiPSC) derived adipocytes and primary human intestinal organoids (hIO). We present preliminary data on the characterization of both cellular compartments and their interactions, particularly in the context of BA treatment. We have recapitulated the basic functionality of each tissue type and have found reciprocal, potentially important changes in gene expression in each. However, we also have encountered numerous technical challenges in the development of this co-culture system and provide methodological observations to assist others seeking to work with a co-culture system of this type.

cell biology↗

bioRxiv2019

Allele-specific DNA methylation is increased in cancers and its dense mapping in normal plus neoplastic cells increases the yield of disease-associated regulatory SNPs

BackgroundMapping of allele-specific DNA methylation (ASM) can be a post-GWAS strategy for localizing regulatory sequence polymorphisms (rSNPs). However, the advantages of this approach, and the mechanisms underlying ASM in normal and neoplastic cells, remain to be clarified. ResultsWe performed whole genome methyl-seq on diverse normal cells and tissues and three types of cancers (multiple myeloma, lymphoma, glioblastoma multiforme). After excluding imprinting, the data pinpointed 15,114 high-confidence ASM differentially methylated regions (DMRs), of which 1,842 contained SNPs in strong linkage disequilibrium or coinciding with GWAS peaks. ASM frequencies were increased 5 to 9-fold in cancers vs. matched normal tissues, due to widespread allele-specific hypomethylation and focal allele-specific hypermethylation in poised chromatin. Cancers showed increased allele switching at ASM loci, but disruptive SNPs in specific classes of CTCF and transcription factor (TF) binding motifs were similarly correlated with ASM in cancer and non-cancer. Rare somatic mutations affecting these same motif classes tracked with de novo ASM in the cancers. Allele-specific TF binding from ChIP-seq was enriched among ASM loci, but most ASM DMRs lacked such annotations, and some were found in otherwise uninformative "chromatin deserts". ConclusionsASM is increased in cancers but occurs by a shared mechanism involving disruptive SNPs in CTCF and TF binding sites in both normal and neoplastic cells. Dense ASM mapping in normal plus cancer samples reveals candidate rSNPs that are difficult to find by other approaches. Together with GWAS data, these rSNPs can nominate specific transcriptional pathways in susceptibility to autoimmune, neuropsychiatric, and neoplastic diseases. Custom genome browser tracks with annotated ASM loci can be viewed at a UCSC browser session hosted by our laboratory (https://bit.ly/tycko-asm)

genomics↗