APC: New Takes on an Old Gene

A Brief History of APC

The APC pathway was discovered in 1982 (more than 40 years ago!). APC is a tumor suppressor gene, meaning it helps the cell division process happen in a controlled way, which helps prevent tumor development. In 1991, Kinzler and Vogelstein discovered that pathogenic variants in the APC gene are responsible for Familial Adenomatous Polyposis (FAP) (Kinzler et al., 1991; Nishisho et al., 1991), a very rare genetic condition primarily characterized by tens to thousands of colorectal polyps and a very high chance of getting colorectal cancer. 

Soon after, we noticed that there were differences in the symptoms depending on where in the gene the pathogenic variant occurred—a phenomenon known as genotype-phenotype correlation. When a pathogenic variant occurs in some locations (typically in the middle of the gene) the phenotype is strong, with innumerable polyps and other stigmata like hepatoblastoma, thyroid tumors and desmoid tumors. On the other hand, when a pathogenic variant occurs near either end of the gene, the phenotype is milder and is sometimes called Attenuated FAP.

A New Phenotype for APC

In 2016 the APC gene gained a new disease-phenotype association with Familial Gastric Adenocarcinoma and Proximal Polyposis of the Stomach (GAPPS), a rare condition with only around 25 families described in the literature (Li et al., 2016). Although they are both caused by pathogenic variants in APC, GAPPS is different from FAP in that it primarily affects the upper gastrointestinal tract causing polyposis in the fundus and the body of the stomach and usually spares the duodenum and the colon. As mentioned, this is a genotype-phenotype correlation as GAPPS is specifically caused by single-nucleotide variation in a very discrete part of the APC promoter 1B called the YY1 binding site.

How Multiple Promoters Influence APC Phenotype 

Speaking of promoters, in genetics, we sometimes forget about non-coding parts of the gene (like promoters) probably because we don’t often understand how changes in these regions influence disease. But for APC we are starting to get a clearer picture. APC has two promoters: 1A and 1B. A gene promoter acts as an assembly location for proteins that allow a gene to be expressed. Promoters essentially control when (e.g. at certain times during development, or in what tissues) and how strongly a gene is turned on—a process called transcription. Promoter 1B drives the majority of APC transcription and we know that the loss of promoter 1B through deletion causes a strong phenotype in both the upper and lower gastrointestinal tract (Yamaguchi et al., 2016). The phenotype is likely strong because it effectively shuts off all transcription of APC drastically reducing the amount of APC protein available to act as a tumor suppressor. 

But what about promoter 1A—can transcription from promoter 1A replace some of that lost APC? Yes…and no—this is genetics, after all—never straightforward! Researchers looked at promoter 1A and found different levels of methylation in different tissues. Methylation can turn off (aka “silence”) gene expression because it physically impedes the assembly of those proteins that are required for transcription. In the upper gastrointestinal tract, promoter 1A is methylated—it’s turned off, so no rescue here. But in the colon, promoter 1A is not methylated—it’s able to drive transcription. This methylation difference may underlie the genotype-phenotype relationships between FAP and GAPPS. Single nucleotide variations in promoter 1B cause GAPPS, which usually only impacts the upper gastrointestinal tract. The lower tract is usually spared, possibly because promoter 1A (which is unmethylated and turned on) is able to restore enough of that missing APC. But since promoter 1A is methylated (turned off) in the stomach, that same rescue doesn’t take place. 

To take the genotype-phenotype correlation even further, a deletion of promoter 1B (as opposed to a single nucleotide variant) is likely much worse and the amount of transcription from promoter 1A is not going to be enough to rescue the total loss of transcription from promoter 1B—so patients with this type of variant are affected throughout the gastrointestinal tract. To further support this concept, a small insertion-deletion at the YY1 site (which can be expected to also be worse than the single nucleotide variations described in the literature) was recently identified in a patient who was affected in both the upper and lower gastrointestinal tract.

Across the globe there are scientists discovering new molecular details about human existence. Sometimes it's hard to see the connections between what is discovered and how it can be applied in a clinically meaningful way. That is largely because, like the above narrative, it takes many, many years to get from point A to point B (or promoter 1A to promoter 1B). While not proven (because few things in science are) the above hypothesis helps us understand the old discoveries in a new and clinically meaningful way. Hats off to all the science that went into the long journey that got us to this new understanding and may it go even further in the future to develop new strategies to counteract these genetic conditions.

Summarizing the influence that multiple promoters have on APC variant interpretation and phenotype: 

APC has two promoters, and the majority of transcription is initiated by the distal one, 1B.
—Factors such as mutation type (point mutation vs deletion) and methylation level can affect phenotypes.
—Breakpoint location relative to these two promoters affects whether an APC deletion is pathogenic and causes disease.


And this is just the beginning! Though we have studied APC for 40 years, we are still learning about APC, different kinds of mutations and genotype-phenotype correlations.  

To learn more about the APC pathway, including additional molecular nuances, check out the the full webinar here.

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