The APC gene is composed of 15 exons encoding a 2844 aminoacid peptide with exon 15 being the largest coding region (6.5 kb); this gene is located on 5q21-q22.
The APC protein (310 kDa) has multiple domains that mediate oligomerization as well as binding to a variety of intracellular proteins, which have an important role in cell adhesion, signal transduction and transcriptional activation. APC is present both in nucleus and in cytoplasm and it has nuclear localization sequences (NLSs) and nuclear export sequences (NESs).
APC acts as acomponent of the wnt pathway and, when the wnt ligand is present, it is able to bind Axin, GSK-3b and b-catenin.
The APC gene encodes multiple protein isoforms through a complicated pattern of expression and alternative splicing. The role that each isoform plays is unknown. The conventional APC (cAPC) splice form is present in many cell types, while other APC splice forms are present only in differentiated cells.
Isoforms of the APC tumor suppressor and their ability to inhibit cell growth and tumorigenicity 2004
CHEMICAL STRUCTURE AND IMAGES
- Crystal structure
The structure of the entire protein is not available, but on PDB database you can find the structure of some portions of APC:
Coiled coil region
b-catenin binding region
Protein Aminoacids Percentage
APC is present both in cytoplasm (it's the predominant location of the full-lenght protein) and nucleus of colic and extracolic cells. The subcellular localization is in cell junction and adherens junction.
APC maintains chromosome stability
- Cell signaling and Ligand transport
APC regulates the level of b-catenin through the modulation of the Wnt pathway (APC is a tumor suppressor)
APC acts as a nuclear-cytoplasmatic shuttling protein with multiple functions
Control in cell cycle progression
- Structural protein
APC plays a role in regulating cell migration and cell-cell adhesion
APC is involved in maintaining cell shape and integrity
Mutational and functional studies indicate that APC acts as a tumor suppressor gene and that FAP is an AD disease in which the patient inherits one mutant allele followed by a somatic mutation in the remaining wild-type allele. Analysis of sporadic colorectal adenomas and carcinomas revealed that APC mutation occurred in nearly 70–80% of all colorectal tumors and it is believed to be an early event in the tumorigenesis process. This mutation doesn’t compromise the function of the gene, but it induces to the acquisition of a second mutation. Moreover, the loss of heterozygosis (LOH) causes formation of polyposis.
APC is expressed and synthetized in a variety of tissues, for example colon, small intestine, prostate, endometrial tissue, adult brain, gastric tract, lung....
- APC is deubiquitinated by ZRANB1/TRABID: Trabid can bind to and deubiquitylate APC
"Trabid, a new positive regulator of Wnt-induced transcription with preference for binding and cleaving
K63-linked ubiquitin chains":http://www.ncbi.nlm.nih.gov.proxy-medicina.unito.it/pmc/articles/PMC2238673/pdf/528.pdf
Recently, using a functional genetic screening approach, a miRNA-mediated mechanism for the control of APC expression and Wnt pathway activity was uncover, suggesting its contribution to colorectal cancer pathogenesis.
The authors identified the miR-135 gene family as a regulator of APC expression and showed its potential to activate the Wnt pathway in the absence of Wnt ligand. In CRC cell lines, it was showed direct and causal suppression of endogenous APC by miR-135a&b. Furthermore, in a significant number of colon tumors, the authors also observed high levels of miR-135a&b that negatively correlated with
Regulation of the Adenomatous Polyposis Coli Gene by the miR-135 family in Colorectal Cancer 2008
In another study it was demonstrated that the expression of APC is regulated by other factors:
- The Level of APC Is Up-regulated by Wnt3a, particularly APC is stabilized after Wnt signaling and it is highly localized in nuclei and decreased upon removal of the Wnt signaling. The domain of APC that is responsible for its down-regulation was identified;
APC is also regulated by phosphorylation: The APC protein contains three 15aa repeats and seven 20aa repeats that are involved in its interaction with β-catenin. Different APC 20aa repeats bind to β-catenin with dramatically different binding affinities.
