Auinash Kalsotra Lab

Auinash Kalsotra wasn’t originally interested in studying cancer. In fact, he wasn’t looking to study any particular disease at all.

Kalsotra wanted to know how the complex machinery of our bodies takes the codes embedded in our DNA and turns them into healthy organ tissues, specifically heart and liver. In other words, he wanted to know how things worked — not why they break or how to fix them.

“There’s a molecular logic to how cells are put together, how something becomes a nerve or muscle cell,” Kalsotra said. “Once these cells have features, how do they mature and give rise to a functioning adult tissue that carries out a particular function?”

But as often happens, scientists start on one path and eventually find themselves pulled onto others. In this case, Kalsotra’s search for a deeper understanding of cellular mechanisms has led to significant findings that show linkages between liver diseases and cancer and may improve our understanding of the origin of these diseases.

Kalsotra’s research has focused on RNA, the workhorse cousin of DNA, which makes up the genetic instructions for living things. RNA is often viewed as important for messaging and other functions, taking DNA’s code and transporting it to and carrying out functions in cells. It’s often taken a back seat to DNA in terms of significance.

In particular, Kalsotra is intrigued by the fact that one gene can give rise to multiple types of RNA based on the type of cell it will encode. A long stretch of RNA will be cut into pieces, called exons, which are spliced together to form messenger RNA (mRNA).The pieces spliced together, their order and other factors determine the type of function the RNA will carry out.

“That means one gene can give rise to multiple mRNAs, and those mRNAs are dependent on the cell type,” Kalsotra said.

Kalsotra knew that RNA binding proteins played a role in the formation of mRNA, so his lab started knocking out these proteins from mouse livers to study their functions.

In liver cells, mice that lost certain RNA binding proteins started displaying signs of fatty liver disease.The condition is common among people who abuse alcohol, but also affects more than 100 million people in the U.S. and more than a quarter of people in the non-developed world as non-alcoholic fatty liver disease.

“One-third of people with non-alcoholic fatty liver disease get an aggressive form of the disease,” Kalsotra said. “In addition to having fat in their livers, they’re going to have a lot of inflammation, scarring and liver cell death.”

The mice eventually developed liver cancer. It got Kalsotra’s lab looking for connections between genes and non-alcoholic fatty liver disease. Analysis revealed that the genes that ranked highest as likely contributing to the disease are associated with RNA splicing.

“Our goal in knocking out these genes was to understand how these cells mature and how RNA splicing plays a role in tissue development,” Kalsotra said. “Instead, what we saw was a very specific disease that seems to match a human phenotype.”

Kalsotra collaborated with the Carle Hospital to analyze biopsy samples of patients with non-alcoholic fatty liver disease. Each patient showed a striking decrease in RNA binding proteins.

The findings raise more questions, such as whether the loss of RNA binding proteins leads to the liver disease and cancer. It’s possible that loss of RNA binding proteins could be a biomarker for fatty liver disease and cancer. Or maybe the opposite is true, that loss of the binding proteins is a result of the liver diseases.

Kalsotra also wants to know if and how the cancer profiles in mice match with humans, who tend to get cancer after fatty liver diseases. And whether there are mutations in genes from birth that lead to liver disease and cancer, or whether there are environmental triggers, such as diet, that are involved.

In addition, the Kalsotra Lab is looking at how the transition from the body making fetal cells to making adult cells might play a role in cancer formation. Fetal cells rapidly proliferate, much like cancer cells. But at some point, the body switches to making adult cells — a few years after birth in humans and a few weeks in mice.

That switch coincides with the creation of adult versions of mRNAs from the same genes. It’s possible, then, that a malfunction in the production of these “adult mRNAs” could reinitiate cell proliferation, a hallmark of cancer.

“What we’re seeing is that it may not only be at the level of mutation in a gene that controls cell proliferation or activating an oncogene that gives a cancer cell an advantage to grow, but also what kind of mRNAs you make,” Kalsotra said. “If you impinge on that regulation, you now produce the wrong kinds of mRNAs that might not be good for that cell at that stage.”

While Kalsotra wasn’t aiming to study cancer, there is a sense of satisfaction knowing that his work might have an impact on the disease. His brother-in-law has advanced-stage esophageal cancer, and the work has become somewhat more personal. His overall goal is to understand the proper function of RNA splicing, but there is an incentive to further exploring the malfunctions as well.

“It kind of gives me extra motivation to see why normal cells all of the sudden become cancerous,” he said. “Maybe one day, if we understand how normal cells work, we can understand what goes wrong in a cancer cell that makes it divide uncontrollably and not listen to the rest of the organ that is telling it to stop growing.”