Newly Developed Triple RNA-Seq Method Used to Expand Gene Expression Studies

A team of scientists from Germany has developed a variation of RNA-seq called triple RNA-seq. They used this method to investigate coinfections with cytomegalovirus and Aspergillus fumigatus, which can pose a serious threat in organ and stem cell transplantation.

According to the study, published in Cell Reports yesterday, triple RNA sequencing dissects the gene expression of three players and their interplay in infection processes. "Up to now, science has in many cases not known why an infection with a certain pathogen can make the affected person more susceptible to an infection with a second pathogen," explains senior author Jürgen Löffler. In such cases, dual RNA-seq was insufficient to provide the desired answers.

In their study, the researchers used the triple RNA-seq method to investigate what happens when monocyte-derived dendritic cells are infected with both Aspergillus fumigatus and the human cytomegalovirus. They were able to prove that the two pathogens influence each other, while also simultaneously affecting the immune cell in a different way than one pathogen alone otherwise would. For example, the cytomegalovirus weakened the fungal-mediated activation of pro-inflammatory signals, while Aspergillus affects viral clearance.

At the same time, the team has identified specific genes in immune cells whose expression profiles differ significantly during an infection with both pathogens, compared to a single infection. These genes could thus serve as biomarkers for the timely identification of a co-infection after transplantation.

The scientists now hope that the triple RNA-seq technology will also help to better understand other cases of common infections, such as viruses and bacteria, and to prevent their potentially serious consequences. "Promising models for understanding how an infection makes the host more susceptible to another pathogen include certain strains of Salmonella and the human immunodeficiency virus (HIV), streptococci and influenza virus, or Chlamydia and human herpes virus," says co-author Alexander Westermann. As a next step, Westermann plans to use the triple RNA-seq technique to investigate infections in which two different types of bacteria jointly influence the course of the disease.