Monitoring kidney transplant rejection in children is akin to sticking your hand into five pots of water, four of which could burn you. The only surefire way to know if a child is rejecting the organ is with a biopsy. The procedure is invasive, requires anesthesia, carries risks of complications and is expensive. In other words, it’s very hot water.
Yet every kidney transplant patient at Children’s of Alabama receives a routine biopsy six months after transplant. Only about one 1 in 5, however, actually show signs of rejection, meaning most of those biopsies were unnecessary. Now imagine there was a simple blood or urine test to tell which children were likely to reject the kidney and need a biopsy. That could mean going from 1 in 5 biopsies positive for rejection to 4 in 5 or 5 in 5, sparing hundreds of children from a painful procedure they don’t need.
Pediatric nephrologist Michael E. Seifert, MD, and his team have been working for years on developing such a test, using a large biorepository of patients’ blood, urine and kidney biopsy tissue collected throughout and after the transplant process.
Their work involves investigating gene expression in the tissue samples to find signals of rejection. But while they are good at identifying abnormalities from a piece of biopsy tissue, the process still has room for improvement. With the way tissue is processed, it’s difficult to determine if the abnormal signals are coming from cells that are relevant for rejection—such as immune cells—or from cells that don’t play a role in rejection.
Now, Seifert and his lab are using a novel technique called spatial transcriptomics, or spatial gene expression assays, which enable them to “see” the signals in the context of their natural habitat without destroying the underlying tissues.
“Spatial transcriptomics allows you to develop non-invasive biomarkers that are more reflective of the underlying biology of the disease you’re interested in, such as rejection,” Seifert said. And those more precise biomarkers could narrow down the number of patients who require biopsies. “This will help us understand the mechanisms of kidney transplant injury and rejection with much higher precision,” he said.
Before this technique, they used one of two methods to study gene expression in the tissue. One is to take the tissue, grind it up, see which genes are high and which are low, then develop a test based on the findings. The other is to separate a piece of biopsy tissue into its component cells and individually examine their gene expression. That’s more precise than the bulk gene expression or grinding method, Seifert said, but you lose any spatial context as to where in the tissue the cell came from.
One way to think about it is having all your furniture jammed into a pod in the front yard, taking a chair into the house, and hoping it’s the right piece for that spot by the window. But without the rest of the furniture in the room, it’s hard to know. With spatial transcriptomics, he said, you’re viewing the chair in context with the rest of the furniture.
“The spatial platform is a really incredible tool in that it allows you to be so precise in the areas of the kidney that you’re studying,” Seifert said. He can also isolate cells he’s interested in from the rest of the tissue without disturbing the tissue itself. “Being able to keep the tissue intact enables you to assign geographic locations for the different signals you’re getting when you test the tissue,” he said.
“We’re just beginning to learn all the ways we can apply it to kidney transplant diseases.”
He and his team presented their first paper on their findings using the new platform at the American Transplant Congress in Boston in June.