NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE239480 Query DataSets for GSE239480
Status Public on Jan 08, 2025
Title The Role of TCF7L2 in Hepatic Metabolic Zonation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Background and Aims: The molecular mechanisms regulating the zonal distribution of metabolism in liver are incompletely understood. Here we used multimodal single nuclei genomics techniques to examine the spatial transcriptional function of the transcription factor 7-like 2 (TCF7L2) in rodent liver. We also determined whether inactivation of TCF7L2 disrupted the normal metabolic architecture of the liver and influenced the development of fibrotic liver diseases. Methods: Multimodal single nuclei RNA- and ATAC-Seq were used to examine the spatial expression and DNA binding activity of TCF7L2 across the liver lobule. The transcriptional activity of TCF7L2 was targeted by removing exon 11 of Tcf7l2, which encodes part of the DNA binding domain (DBD). The effect of TCF7L2 inactivation on transcriptional regulators of zonation, hepatic metabolism, and the development of fibrosis was investigated in Hep-TCF7L2ΔDBD mice fed the Gubra Amylin Nash (GAN) or choline-deficient amino acid-defined high fat (CDAHFD) diet for 24- and 8-weeks, respectively. Results: Tcf7l2 mRNA expression was ubiquitous across the liver lobule, but the presence of the consensus TCF/LEF DNA binding motif in open chromatin was enriched in pericentral (PC) hepatocytes in zone 3, but not periportal (PP) or mid-lobular hepatocytes in zones 1 and 2. Consistent with this, PC hepatocyte gene expression was lost in Hep-TCF7L2ΔDBD mice, which we link to alterations in the transcriptional activity of zonal repressors Tbx3 and Tcf7l1. The absence of PC hepatocyte gene expression resulted in impaired bile acid synthesis and hepatic cholesterol accumulation, and disrupted metabolic pathways linked to ammonia detoxification, most notably glutamine/glutamate homeostasis. Following the CDAHFD, Hep-TCF7L2ΔDBD mice developed more severe hepatic fibrosis. Finally, TCF7L2 expression declined in human livers as the severity of fibrosis progressed. Conclusion: TCF7L2 is an important transcriptional regulator of PC hepatocytes in zone 3, and regulates multiple zonated metabolic pathways that may contribute to the development of fibrotic liver diseases.
 
Overall design Animal models Mice with LoxP sites flanking exon 11 of the Tcf7l2 gene, which encodes part of the DNA binding domain of the TCF7L2 protein, have been described previously [23]. Albumin-Cre (Alb-Cre) mice were obtained from The Jackson Laboratory (stock # 003574). Mice were fed either regular chow (Envigo, cat # 7012), a Gubra Amylin NASH (GAN) diet (40% fat, 20% fructose, 2% w/w cholesterol; Research Diets Inc, D09100310) for 24-weeks, or a methionine and choline deficient, 60% HFD diet (CDAHFD, Research Diets cat#: A06071302) for 8-weeks. Tcf7l2 expression was examined in a cohort of rats fed the same CDAHFD diet for 14-weeks, supplemented with NaNO2 (25 mg/kg i.p. three times a week between weeks 4 and 14), and in mice fed a fast food diet (FFD) for 11 months. This consisted of a commercially available high fat, high cholesterol diet (Research Diets Inc, D12079B) and drinking water containing 23.1 g fructose and 17.2 g glucose per 1000 mL of water. The TCF/Lef:H2B-GFP reporter mouse was obtained from The Jackson Laboratory (stock # 013752) and was used to examine TCF/LEF activity in liver sections. Mice were provided ad-libitum access to acidified reverse osmosis water (pH 2.5 – 3.0) and Nestlets. All mice were housed in ventilated cages (Allentown Caging Equipment Company, cat # 75JAG) with irradiated Sani-Chip bedding in a room maintained at 75 ± 3°F and on a 14 h light/10 h dark cycle. Littermate LoxP/LoxP controls were used in all experiments. All rodent studies, with the exception of those carried out by Gilead Sciences Inc (Mouse FFD and rat CDAHFD), were approved by the UT Health San Antonio Institutional Animal Care and Use Committee (IACUC). Single-nuclei multiomics Nuclei were isolated from approximately 20 mg of frozen mouse liver harvested from control (TCF7L2LoxP/LoxP) and liver-specific TCF7L2 mutant mice (Hep-TCF7L2ΔDBD). 10X Genomics Chromium single nuclei multiome gene expression and Assay for Transposase-Accessible Chromatin (ATAC) libraries were prepared from approximately 5000 nuclei/mice at the Genome Sequencing Facility at the University of Texas Health at San Antonio (UTHSA). Liver samples were processed in pairs (one control and one mutant) on three consecutive days to minimize batch effects. Library quality and quantity were assessed using the 2100 Bioanalyzer and were sequenced on a NovaSeq 6000 (Illumina, CA, USA). We performed two distinct analyses that relied on separate clustering. First, we used the control samples to establish the methodology of quantifying zonal gene expression and transcription factor occupancy, including TCF7L2. In a distinct analysis, we then examined the consequences of TCF7L2 transcriptional inactivation on zonation in control vs. mutant livers. A detailed description of the computational methodology used to integrate and analyze the multiomic data described throughout the manuscript is provided in the Supplementary Materials.
 
