“This is a surface where pathogens can sneak in,” says La Jolla Institute for Immunology (LJI) Assistant Professor Miguel Reina-Campos, Ph.D. “That’s a massive challenge for the immune system.”

So how do immune cells keep the gut safe? New research led by scientists at LJI, UC San Diego, and the Allen Institute for Immunology shows that pathogen-fighting immune cells called tissue-resident memory CD8 T cells (T_RM cells) go through a surprising transformation — and relocation — as they fight infections in the small intestine.

In fact, these cells literally rise up higher in the tissue to fight infections before pathogens can spread to deeper, more vulnerable areas.

“The tissue in the gut has evolved to provide signals to immune cell infiltrates — to put immune cells in specific places so they have a better ability to stop pathogens,” says Reina-Campos, who served as first author of the new Nature study alongside co-first author Alexander Monell of UC San Diego and co-senior authors Maximilian Heeg, M.D., and Ananda W. Goldrath, Ph.D., of the Allen Institute for Immunology and UC San Diego.

The new findings add to the growing body of evidence that immune cells adapt to protect specific tissues. Reina-Campos thinks these “tissue-resident” immune cells may be key players in future cancer immunotherapies that target tumors in specific organs.

T cells on the move

Reina-Campos and his colleagues investigated the formation of T_RM cells in the small intestine. The team harnessed a cutting-edge technology called spatial transcriptomics to track these cells in both human and mouse tissue samples.

Their work showed that the small intestine holds two types of T_RM cells. These cells are split between the tiny, finger-like “villi” structures that line the small intestine or the “crypts” between the protruding villi.

The researchers found that progenitor-like T_RM cells live closer to the crypts between the villi. On the other hand, differentiated T_RM occupy more exposed regions at the top of the villi. “Differentiated immune cells are more exposed at the top of the villi, and that’s where they have a better ability to protect you from infections,” says Reina-Campos.

Meanwhile, a reserve population of progenitor-like T_RM cells continues to lie low in the crypts. “These cells can replenish the pool of effector T cells, so the immune system keeps them as back-ups in the deeper parts of the tissue,” adds Reina-Campos.

What keeps these populations organized and in check?

To spy on these important immune cells within their natural habitat, Reina-Campos and colleagues used a new technology — called spatial transcriptomics — to observe millions of messenger RNA molecules simultaneously at subcellular resolution.

“For the first time, we were able to capture the formation of immunological memory in space and time,” says Reina-Campos.

Looking at small intestines after a viral infection, the scientists found that the gut releases chemical signals to instruct immune cells where to go and what to do. “This study offers a new resource for finding signals that position immune residents to strengthen our gut immunity,” says Reina-Campos.

Checkmate for disease?

Reina-Campos credits his mentor, Goldrath, as well as Heeg’s and Monell’s expertise for making this study possible. As Reina-Campos explains, Heeg and Monell developed new computational approaches to make sense of the massive amounts of data captured through spatial transcriptomics.

“It’s led to a breakthrough in our ability to look at hundreds to thousands of genes simultaneously in intact tissues,” says Reina-Campos. “With this study, we’ve opened up a new path for discovery.”

Reina-Campos compares the battle between immune cells and pathogens to a chess match.

“To be a chess grandmaster, you need to know not only about the pieces: the bishops, pawns, rooks, etc, but also how they move in concert on the chessboard,” he says.

For a long time, scientists have studied the chess pieces — by analyzing cells extracted from tissue — but they haven’t gotten a good look at the chess match itself. “We don’t know as much about how the chessboard works — and we know even less about the rules that apply to our chess pieces as they move across the board,” says Reina-Campos.

The new study gives researchers a detailed look at how immune cells interact with each other and their cellular gameboard.

Reina-Campos says the new finding should guide future research into how immune cells develop and move through other organs with different tissue structures, such as the kidneys and lungs — and how immune cells might fight tumors in these organs.

