Rewriting Cancer Pathways with Agnieszka Bialkowska

For Agnieszka Bialkowska, cancer research begins with a deceptively simple question: how do normal biological processes meant to heal the body become drivers of disease? At Stony Brook University's Renaissance School of Medicine, her work sits at the intersection of fundamental biology and therapeutic possibility, with a recent patent marking a significant step toward translating long-standing discoveries into tools that could reshape cancer treatment.

Bialkowska is a cancer biologist whose research focuses on transcription factors, molecular regulators that control how genes are turned on and off inside cells. While these proteins are essential for normal tissue function, her work has shown how their misregulation can accelerate tumor development, particularly in cancers of the gastrointestinal tract and pancreas.

Her research environment at Stony Brook plays a central role in that work. As a member of the Oncogenic Drivers and Mechanisms of Carcinogenesisprogram, Bialkowska collaborates with researchers studying cancer across diverse models and organ systems. That exposure, she says, strengthens how questions are framed and how experiments are designed. "Collaboration is fundamental," she explained. "Sharing ideas with people who may not work in your exact field helps you look at scientific questions from completely different angles."

When Healing Fuels Disease

At the center of Bialkowska's research is Krüppel-Like Factor 5, or KLF5, a transcription factor critical for maintaining the intestinal lining. The intestinal epithelium is one of the fastest-renewing tissues in the human body, replacing itself every few days as it responds to constant exposure from food, bacteria and environmental stress.

"You need KLF5 for proper growth and regeneration of the intestinal epithelium," she said. "But the same pathways that support healing can be hijacked during cancer development."

In healthy tissue, KLF5 promotes controlled cell proliferation after injury. In cancer, its elevated expression can fuel tumor growth. Bialkowska's work explores how inflammation, injury and regeneration overlap and how chronic activation of these processes can push cells toward malignancy. "Inflammation is necessary for healing," she noted. "But when it becomes excessive or chronic, it increases the risk of cancer development."

That balance between protection and risk is what makes her work particularly relevant for therapeutic intervention. Rather than eliminating regenerative signals entirely, her research aims to understand how moderating them might slow or prevent tumor progression.

From Mechanism to Molecule

That long-term focus culminated recently in a U.S. patent for small molecules that reduce the expression of transcription factors including KLF5 and EGR-1 (US12486227B2). Co-invented with longtime collaborator Vincent Yang, the patent represents both a scientific milestone and a translational breakthrough.

"Targeting transcription factors is still relatively unusual," Bialkowska said. "There are not many compounds designed to regulate them directly. That is what makes this approach exciting."

Initially, the compounds were developed as research tools to better understand how transcription factors drive carcinogenesis. Over time, their potential therapeutic value became clear. Elevated KLF5 expression is observed in colorectal and pancreatic cancers, making it an attractive target across multiple disease contexts.

The patent, she emphasized, does not represent an endpoint. Instead, it opens the door to combination therapies, where transcription factor inhibitors could be paired with existing treatments to enhance effectiveness or overcome drug resistance. "Cancer cells are highly plastic," she said. "They adapt. Having additional tools gives clinicians more options over time."

Bridging Discovery and Impact

For Bialkowska, the movement from basic research to intellectual property was not planned but organic. "You do not start a project thinking about a patent," she said. "You start by asking a scientific question. The translation happens when the science leads you there."

That transition, she believes, underscores the importance of sustaining both fundamental and applied research. "One cannot exist without the other," she said. "We learn from basic biology, translate that knowledge to patients, and then bring insights from the clinic back to the lab."

It is a perspective shaped by years of mentorship and collaboration. In her own lab, Bialkowska encourages young scientists to remain flexible, ask questions freely and seek input beyond their immediate expertise. "The era of doing research in isolation is over," she said. "Progress depends on listening, adapting, and working together."

As her patented work moves forward, Bialkowska remains focused on the same core goal that drew her into cancer research in the first place: understanding how cells behave, and how that knowledge can be used responsibly to improve human health. "Every day we learn something new," she said. "That is what keeps the work moving forward."