Mapping uncertainty

Mapping Uncertainty

Can gene regulatory networks help scientists predict cell behavior and improve therapeutics for cancer and other diseases?

By Bernard Cook III

It’s one of the big mysteries of biology. Why do genetically identical cells often differ in the way they move, which proteins they produce and how they respond to their surroundings? Casim Sarkar, a professor in Biomedical Engineering and a member of the BioTechnology Institute, is working to solve this enigma by studying gene regulatory networks — the interaction between genes and the proteins they produce.

Sarkar likens these gene regulatory networks to computer code that governs which genes are turned on, what proteins they produce and in what quantity. As it turns out, a cell’s behavior (for example, how it moves) and the decisions it makes (whether to move) are largely determined by gene regulatory networks and how they interact with the cell’s environment.

To begin unraveling the link between gene regulatory networks and cell behavior, Sarkar’s lab borrowed the concept of the “epigenetic landscape” from developmental biologists. Initially, the epigenetic landscape was developed as a visual metaphor to demonstrate how a stem cell (a cell that has not yet developed a specific function) becomes one of many cells with a defined function, like a neuron or a muscle cell. According to Sarkar, “The landscape looks like a ski slope where you can take different paths all starting from the same point.”

Like a ski slope, the epigenetic landscape has defined features like height, steepness and surrounding hills and valleys, which collectively inform what a cell — in this case, the skier — will do next. Picture placing a marble on a Pringle: in some directions, it may move downward and in others it can only go up. Let go, and the marble will most likely move downward. Like this, a cell on or near a crest is likely to move downhill and perform actions that are more likely, while a cell in a valley is met with resistance and likely won’t change its behavior at all (unless, like a skier, it has accumulated sufficient prior momentum to move upwards).

Instead of simply using the landscape to conceptualize cell behavior, Sarkar’s lab is developing a computer-based epigenetic landscape to predict what a cell in a given state might do next — and the likelihood of that outcome. This approach is particularly useful because it allows him to incorporate elements like cell-to-cell variability and DNA modifications, two features of gene regulatory networks that may push two otherwise identical cells to do different things in the same circumstances. In his model, these elements play a role in determining the shape of the landscape, which allows Sarkar and his team to make predictions about cellular behavior by accounting for these confounding elements. Importantly, this approach also allows him to pinpoint facets of the gene regulatory network that drive two identical cells to behave differently.

Understanding why identical cells take different paths may help improve therapies for cancer and other conditions. In cancer, for example, tumors consist primarily of cells that proliferate rapidly. But some cancers also contain dormant cells that evade standard chemotherapy and often cause relapse. Sarkar’s approach could identify aspects of the gene regulatory network that push some cells to choose dormancy, which in turn, may help researchers keep these cells dormant or identify an intervention that awakens dormant cells and renders them vulnerable to standard chemotherapy.

Sarkar’s long-term goal is to make concrete predictions about what a cell might do in specific environmental conditions as a result of the underlying gene regulatory network. Solving this mystery could help engineers working with stem cells create tissues with the desired structure and function and improve therapeutic strategies to combat antibiotic resistance.

Undercover Operative: Environmental Microbiologist Infiltrates the World of Human Microbiome Research

BTI Researcher Christopher Staley uses an ecology framework to tackle the human microbiome and its intricate secrets.

By Emerson Mehring

Can your poop cure disease? Sounds ridiculous until you hear stories from patients helped by a fecal microbiota transplant (FMT). BTI Researcher Christopher Staley left the banks of the Mississippi River and dove head first into the diverse ecosystem living inside our digestive tract: the microbiome. But how did he get there?

During his undergraduate and graduate studies, Staley met Michael Sadowsky, a distinguished microbiologist and then director of the University of Minnesota BioTechnology Institute. After mingling at several research conferences, Sadowsky offered Staley a job studying water quality at pollution sites along the Mississippi River. Staley’s role was to isolate and analyze DNA sequences from microorganisms living in the water and sediment.

With no expertise in mathematical modeling for biological systems or computational biology, Staley was concerned about his new position, but Sadowsky reassured him he was a good fit. Staley offered a new perspective to the team of bioinformatic scientists that would process the data. He understood the connections to the larger ecosystem.

“I learned how to speak both languages,” recounts Staley. “And we found eight stories hidden in their data which were all eventually published.”

Much like the waters of the Mississippi, the digestive tract harbors countless microbial communities. When Sadowsky introduced Staley to fellow BTI researcher Alexander Khoruts’ work on the microbiome, a natural partnership emerged.

Khoruts and Sadowsky were instrumental in developing the modern use of microbiota transplant therapeutics (MTT), though the practice dates to fourth-century China when people suffering from severe diarrhea were treated using a soup of dried fecal matter (yes, you read that correctly) to restore the balance of bacteria in the gut. Khoruts and Sadowsky sought a modern approach to help patients suffering from stubborn Clostridium difficile infections that cause severe stomach cramping, diarrhea, and abdominal pain. But faced with the complexity of the microbiome, Khoruts and his team had many unanswered questions.

After analyzing their dataset, Staley recognized that environmental science offered some solutions. “The tools and techniques we used studying the river are the same for fecal samples. They thought their questions were hard, but I saw them through a different lens.” He recalls the collaboration as a success because they respected each other’s expertise, which presented complementary analytical perspectives.

After dabbling in clinical research, Staley’s curiosity was piqued, so he pursued a position in the Department of Surgery at the University of Minnesota.

Navigating the transition from environmental to clinical research was challenging. Staley built on his background in ecology to explore links between the microbiome and human disease while working with University of Minnesota physician Armin Rashidi, who studies the effects of leukemia treatment on the microbiome.

Knowing that antibiotics can wreak havoc on the microbial balance in the body, Rashidi sought to understand the potential impact on his patients. Working together, Rashidi and Staley determined that antibiotics—while effective in treating harmful infections—also destroyed the helpful bacteria that keep our bodies healthy. This paradox proved fundamental to understanding the connection between the microbiome and disease and how microbial communities interact to support and undermine human health.

The microbiome has been linked to obesity, colorectal cancer, and almost every illness researchers could find. And while microbiome research has blossomed over the last decade, Staley estimates about 15 percent of studies pay adequate attention to microbial community function, and even fewer explore a critical component of bacterial communication: quorum sensing. Staley’s new focus is on disrupting the signaling molecules bacteria use to communicate with quorum quenching techniques, in collaboration with BTI investigator Mikael Elias, which prevent synchronized behavior in microbial communities.

“Of course, they’re talking in there,” says Staley. “Did you think the bacteria were just sitting there, ignoring each other? There are trillions of them!”

In preliminary testing in mice, Staley found evidence that quorum sensing could play a significant role in the gut-body connection. When fed a Western diet, quorum-quenching mice were more resistant to diet-induced obesity than mice in the control group. While only a preliminary trial, Staley is enthusiastic about digging into the mechanics of bacterial communication and its impact on the human body.

Does he miss the Mississippi and his work in environmental science? Staley’s lab is a short walk from the mighty river, and as he points out: “First, I was looking for the effects of pollutants on a body of water, and now I’m analyzing fecal matter for how bacteria impact the body … it’s almost the same!”