Contributor(s) Ayala I, Hebbale S, Mononen J, Sholto M, Shannon C, Valdez I, Fourcadot M, Bakewell T, Romero G, Asmis M, Freitas L, Aguiar Vallim T, Heikkinen S, Norton L
Citation missing Has this study been published? Please login to update or notify GEO.
BioProject PRJNA997726
Submission date Jul 27, 2023
Last update date Jan 08, 2025
Contact name Luke Norton
E-mail(s) nortonl@uthscsa.edu
Organization name UTHSCSA
Street address 7703 Floyd Curl Dr
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (12)
GSM7665993 Control GEX Sample 1
GSM7665994 Control GEX Sample 2
GSM7665995 Control GEX Sample 3

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE239480_2606_M_barcodes.tsv.gz 18.0 Kb (ftp)(http) TSV
GSE239480_2606_M_features.tsv.gz 2.9 Mb (ftp)(http) TSV
GSE239480_2606_M_matrix.mtx.gz 158.2 Mb (ftp)(http) MTX
GSE239480_2607_M_barcodes.tsv.gz 20.6 Kb (ftp)(http) TSV
GSE239480_2607_M_features.tsv.gz 3.1 Mb (ftp)(http) TSV
GSE239480_2607_M_matrix.mtx.gz 201.8 Mb (ftp)(http) MTX
GSE239480_2618_M_barcodes.tsv.gz 21.0 Kb (ftp)(http) TSV
GSE239480_2618_M_features.tsv.gz 3.1 Mb (ftp)(http) TSV
GSE239480_2618_M_matrix.mtx.gz 199.0 Mb (ftp)(http) MTX
GSE239480_2643_C_barcodes.tsv.gz 16.2 Kb (ftp)(http) TSV
GSE239480_2643_C_features.tsv.gz 2.9 Mb (ftp)(http) TSV
GSE239480_2643_C_matrix.mtx.gz 150.7 Mb (ftp)(http) MTX
GSE239480_2645_C_barcodes.tsv.gz 18.1 Kb (ftp)(http) TSV
GSE239480_2645_C_features.tsv.gz 3.1 Mb (ftp)(http) TSV
GSE239480_2645_C_matrix.mtx.gz 167.8 Mb (ftp)(http) MTX
GSE239480_370_C_barcodes.tsv.gz 16.7 Kb (ftp)(http) TSV
GSE239480_370_C_features.tsv.gz 2.9 Mb (ftp)(http) TSV
GSE239480_370_C_matrix.mtx.gz 132.7 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap