Correcting for tuberculosis susceptibility

If a person infected with Mycobacterium tuberculosis (Mtb) coughs and releases the bacteria into the air, anyone who inhales the pathogen could develop tuberculosis. But not everyone is susceptible to the severe form of the disease. People can resist the infection if their macrophages destroy the invading bacteria after engulfing them. On the other hand, the macrophages in a susceptible individual provide the Mtb safe harbor and instead damage the body through an excessive inflammatory response.

In a recent Science Advances study, scientists described a method for conferring tuberculosis resistance to individuals with susceptible macrophages (1). The researchers compared the immune cells in resistant mice and susceptible mice and identified a combination of drugs to alter the latter’s macrophages so that they behaved like the former’s.

Igor Kramnik, a pathologist at Boston University and one of the study authors, first characterized the mouse model of tuberculosis susceptibility used in this study decades ago (2). Whereas other animal models had failed to recapitulate the precise symptoms observed in the lungs of people with tuberculosis, Kramnik’s mice provided an accurate representation of the disease in humans, making them useful for drug development.

Kramnik’s team showed that a mutation in the sst1 gene made a mouse’s macrophages susceptible to Mtb infections and allowed Mtb to grow unchecked in its lungs. The sst1 mutation did not lead to a clearly discernible, easily correctable change in the macrophages, however. Rather, it created widespread changes in the macrophages through its interactions with other genes and proteins. In other words, changing a susceptible macrophage into a resistant one would require an intricate understanding of the network of genes expressed in each.

Boris Kholodenko wears a white button down shirt and stands in a front of window.

Boris Kholodenko is a systems biologist who looks for ways to reverse pathogenic cell states.

credit: Boris Kholodenko

The complex molecular interactions that determine a cell’s state have always fascinated Boris Kholodenko, a systems biologist at University College Dublin and a study coauthor, and that made him the perfect research partner for Kramnik. Prior to the current study, Kholodenko described an approach, cell state transition assessment and regulation (cSTAR), for mapping the gene expression profiles that differentiate cell states and identifying drugs or other interventions that could drive a cell to transition from one state to another (3). Kholodenko initially envisioned cSTAR as a method for identifying cancer treatments. “Instead of killing cells, we may actually reverse oncogenic transformation,” he said. But through his work with Kramnik, Kholodenko saw an opportunity to demonstrate the far-reaching utility of cSTAR to find drug combinations that could reverse pathological cell states in any number of diseases, including tuberculosis.

Kholodenko and Kramnik’s teams collected macrophages from the bone marrow of Kramnik mice and mice with the resistant form of the sst1 gene. The researchers exposed each type of macrophage to tumor necrosis factor (TNF), a signaling protein that activates immune cells and induces fever and inflammation. From previous work, they knew that TNF would only prime macrophages equipped with a resistant sst1 gene to control an Mtb infection, so they sequenced the RNA transcribed in each type of macrophage after TNF exposure.

Focusing on the expression levels of 46 genes that they identified as responsive to TNF, the researchers used machine learning to differentiate resistant and susceptible macrophages and to quantify the separation between the two types. To force the susceptible macrophages to respond to TNF in the same way that resistant macrophages do, they tried treating the susceptible macrophages with a variety of drugs.

The plant-derived compound rocaglamide A, which interacts with inflammatory pathways, changed the gene expression profiles of susceptible macrophages to match that of resistant macrophages. When the researchers administered the compound to Mtb-infected macrophages, TNF-exposure reduced the number of Mtb in the immune cells, suggesting that the macrophages killed the bacteria that they engulfed. The treatment also promoted the immune cells’ antioxidant defenses.

You might use one tenth of the toxic dose, which is not terrible.
- Boris Kholodenko, University College Dublin

One potential challenge, though, is that rocaglamide A is highly toxic, and patients with tuberculosis may not tolerate large doses. When the researchers checked the effects of different drugs on susceptible macrophages, they also saw positive effects from a class of molecules that inhibit c-Jun N-terminal kinase (JNK) signaling, which is involved in a number of important cellular processes. The cSTAR analysis suggested that JNK inhibitors could complement the effects of rocaglamide A, so the researchers tried treating Mtb-infected macrophages with low doses of both drugs. Kholodenko said, “You might use one tenth of the toxic dose, which is not terrible.” In fact, the combination proved effective at lowering Mtb numbers in the immune cells.

Robert Wallis, an infectious disease physician with the Aurum Institute, had never heard of rocaglamide A as a treatment for tuberculosis prior to reading this study, with which he was not involved, but he’s excited to see Kramnik and Kholodenko’s team take the next step. “They’re in a very good position to advance this to the level of testing in animals instead of just in cells,” said Wallis.

Wallis is interested in tuberculosis therapeutics that target the response of human cells, but such treatments have tended to lag behind drugs designed to kill Mtb themselves. Nevertheless, Wallis is confident that accruing knowledge from studies like this one will ultimately lead to useful host-directed therapies for tuberculosis. It will take a little more patience, though. He said, “We’re just beginning.”