Mapping the liver

The “Human Cell Atlas” project, launched by international researchers in October 2016 to decipher the totality of all human cells, is one example, and is quite reminiscent of the scope and depth that was brought to the Human Genome Project before it. As part of the Human Cell Atlas effort—which aims to provide a precise overview of which genes, proteins and other molecules are active in which cell type, and where precisely the cells are located—the laboratory of Dr. Dominic Grün at the Max Planck Institute for Immunobiology and Epigenetics says it has created a comprehensive map of all cell types in the healthy human liver using single-cell RNA sequencing tools.

Focusing on the liver makes a great deal of sense, given that it is one of the most important organs of the human body and plays an essential role in the metabolism, immune response and detoxification of the body—yet its cellular composition has remained rather incompletely understood.

But what makes the work at the Grün lab all the more notable is that the researchers there not only mapped out the liver’s cells, but also discovered new subpopulations of important liver cell types; moreover, as the Max Planck Institute noted, they “also demonstrated the usefulness of their human liver cell atlas as a resource to reveal how cells change in liver cancer. This shows that the atlas provides a powerful resource for basic research of liver diseases and a basis for developing novel therapies.”

Their comprehensive cell atlas of the liver was the focus of research they recently published in Nature on July 10, in a paper titled “A Human Liver Cell Atlas reveals Heterogeneity and Epithelial Progenitors.”

Based on the analysis of 10,000 cells from nine human donors, the cell atlas reportedly maps all important liver cell types, including hepatocytes, the major metabolic cells of the liver, endothelial cells lining the blood vessels, liver resident macrophages and other immune cell types, as well as bile duct cells and liver epithelial progenitors. With this data, the researchers say it is possible “to capture the diversity of cell types and cell states at an unprecedented resolution and to understand how they change during development or upon disease progression.”

The researchers also report they uncovered “an astonishing diversity” among individual cells of the alleged same cell type. They found new subtypes of hepatocytes, endothelial cells and macrophages, which, although not very different from one another in their morphological appearance, nonetheless possess discrete gene expression profiles. These discoveries were made possible by the significant progress of experimental and computational single-cell analysis methods, which enable cells to be examined at high resolution.

In single-cell RNA sequencing, the organ tissue to be investigated is dissociated into individual cells; these cells are then isolated and sequenced separately. The sequencing is used to determine how many messenger RNA molecules of each gene are present in the cell.

“The messenger RNA transmits the blueprints stored in the DNA to the protein factories. By measuring which RNA molecules are present in a cell at a certain point in time, we can identify which genes are active. This gives us a kind of fingerprint that provides us with a comprehensive insight into the very nature of each cell. This enables us to understand which functions the cell performs, how it is regulated and also what happens when diseases develop,” explained Grün.

The data obtained in this way are not both extensive and very complex, because the RNA molecules of thousands of genes in thousands of cells have to be quantified and interpreted simultaneously. In recent years, Grün has developed custom algorithms to assist him and his team in characterizing the different cell types and understand their developmental pathways.

Among their finding was the elucidation of a subpopulation of bile duct cells; bile ducts run through the entire liver to transport bile to the gallbladder.

“Our data show that cells within this rare subpopulation are precursor cells or progenitors. They are not only able to form organoids, which is a marked characteristic of stem cells, but also have the potential to develop into different cell types,” said Nadim Aizarani, the first author of the study. These progenitor cells either differentiate into hepatocytes or bile duct cells when cultivated in a culture medium. The Max Planck researchers are convinced that this precursor cell population plays an important role in liver regeneration and could also be involved in the development of liver diseases or tumors.

And while a great deal of liver research right now is focused on fatty liver disease, such as nonalcoholic fatty liver disease and nonalcoholic steatohepatitis, the new cell atlas also has a great deal of potential in cancer therapeutics research.

As the Max Planck Institute notes, “current approaches to analyze diseased tissue, such as tumor tissue, only provided an average value of the concentration of active genes for the entire tissue sample and thus only an average view of the tumor’s molecular profile.”

“The contribution of rare cell types or even individual cells is lost in this average value,” added Grün, “although it is perhaps precisely these few cells that determine whether a tissue is healthy or degenerates into cancer.”

But single-cell sequencing, on the other hand, captures the molecular signature of each healthy or diseased cell in the sample to be examined. The comparison with reference data from healthy tissue enables scientists to target the disease-causing molecular properties of tumor cells and may help to develop improved treatment options in the future.