Influence of very early life stages

The research team investigated how maternal stress affects the stress hormone system of the offspring. They found that the activation of the hypothalamic-pituitary-adrenal (HPA) axis, which plays a central role in coping with stress, can be significantly influenced by exposure to maternal glucocorticoids during development. The early phase of organ differentiation in the first half of pregnancy proved to be a particularly critical period. “Our results show that the HPA-axis activity of offspring was enhanced, the more adversity the other had experienced during early pregnancy — which could be food shortages or social conflicts for example,” says Simone Anzá, former doctoral student at the University of Göttingen and the German Primate Center and first author of the study.

Investigation in the wild

In contrast to studies in the laboratory, the monkeys were observed in their natural habitat. Over a period of nine years, the researchers repeatedly collected fecal samples from pregnant females and measured the concentration of glucocorticoid metabolites in them in order to determine the animals’ exposure to environmental factors such as food scarcity, temperature fluctuations and social interactions. These values were compared with the stress hormone levels of the offspring at different ages. The effects on the stress axis of the offspring were evident from infancy through the juvenile period and into adulthood at nine to ten years of age. Previous analyses from the same study had already shown that early prenatal stress was also associated with altered growth, negative changes in the gut microbiome and impaired immune function, underlining the comprehensive influence of the environment in the early prenatal period on various physiological systems. In contrast, maternal glucocorticoid levels in late pregnancy or during lactation had no or different influences.

Relevance for health research

“Our research results indicate that the timing of maternal stress hormone exposure during and after pregnancy crucially affects the consequences for the development and health of the offspring. It is also important to note that these effects do not require catastrophic events, but that even moderate changes in environmental conditions are sufficient,” says Oliver Schülke, scientist at the University of Göttingen and the German Primate Center and head of the study. Stress in early pregnancy can also have a long-term effect on health in humans and increase the risk of stress disorders and immune problems. “Our findings may help to identify the timing and mechanisms that preventive measures should address in order to reduce long-term health risks,” says Oliver Schülke.

The Geiseltal Saxony-Anhalt is located south-west of Halle and was a lignite mining area until 1993. Numerous exceptionally well-preserved animal fossils have been unearthed here. The Geiseltal Collection at MLU comprises 50,000 fossils and is considered a national heritage asset. These fossils offer unique insights into the evolution of animals and the Eocene Epoch around 45 million years ago. At that time, the Geiseltal was a warm, tropical swamp. Ancient horses, early tapirs, large land crocodiles as well as giant tortoises, lizards and numerous birds lived here. Some of the latter were flightless and the largest of these was Diatryma, a herbivore with a gigantic beak which stood around 4.6 feet high.

For many years no one knew that an almost completely preserved skull of Diatryma was part of the collection. “The find was initially misidentified as a crocodile skull,” says Michael Stache, a geological preparator at MLU’s Central Repository of Natural Science Collections. Stache came across the fossil again by chance several years ago. He realised the mistake and got down to work, restoring and then analysing the piece of skull. He combined the fossil with another object from the collection, reconstructing an almost entire skull. Dr Gerald Mayr, a researcher at the Senckenberg Institute, examined the find more closely and realised its importance: the skull clearly belonged to a Diatryma. Only one other fully preserved skull is known to exist in the world and is housed in the American Museum of Natural History in the USA.

“This shows once again that many of the most interesting discoveries in palaeontology occur in museum collections. Just a few years ago, nobody would have thought that the Geiseltal Collection would contain such surprises,” says Gerald Mayr. Michael Stache also reports that there is great scientific interest in the fossils. Researchers from Germany and abroad come to MLU on a regular basis to investigate the objects. “This research expands our understanding of the Eocene Epoch in the Geiseltal even though the excavations were completed long ago,” says Michael Stache. Up until ten years ago, for example, it was assumed that Diatryma hunted prehistoric horses in the Geiseltal. More recent investigations have found that the bird was, in fact, a herbivore.

There are around 40 specimens of the bird in the Geiseltal Collection. “Diatryma was probably a rare guest in the Geisetal. Otherwise, there would probably be more fossils,” concludes Stache.