Genome- The Cell’s Recipe Book

“Every cell in your body is using an identical ‘recipe book’ to make them into the cells they need to be. Interpreting the book incorrectly can lead to changes in the cells which can lead to malignant cell degeneration and cancer”. Image: Pexels.com

By: Aurora Taira

What a perfect day for baking a pie! You take your recipe book and check the page you have bookmarked. Perhaps you have other favorites that are also bookmarked, while the page with blue cheese flavored mushroom soup is being completely ignored…or even being marked with a red flag!

Every cell in your body is actually using an identical recipe book to make the proteins they need to be the cells they are. This might sound unlikely as the cells in your eye and the cells in your big toe are quite different. The trick is that the cells have bookmarked different pages of the same recipe book; despite the genome being identical in all cells, not every gene is being translated in every cell.

Bookmarks may help you to find your favorite recipes when you need them or to mark the ones you dislike. Similarly, epigenetic marks are necessary for the cell to make proteins in the right place at the right time. Image: Pexels.com

We geneticists call this kind of bookmarking “epigenetic regulation”. DNA methylation is perhaps the most studied mechanism of epigenetic regulation and is often associated with silencing of gene expression. Accurate regulation of epigenetic factors is absolutely vital for normal cells to differentiate, develop and function. 

What happens when the recipe book is not interpreted correctly? – An example of a lymphoma predisposition family.

Reading the recipe book (in this case the genome) of a cell can go wrong in many ways. If cells harbor mutations, the recipe book itself might break. This may cause the cells to make nonfunctional proteins. The wrong pages might be bookmarked resulting in abnormal gene regulation. These changes often predispose cells to malignant degeneration and cancer.

Lymphomas are forms of cancer that affect the lymphatic system. Image: Aurora Taira, created with BioRender

We recently identified a Finnish family with many individuals diagnosed with lymphoma. As they were all from the same family, we reasoned that they probably have an inherited mutation which predisposes these individuals to hematological neoplasia. After mutation analyses we noted that some of the family members were carrying germline heterozygous mutations in a gene called TET2.

The TET2 story

TET2  is an important regulator of DNA demethylation in hematopoietic cells and is often somatically mutated in patients diagnosed with hematological diseases. The family members with mutated TET2 carry only one functional copy of this enzyme, and importantly, showed excess hypermethylation in their genome. The epigenetic regulation has gone wrong: as the amount of functional TET2 is decreased, demethylation is not taking place as normal and methylation keeps accumulating in the wrong places in the genome. So, a mutation in an important epigenetic regulator gene was causing errors in the genome bookmarking, eventually resulting in an increased risk for developing lymphoma.

This family had elderly mutation carriers diagnosed with lymphoma, but also younger unaffected adults carrying the mutation and showing an excess of hypermethylation. Could we do something about the hypermethylation and thus perhaps decrease their risk for developing lymphoma?

Fixing the bookmarks with vitamin C

Translational research and new treatment options are non-existent without basic research. Previous studies on mice and cell lines had found a fascinating feature of our gene of interest: TET2 activity is shown to be boosted by vitamin C. We became inspired by this and asked if vitamin C could also boost the activity of TET2 in humans. Family members from this same lymphoma predisposition family consented to take part in a clinical trial where they took 1g of vitamin C daily for one year. Through blood samples collected before, and at 6 and 12 months of the trial, we analyzed the genome wide methylation and gene expression patterns of these individuals.

“TET2 activity is shown to be boosted by vitamin C in mice and in cell lines, but could it also boost activity of TET2 in humans?” Image: Any Lane, pexels.com

Indeed it seemed to work! We saw that vitamin C reinforced the DNA demethylation cascade and reduced the proportion of hypermethylated loci at enhancer regions. The TET2 mutation status was elevating the binding site methylation levels of master hematopoietic transcription factors (such as TBX21 and SPI1) at the beginning of the trial but not after 12 months of vitamin C intake. The number of differentially expressed genes between mutation carriers and controls from the same family decreased after the vitamin C trial.

Spill the beans, cytosine!

Interpretation of the results was not trivial as the demethylation cascade is not as simple as a PhD student would hope it to be. Demethylation can occur either passively during cell division or actively via oxidation by TET2. When TET2 is involved, the first step in the reaction results in 5-hydroxymethylcytosine and in further oxidation steps, 5-formylcytosine and 5-carboxylcytosine are produced. Eventually, unmodified cytosine can be restored. With our nanopore sequencing machine, Promethion, we were able to detect both methylation and hydroxymethylation calls. 

What we actually saw after the trial was a genome wide decrease in hydroxymethylation levels and not methylation levels. With modeling of the reaction rates in the demethylation cascade we saw that vitamin C specifically enhanced the rate of the later oxidation steps and repair rate in the mutation carriers. Thus, we reasoned that vitamin C is boosting TET2 activity by driving the cytosine oxidation cascade to completion at a higher overall rate and that our results from mixed blood cells after 12 months of daily vitamin C likely reflect a new steady state in the system.

Next piece of the puzzle

Research is about searching for the truth through carefully conducted studies and experiments, but it is also about questioning the results previous scientists have published. Our results suggest that vitamin C may be of value in the prevention of hematological neoplasia for individuals carrying TET2 mutations. At this stage it is important to remember that further studies are needed to confirm our findings. While our results are promising, no official recommendations can be established at this point. We look forward to hearing how the scientific community will respond to our study and hope that it has given inspiration to researchers who are puzzling with the prevention of hematological diseases.

Aurora Taira, Doctoral researcher, Tumor Genomics group at the University of Helsinki. Photo: University of Helsinki, Credit: Iikki Donner.

Taira, A., Palin, K., Kuosmanen, A., Välimäki, N., Kuittinen, O., Kuismin, O., … & Aaltonen, L. A. (2023). Vitamin C boosts DNA demethylation in TET2 germline mutation carriers. Clinical Epigenetics15(1), 7.