Can losing one gene do all that? Yes it can — there’s still hope

The Cancer Genome Atlas has dashed our hopes of finding ‘the’ cause of cancer. It has sequenced the genomes of a large number of cancers — the following paper looked at 21 tumor types sequencing the protein coding parts (exomes) of 4,742 specimens, along with that of normal tissues [ Nature vol. 505 pp. 495 – 501 ’14 ].

The problem is that lots of mutations have been found in every type of cancer studied this way.

The following is typical — 178 cases of lung cancer (squamous cell variety) were studied. Some 360 mutations in exons, 165 genomic rearrangements, and 323 copy number alterations were found — but this doesn’t represent the results for the 178 cases as a whole. This was the average amount of genomic mayhem seen in each individual tumor . How do you find ‘the’ cause of the cancer in this mess? One way might be to find a gene mutated in all 178 cases (e. g. recurrent mutations). This would be the holy grail — the mutation driving cancer formation, the rest being the chaff of the well known genomic instability due to the high mutation rate of cancer cells. They found 11 such genes, but they were far from mutated in all cases. Pretty depressing isn’t it?

A recent paper [ Proc. Natl. Acad. Sci. vol. 111 pp. 14009 – 14010, E4066 – E4075 ’14 ] gave an example of a huge number of changes in the clinical activity of a cancer cell line due to the functional loss of just one gene (called COSMC). Here’s what happened. In a pancreatic cancer cell line, COSMC knockout produced malignant xenografts (e.g. placing the cells in an immunodeficient animal and watching what happens), which could be reversed by reintroduction of COSMC. The changes include (1) increased proliferation, (2)loss of contact inhibition of growth, (3) loss of tissue architecture, (4) less basement membrane adhesion and (5) invasive growth — remarkable that knocking out just one gene could do so much. Perhaps not a driver mutation, but certainly a delicious drug target. Before getting too excited, remember that this occurred in a cell line which was cancerous to begin with.

The quick and dirty explanation of what is going on is that COSMC is a protein chaperone for an enzyme adding a sugar to proteins destined either for secretion or for insertion into the cell membrane. Lose COSMC and the whole pattern of sugar attachments to these proteins changes. There are a lot of proteins modified by adding sugars (glycosylated proteins), actually 446 of them, with 1,471 sites for this to happen.

The rest of the post is for the cognoscenti and concerns the gory details.

From the paper itself — “Neoplastic transformation of human cells is virtually always associated with aberrant glycosylation of proteins and lipids.” The most frequently seen glycophenotype are the Tn and STn carbohydrate epitopes of epithelial cell cancers. They arise when mucin-type O-linked glycans (normally more complex) are truncated so that only a single -N-acetylgalactosamine (Tn) or N-acetylgalactosamine modified with sialic acid (STn) remains attached to the protein by a serine or a threonine. There are ‘up to’ 20 GalNAc transferases adding GalNAc to serine or threonine. Overall there are some 200 glycosyltransferase found in the secretory pathway. In most cases the GalNAc is modified with beta 1 –> 3 galactose by a single enzyme (called C1GalT1). This reaction is dependent on COSMC, a protein chaperone.

Although there weren’t mutations in the glycosyltransferases studied in 46 cases of pancreatic cancer, 40% of them showed hypermethylation of the COSMC (e.g. methylated cytosines in the promoter region, which shut down transcription of COSMC). This correlated with expression of truncated O-Glycans (e.g. the Tn and STn antigens) and loss of C1GalT expression.

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