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Epigenomic analysis of micro-dissected human liver reveals principles of zonated morphogenic and metabolic control

ABSTRACT: Epigenomic analysis of micro-dissected human liver reveals principles of zonated morphogenic and metabolic control

PROVIDER: PRJNA414905 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6188610.fastq.gz	Fastqsanger.gz
	SRR6188620.fastq.gz	Fastqsanger.gz
	SRR6188630.fastq.gz	Fastqsanger.gz
	SRR6188640.fastq.gz	Fastqsanger.gz
	SRR6188650.fastq.gz	Fastqsanger.gz

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Epigenomic analysis of micro-dissected human liver reveals principles of zonated morphogenic and metabolic control

Project description:To investigate the underlying molecular principles of metabolic and morphogenic zonation of the human liver lobule, we generated an integrated epigenetic map across three zones (pericentral, intermediate and periportal) by methylation and transcriptomic analysis of hepatocytes captured by laser micro-dissection. We observe a deep link between epigenetic zonation of human liver and a zonated expression of metabolic and morphogenic pathways: Key transcriptionally zonated enzymes in xenobiotic and glutamine metabolism show a strong anticorrelated methylation gradient indicating that zonal expression of these genes is partly controlled by epigenetic programs. Zonated DNA-methylation at binding sites of uniformly expressed transcription factors such as HNF4A and RXRα points to an epigenetic layer in regulatory networks and a zonated activity of their nuclear ligands and drugs such as fibrates and bile acids. The same holds for genes of the wnt morphogen pathway whose expression show a zonated methylation at binding sites of TCF4L2. A strong pericentral expression of LGR5 and AXIN2 and a corresponding expression gradient of the liver progenitor marker TBX3, indicates a predominant pericentral source of hepatocyte regeneration under steady-state conditions in humans. Conversely, the periportal expression of NOTCH and EPCAM at the border to the biliary tree as source of regeneration under injury conditions. Overall our data provide a deep understanding of molecular control of the zonal organisation in the human liver.

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Epigenomic map of human liver reveals principles of zonated morphogenic and metabolic control.

Project description:A deeper epigenomic understanding of spatial organization of cells in human tissues is an important challenge. Here we report the first combined positional analysis of transcriptomes and methylomes across three micro-dissected zones (pericentral, intermediate and periportal) of human liver. We identify pronounced anti-correlated transcriptional and methylation gradients including a core of 271 genes controlling zonated metabolic and morphogen networks and observe a prominent porto-central gradient of DNA methylation at binding sites of 46 transcription factors. The gradient includes an epigenetic and transcriptional Wnt signature supporting the concept of a pericentral hepatocyte regeneration pathway under steady-state conditions. While donors with non-alcoholic fatty liver disease show consistent gene expression differences corresponding to the severity of the disease across all zones, the relative zonated gene expression and DNA methylation patterns remain unchanged. Overall our data provide a wealth of new positional insights into zonal networks controlled by epigenetic and transcriptional gradients in human liver.

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Single-cell RNA-seq of sorted and micro-dissected mouse bone marrow cells

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Project description:We here systematically studied the interaction network of bone marrow cells. To this end, we micro-dissected many small interacting structures (cell doublets, triplets etc.) into single cells, and sequenced their mRNAs, to infer cell identity. After grouping the cells into cell types (based on the single-cell transcriptomes), we identified actual physical interactions that occurred more, or less, than what would be expected by chance. We compared the micro-dissected data to sorted hematopoietic stem cells. After mild dissociation of the bone marrow, we micro-dissected many small interacting structures (cell doublets, triplets etc.) into single cells, and sequenced their mRNAs. In addition, single hematopoietic stem cells were sorted (Lineage- Kit+ Sca1+ CD150+ CD48-) to sequence their transcriptome. In detail, the bone marrow was mildly flushed. Structures composed of about 10 to 20 cells were set apart. With needles and a micro-dissection microscope, we trimmed of smaller structures from these big structure. These smaller structures are mainly two to four cells attached together. These small structures were then further micro-dissected to single cells. The goal of doing these sequential dissections was to keep track of which cells were interacting with which. Each micro-dissected cell sample contains RNA-seq data for 96 single cells. Each single cells received a different barcode that allow us to entangle them, and to produce the processed .coutt.csv file. Each sorted hematopoietic stem cell sample represents a single cell. The processed data file expdata_BMJhscC.csv contains transcript counts for all analyzed cells.

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Project description:We report the continuous patterning and dynamic morphogenesis of hepatic, biliary and pancreatic structures, invaginating from a three-dimensional culture of human pluripotent stem cell (PSC). The boundary interactions between anterior and posterior gut spheroids differentiated from human PSCs enables autonomous emergence of hepato-biliary-pancreatic (HBP) organ domains specified at the foregut-midgut boundary organoids in the absence of extrinsic factor supply. The regional identity of the boundary region of anterior-posteior spheroids was analyzed by RNA-sequencing with micro-dissected boundary organoid into anterior, posterior, and boundary regions. Each region expressed the corresponding gut lineage markers. The early HBP specification markers including HHEX1 and PDX1 at the boundary were highly upregulated compared with the other two regions, indicating that the anterior-posterior boundary interactions autonomously generate HHEX and PDX1 positive cells in the absence of exogenous inductive factors. To delineate the HBP progenitor self-inductive mechanism, we evaluated the boundary specific expression profiles of known inductive signaling pathways that includes FGF, BMP, Hedgehog, NOTCH and retinoic acid (RA) signals, and found that the signal downstream of RA were activated prominently at the boundary region but not in the anterior or posterior regions.

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