Nat methods & Immunology: scientists have developed a new technology to study information exchange between cells - nichenet

February 18, 2020 / BIOON / -- recently, in two research reports published in the international journal Nature Methods and immunology, scientists from VIB ugent research center and other institutions in Belgium developed a new bioinformatics method to better study the molecular mechanism of communication between cells The method, called nichenet, can help researchers understand how gene expression in cells is regulated by interacting cells Meanwhile, nichenet technology can be widely used in research fields such as immunology and tumor biology Photo source: cc0 public domain In multicellular organisms, cells themselves do not play a role, but they can produce signal molecules that affect gene expression in the interacting cells This kind of cell-cell communication plays a very important role in many biological processes, such as cell development and function It is very important to study the communication mechanism between cells not only for understanding the basic biological process, but also for understanding the basic biological process It can also help to reveal the pathogenesis of many diseases, such as cancer In the tumor microenvironment, the interaction between cancer cells and other cells is very important for the growth of cancer cells The differentiation of macrophages is an essential key process of cell-cell communication, which is affected by other types of cells in macrophage environment or habitat The researchers worked with Kupffer cell, a macrophage living in the blood stream of the liver, to produce a large number of gene expression data of related cells According to researcher YVAN saeys, it may not be a simple task to use such data to reveal the communication between cells We need to develop a new and complex algorithm to solve such problems; based on the previous research results, researchers have developed a new method to analyze the molecular mechanism of the communication between cells The idea, the researchers explained, is to take advantage of the vast amount of knowledge available over the years about intercellular signals and use that knowledge to clarify which intercellular communication processes are taking place To do this, researchers must use a variety of machine learning and complex technologies, such as network algorithms for analyzing social networks Researcher saelens said that in essence, we can compare the nichenet technology with an imaginary biologist The imaginary biologist can not only know everything about intercellular communication, but also apply this knowledge to a complex large-scale database In the past, it took weeks of literature research to make a reasonable prediction of intercellular communication, But now researchers can do it with just one button The first case of nichenet test is the Kupffer cell habitat data obtained by the researcher guilliams laboratory The researchers in the laboratory can now confirm some signals predicted by nichenet technology through experiments It is nichenet technology that enables researchers to study some factors that they would not think of, and the technology can also be used as a necessary tool Help to reveal the habitat of Kupffer cells In addition to the Kupffer cell story, researchers can also use the nichenet technology in the tumor microenvironment to study the communication mechanism between cells The researchers used the technology in the previously published single cell data, but now they are studying the newly generated single cell database, how different types of therapies affect the cell interaction mechanism in the tumor microenvironment, and this Later researchers will use nichenet technology to further study how these effects affect tumors Finally, the researchers say these applications illustrate the value of nichenet technology, which plays a key role in cell communication in biological processes and disease development Reference materials: [1] Scientists' twitter 'for cells by VIB (the Flanders Institute for Biotechnology) [2] Robin browaeys et al Nickel: modeling intercellular communication by linking lives to target genes, nature methods (2019) Doi: 10.1038/s41592-019-0667-5 [3] Johnny bonnardel et al Stellate cells, hectocytes, and Endothelial Cells Imprint the Kupffer Cell Identity on Monocytes Colonizing the Liver Macrophage Niche , Immunity (2019) DOI: 10.1016/j.immuni.2019.08.017