The phosphorylation of any of the 20aa repeat fragments increases the binding affinities by at least 140-fold. This suggests that the function of all 20aa repeats, and likely the entire central region of APC, is tightly regulated by phosphorylation. Then, phosphorylation has a critical regulatory role in APC function. In addition, it was demonstrated that the central region of APC is unstructured in the absence of β-catenin and Axin, suggesting that β-catenin may interact with each of the APC 15aa and 20aa repeats independently.
The Third 20 Amino Acid Repeat Is the Tightest Binding Site of APC for β-Catenin 2006
DOMAINS, FEATURES, VARIATIONS OF APC PROTEIN
See Ensemble Genome browser
DISRUPTION OF APC FUNCTIONS
Interestingly, the number of polyps in FAP is determined in part by the location of the germline mutation within the APC sequence. Disease-causing germline mutations in APC are always either deletions or premature truncations.
In the present, more than 300 different types of mutations are recognized as the cause of FAP. Most of these mutations (insertions, deletions, nonsense mutations, etc.), result in a truncated protein. The most common mutation, occurring in about 10% of FAP patients, is a deletion mutation in codon 1309; the second, occurring in 5% of the patients, is a deletion at codon 1061.
FAP patients tend to present with different phenotypic variants, depending upon the location of the truncating mutation.
Truncation mutations of APC
Over 95% of the germline mutations identified in the APC gene are frameshift or nonsense mutations that result in a truncated protein product. The majority of germline mutations in APC occur in the 5’ half of the gene leading to the elimination of most of the 20-amino acid repeats involved in regulating b-catenin levels and the repeat sequences involved in axin binding. However, these truncated proteins also lack the microtubule and EB1 binding domains located in the C-terminal end of the protein. A careful analysis of the location of the APC germline mutation compared to the polyposis phenotype reveals that patients with mutations near codon 1300, between the first and second 20-amino acid repeats, develop particularly severe disease characterized by >2000 polyps and earlier-onset cancer formation.
The location of the original germline mutation in APC may also influence the position and type of mutation in the remaining wild-type allele during tumorigenesis. Patients with a germline mutation near codon 1300 tend to undergo loss of heterozygosity (LOH) mutations as the second ‘hit’. In tumors from patients with germline mutations elsewhere in the APC gene, the second ‘hit’ was more commonly a protein truncating mutation; most within a specific region between codons 1250 and 1450 referred to as the mutation cluster region (MCR).
The location of the protein truncating mutation affects the number of 20-amino acid repeats remaining. Mutations near codon 1300 would result in an APC protein with one 20-amino acid repeat. The ability of APC to regulate b-catenin activity appears to depend upon the number of 20-amino acid repeats present in the protein. Even truncated APC with one 20-amino acid repeat is capable of exporting b-catenin out of the nucleus, suggesting APC proteins truncated near codon 1300 still maintain some b-catenin downregulating activity. Following LOH and gene duplication, the cell would be left only with an APC protein containing one repeat.
Missense mutations in APC
A small number of missense variants of APC have been identified in the germline of patients with multiple polyps and CRC that may contribute to disease.
The immediate effect of these single amino acid changes on function of the APC protein is difficult to predict. Two missense variants most frequently reported are I1307K and E1317Q.
The I1307K variant has been identified almost exclusively in patients of Ashkenazi Jewish descent and has been associated with increased risk of multiple adenomas and CRC similar to an AFAP phenotype. The nucleotide change that results in the I1307K allele is a T→A transversion at position 3920 which changes an A3TA4 sequence to an A8 tract (AAAAAAAA). This mononucleotide repeat appears susceptible to polymerase slippage and mispairing during DNA replication resulting in increased frameshift mutations in this new poly-A sequence.
Even if the I1307K variant has been associated with increased adenomas in certain select populations, other studies have identified no increased risk of CRC in carriers of this germline variant. Possibly the association is not between I1307K and CRC risk, but rather some genetic or environmental factor that increases the risk of frameshift mutations in this newly created A8 tract.
The relationship between the E1317Q variant of APC and CRC risk is even less clear. An association between E1317Q and multiple adenomatous polyps has been reported along with a weak association with CRC. However, more recent studies examining larger numbers of CRC patients and controls observed almost no association between the variant and increased CRC risk. In total, more than 60 different germline missense variants of APC have been described in the literature or APC mutation databases as potentially pathogenic. However, the number of patients and controls examined is small for most of the variations.
