For all its mysteries, cancer can be boiled down to a disease caused by cell division gone haywire. But what determines the rate at which cancer cells can grow? They need cell building materials—amino acids, proteins, lipids, metabolites, etc.—and they need to assemble them and make essential structures quickly.
The classic example is DNA replication. Cancer cells copy their genomes super-fast to fuel their rapid division, and they often do so sloppily; their replication is notoriously rife with mitotic errors and other genome instability. As a result, over 75% of all cancers have some kind of chromosome mis-segregation, breakage, gain, or loss. Aneuploidy, or a funky number of chromosomes, is a hallmark of cancer that we’ve known about 100 years, with a variety of mechanisms proposed to explain why it happens (keep this in mind for later!).
Then, there’s RNA. It’s well established that oncogene transcription factors can misregulate a variety of gene programs to transform cells. Less understood is the phenomenon of hypertranscription—or global upregulation of gene expression across the entire genome—which is common in tumors and associated with aggressive disease. However, the root cause of hypertranscription remains unclear. Is it caused by oncogenic transcription networks? Could it be a driver of genetic instability, or is it just a downstream consequence of oncogenesis? It’s also unclear which hypertranscribed genes might be important for cancer survival, or if hypertranscription is crucial at all, although current evidence says that the latter is likely true.
A new study published in Science from the Henikoff Lab—co-lead by Drs. Steve Henikoff and former postdoc Ye Zheng, now running a lab at MD Anderson—sought to understand hypertranscription in cancer, but with a twist. Instead of relying on traditional RNA profiling methods, which are plagued by issues of RNA stability, they instead used a DNA-based method to map the location of RNA polymerase II (RNAPII) in paraffin-embedded tissue samples from a variety of tumors. These tissue samples were provided by the Holland Lab, underscoring the spirt of collaboration that the Hutch is known for.
Recently developed in their lab, the principle of CUTAC—cleavage under targeted accessible chromatin—is this: a transposase enzyme is directed to RNAPII via antibody tethering, where it then inserts sequencing adapters in the accessible chromatin nearby. A few PCRs later, and you have a map of RNAPII hot spots across the genome, and, therefore, can infer where and how much transcription is occurring.
Using CUTAC, the authors found hotspots of hypertranscription at thousands of cis-regulatory elements in many tumors including breast, colon, liver, rectum, and stomach samples. However, not all cancers had the same levels of hypertranscription, indicating that it is, as the authors put it, “a common, but not defining, feature of cancer.”
In breast and colon samples in particular, they found high RNAPII occupancy centered over the gene that encodes human epidermal growth factor receptor 2 (HER2), an oncogene that is an attractive target for breast cancer therapies. By looking just at CUTAC signals in this region, they were able to detect genomic amplifications—not just overexpression—of this region, consistent with known HER2 amplifications in breast cancer.
But beyond known oncogenes, Drs. Henikoff and Zheng soon turned their focus to histone hypertranscription in cancer. Histones, which are the proteins needed to package DNA, are frequently left out of these kinds of analyses because they cannot be picked up by traditional RNA sequencing methods that rely on polyA enrichment. But Dr. Henikoff has long been fascinated by how histones are involved in cancer (see this article, this one, and this one too for examples of this kind of work from his lab).
His interest is because histones are necessary to package replicating genomes in nucleosomes, and a whopping 5% of all proteins in the cell are histones (it takes 64 genes to crank this level of protein out). Therefore, the rate of histone production can limit the rate of DNA replication.
“If histone production at S-phase is rate-limiting for proliferation,” the authors hypothesized, “then we would observe a correlation between cancer aggressiveness and RNAPII, specifically over histone genes.” Indeed, when they looked at hypertranscription at the 64 histone genes, they found that histone hypertranscription correlates with cancer aggressiveness and recurrence in meningiomas. Histone hypertranscription also appears to be a common feature of several different cancers, as clustering cancers by RNAPII signal at histone genes showed fewer distinct clusters than looking at any particular cis-regulatory elements.
Intriguingly, the authors found that the level of histone hypertranscription was highly correlated with genome instability, specifically correlating with whole-arm chromosome losses. “What makes this especially interesting from a scientific perspective is that aneuploidy in cancer was first described in 1890, and ever since, mitotic errors have been proposed to underlie the phenomenon,” Dr. Henikoff says. In a brand-new preprint, which is now in press at PNAS, he and his co-authors have proposed a new mechanism: that histone overexpression competes with proteins required to form stable centromeres, leading to centromere breaks and whole-arm losses.
In summary, the authors posit that “the single functional role of hypertranscription in cancer is to produce enough histones” to package the replicated genomes cancer cells need for quick proliferation. But, in this race to replicate, genome stability is sacrificed, and cancer cells gain the potential for further tumorigenesis.
This publication was also featured by the Fred Hutch News Service. Click here to check out their story.
Fred Hutch/University of Washington/Seattle Children’s Cancer Consortium Members Drs. Steven Henikoff, Sita Kugel, and Eric Holland contributed to this research.
The spotlighted research was funded by the Howard Hughes Medical Institute, the National Cancer Institute, and the National Institutes of Health.
Henikoff S, Zheng Y, Paranal RM, Xu Y, Greene JE, Henikoff JG, Russell ZR, Szulzewsky F, Thirimanne HN, Kugel S, Holland EC, Ahmad K. 2025. RNA polymerase II at histone genes predicts outcome in human cancer. Science. Jan 2;387(6735):737-743.
Hannah Lewis is a postdoctoral research fellow with Jim Boonyaratanakornkit’s group in the Vaccine and Infectious Disease Division (VIDD). She is developing screens to find rare B cells that produce protective antibodies against human herpesviruses. She obtained her PhD in molecular and cellular biology from the University of Washington.
For the Media