Colon cancer remains a major global health concern, ranking third among the most diagnosed cancers and leading causes of cancer-related death worldwide. One critical factor that makes treating colon cancer challenging is the presence of cancer stem cells. Though typically present in small populations, these powerful cells drive tumor growth, resist standard treatments, and often contribute to relapse. They achieve this through their “stemness,” a set of properties that enable these cells to self-renew and differentiate into other cell types. Thus, understanding how stemness might be controlled at the molecular level is essential for developing effective therapies for colon cancer.
Over the past two decades, researchers have identified several key molecules involved in both the development of the colon and the progression of colon cancer. Among them are CDX1 and CDX2, two homeobox transcription factors that help establish and maintain the identity of intestinal epithelial cells. Another example is the protein β-catenin, a well-established driver of colon cancer whose dysregulation can lead to uncontrolled cell growth. While prior studies have shown that CDX1 and CDX2 inhibit tumor growth, the exact mechanisms by which they counteract β-catenin and suppress stemness remain largely unknown.
Now, a recent study led by Professor Koji Aoki from the Department of Pharmacology, Faculty of Medicine at the University of Fukui, Japan, along with Dr. Akari Nitta and Dr. Ayumi Igarashi from the same university, provides new insights. Sharing the motivation behind their study, Prof. Aoki states, “We want to understand the transcriptional mechanisms underlying colon cancer progression, as well as those regulating differentiation and stemness in colon cancer.”
Their paper, published in Volume 16 of the journal Cell Death & Disease on May 21, 2025, reveals how CDX1 and CDX2 interfere with β-catenin and affect gene expression pathways that sustain stemness in colon cancer cells.
The researchers used genetically engineered mouse models, human colon cancer cell lines, and organoid cultures to analyze how deletion or overexpression of CDX1/2 affected tumor behavior. They found that the complete loss of CDX1, or the combined loss of CDX1 and CDX2, increased the aggressiveness of tumors in mice. These tumors showed higher expression of LGR5 and CD44-two genes strongly associated with cancer stemness-and were more invasive. When CDX1 or CDX2 was artificially reintroduced into cancer cells, the expression of these stemness-related genes sharply decreased, suggesting a suppressive role of CDX1/2.
To understand the underlying molecular mechanisms, the team delved into the finer details of how CDX1/2 influence gene expression. They observed that CDX1/2 bind to a specific region downstream of the starting point of the LGR5 gene, a region also targeted by β-catenin. Surprisingly, even though CDX1/2 promoted an open chromatin structure usually associated with active gene expression, they still significantly reduced the presence of key transcriptional components, namely RNA polymerase II (Pol II), DRB sensitivity-inducing factor (DSIF), and RNA polymerase II-associated factor 1 (PAF1), around LGR5’s starting site. These proteins are essential for DNA transcription and its regulation.
Through further experimentation and analyses, the researchers found that CDX1/2 directly interfere with β-catenin’s ability to assemble the active form of Pol II complexes, which include DSIF and PAF1. This suppression occurred because CDX1/2 prevented the direct interaction between β-catenin and these transcription factors due to their functional homeodomains. Hence, CDX1/2 effectively cut off the supply chain needed for LGR5 expression and promotion of cancer stemness.
According to Prof. Aoki, identifying the roles of DSIF and PAF1 in the context of colon cancer was one of the key findings of the study. “Our results suggest that DSIF and PAF1 complexes act as transcriptional platforms that integrate and funnel both tumor-suppressive and oncogenic signals into the expression of genes that control colon cancer stemness,” he explains. This positions DSIF and PAF1 complexes as central players in the pathophysiology of colon cancer, marking them as potential therapeutic targets of future drugs.
Targeting the genes and proteins that regulate stemness may become a cornerstone of new cancer therapies, although more studies will be needed to understand and leverage these complex cellular processes. “Further investigation of stemness-related transcriptional mechanisms will aid in the development of drugs to effectively treat colon cancer,” surmises Prof. Aoki.