Genotype to phenotype: Analyzing the effects of inherited mutations in colorectal cancer families2009
Variants of the splicing
In addition to an alteration of the amino acid sequence, missense variants may also affect the final protein product by disrupting splicing of the primary transcript. The variations may disrupt regulatory sequences such as splicing enhancers or silencers that result in the splicing machinery skipping exons in the mutant gene. Silent variants which affect the genomic sequence but are still predicted to encode for the same amino acid may also affect splicing, particularly if they fall near an exon–intron boundary. An evaluation of the primary transcript from different patients harboring missense or silent variants in APC revealed that the majority of them result in exon skipping due to aberrant splicing. Variants that result in the skipping of exons 4, 11, and 14 result in premature stop codons and a truncated protein product suggesting that these variants are likely pathogenic.
A variant from an AFAP patient that leads to the skipping of exon 13 did not result in loss of the reading frame. However, it is believed that this variant may be pathogenic because it results in the removal of a complete A8 repeat region from the APC protein. Thus, while often missense and, especially, silent variants are excluded from further consideration during screens for cancer-associated mutations, these variants may very likely have pathogenic consequences.
Genotype to phenotype: Analyzing the effects of inherited mutations in colorectal cancer families2009
Inactivation of APC gene through methylation
Some colorectal tumours have been shown to have acquired hypermethylation of the APC promoter. Promoter methylation has been shown to silence transcription and to provide an alternative mechanism of inactivation of several genes.
APC promoter methylation has therefore been proposed as an alternative mechanism of gene inactivation. Another cause of promoter methylation in colorectal tumours is the molecular pathway known as the CpG island methylator phenotype (CIMP), in which extensive methylation is found, probably secondary to some unknown epigenetic alteration. Therefore, an alternative explanation for APC promoter methylation is that it takes part to the CIMP pathway.
The APC gene has two promoter regions, 1A and 1B; the second produces three transcripts, 1B1, 1B2 and 1B3, through an alternative splicing. 1A is the predominant form in normal colonic
tissue. Early observations revealed heavy hypermethylation of APC promoter 1A in sporadic CRCs, but no hypermethylation was observed in normal mucosa and adenomas, suggesting that this could be a pathogenic event in cancerogenesis. But in this study no correlation with clinico-pathological features could be established. In contrast, no aberrant methylation of promoter 1B has been detected.
APC promoter hypermethylation has been suggested as an alternative to mutation or LOH as a way to inactivate the gene in colorectal tumours, but this recent study show that this is not the case.
Methylation affects mutant, as well as wildtype, APC alleles and is not more common in tumours with only one identified ‘hit’ at APC. Moreover, APC methylation does not seem to be a consequence of CIMP. Methylation causes a marked reduction in 1A transcript and total APC mRNA levels. However, this does not lead to detectably consistent changes in Wnt activation.
This study and others suggest that APC promoter 1A hypermethylation is an early event in colorectal tumorigenesis, because it was seen in small adenomas. Why only promoter 1A is affected remains unclear. Promoter 1B seems resistant to methylation in multiple cancer types; maybe it is possible that silencing of the major APC isoform, 1A, is ineffectual in causing tumours to grow. Another possibility is that methylation is not an alternative to APC mutation, but a consequence of it. Maybe relatively subtle differences in APC expression caused by promoter methylation are selected to fine regulate Wnt signalling in colorectal tumours, including early lesions.
Promoter hypermethylation leads to decreased APC mRNA expression in familial polyposis and sporadic colorectal tumours, but does not substitute for truncating mutations 2008
The analysis of the sequence of the APC gene can be used for the diagnosis of Familial Adenomatous Polyposis Syndrome.
Today a good number of genetic tests are available to test for APC germline mutations. Among these are sequencing of the full APC gene, combination of conformation strand gel electrophoresis (CSGE) screening and protein truncation test (PTT), protein truncation test alone and finally linkage analysis. The most commonly used today is direct sequencing of the APC gene.
The mutation detection rate is 70%. Large insertions and deletions need other tests and add about the 5% of the cases.
Molecular Pathogenesis of Colorectal Cancer 2005