Van Boxtel group

 

Mutation accumulation in normal cells is required for the development of cancers. Because aging is the biggest risk factor for cancer, it is thought that mutation accumulation is rate limiting for disease initiation. Indeed, as our cells age, they gradually accumulate mutations in their genomes. If a cell by chance acquires a bad mutation at the wrong time and place, malignant transformation can be triggered. According to this model, we should target these mutations, or their functional effects, in order to remove the driving force of the cancer and kill it.

However, with the recent developments of sequencing normal, noncancerous cells, we see that the mutation loads in normal tissues are already so high that it is very likely that there are always cells in our bodies with the right set of mutations, which are required for malignant transformation; yet we don’t have cancer. For example, in quite some newborns we can detect leukemia-driving fusion genes in their blood, yet these babies are perfectly healthy and do not develop leukemia. In addition, for certain cancer types, such as leukemia, young children show a higher incidence compared to young adolescents. This phenomenon represents an apparent paradox, as young cells should have less somatic (oncogenic) mutations than adult cells. It is very likely that mutation accumulation, although very necessary, is not the rate limiting step in cancer development.

Why then, do certain individuals develop cancer and others don’t? If mutation accumulation is not rate limiting for disease development, what is? And more importantly, shouldn’t we be targeting those rate limiting factors? In other words, if getting cancer is default, because of the relatively high mutation burden in normal tissues, how do our bodies keep the initiation of cancer in check and why does this sometimes fail?

Pinpointing the rate limiting steps in cancer initiation is challenging as many factors can play a role: ecological features within the various tissues, tissue damage responses, age, carcinogenic exposure, etc. Still, an increased understanding in how the body can keep cancer in check might revolutionize how we battle the disease: we have “stolen” our best ideas from nature, so why not this?

To answer these questions, we have 3 research themes in our lab.
Theme 1: Tissue-specific mutation accumulation in human stem cells
Theme 2: Tracking the origin of cancer
Theme 3: The etiology of therapy-related malignancies in cancer survivors

 

Organ-specific cancer incidence varies significantly throughout the human body, which cannot be solely explained by different exposures to mutagenic environmental factors, such as smoking, ultra-violet light or alcohol use. Adult stem cells are likely the cellular targets for accumulation of pre-cancerous successive oncogenic hits, which eventually can give rise to tumor development, owing to their life-long capacity to propagate mutations to both self-renewing progeny and downstream progenitors. We aim to identify and study the mutational processes that are active in adult stem cells of various organs and precede oncogenic transformation.

Strategy 1: Characterizing mutation accumulation during healthy life
Cataloguing rare somatic mutations in physiologically normal cells is technically challenging due to polyclonal nature of healthy tissues and the high error rate of single cell sequencing techniques. To overcome these challenges, we expand individual stem cells in vitro into clonal cultures, which reflect the genetic makeup of the original cell (i.e., mutations in the original cell will be shared by all other cells in the culture). Subsequently, sufficient DNA can be obtained to accurately catalogue the very rare somatic mutations present in the original cell. Using this approach, we have studied mutation accumulation in various tissues, such as blood, small intestine, colon and liver, and correlated this with organ-specific cancer incidence.

Publications:
Blokzijl et al., Nature 538:260-264 (2016) PMID: 27698416 Jager et al., Nature Protocols 13:59-78 (2018) PMID: 29215633 Osorio et al., Cell Reports 25:2308-2316.e4 (2018) PMID: 30485801
Rosendahl Huber A, Manders F, Oka R, van Boxtel R. Characterizing mutational load and clonal composition of human blood. J Vis Exp. 2019 Jul 11;(149)

Strategy 2: Study mutation accumulation in individuals at risk
Some individuals are at risk of developing cancer due to predisposing factors, such as germline mutations in DNA repair genes or a constitutive trisomy of chromosome 21 underlying Down syndrome. Indeed, newborns with Down syndrome have an increased risk of developing childhood leukemia, while they seem protected against solid tumors throughout life. We hypothesize that by characterizing mutation accumulation in stem cells of different tissues of individuals at risk for cancer, we will gain mechanistic insight into the rate limiting factors underlying carcinogenesis. Using this strategy, we found that fetal Down syndrome cells accumulate more mutations during early development as karyotypically normal cells. This increased mutation burden may contribute to the increased risk of leukemia early during life in Down syndrome.

Publications:
Hasaart et al., Scientific Reports 10:12991 (2020) PMID: 32737409 Hasaart*, Bertrums* et al., Expert Rev Mol Med. 23:e5 (2021) PMID: 33902785

DNA is the largest biomolecule in the cells, which unlike other biomolecules is irreplaceable. Consequently, mutations resulting from incorrectly or unrepaired DNA damage will gradually accumulate throughout the life of a cell. The processes causing these mutations leave characteristic patterns in the DNA, such as specific base substitutions in certain nucleotide context (i.e., mutational signatures/footprints). These patterns can serve as a functional readout of mutagenic and/or DNA repair activity. In addition, cells with disadvantageous mutations will be selected against causing a disbalance between damaging and neutral mutations at functionally important loci, such as genes. This phenomenon can be exploited to measure selective pressure. Finally, cells with a more recent common ancestor will share a larger number of somatic mutations than cells that separated early during development, providing means to measure clonal lineages within tissues. Therefore, the complete catalogue of somatic mutations in a genome can serve as an archive containing information on the life history of the cell. By studying mutation accumulation in noncancerous cells of individuals who developed cancer, we aim to determine the mechanisms and rate-limiting steps underlying carcinogenesis.

Strategy 1: Dissecting the etiology of mutational signatures in cancer
A multitude of mutational signatures have been identified in cancer genomes. However, the mechanisms underlying many signatures remain unknown, which hampers their use in cancer diagnostics. We aim to functionally characterize the etiology of mutational signatures in cancer genomes. To achieve this, we combine experimental and bioinformatics approaches to systematically identify and characterize the processes underlying mutational signatures. For this, we apply CRISPR/Cas9 genome editing or specific carcinogenic exposure in human organoid cultures as well as cell lines. Using this strategy, we discovered a novel signature induced by common gut bacteria that can cause colorectal cancer. Also, we found a signature that can be predictive for genetic predisposition to cancer as a consequence of germline mutations in the DNA repair gene NTHL1.

Publications:
Drost et al., Science 358:234-238 (2017) PMID: 28912133 Blokzijl et al., Genome Medicine 10:33 (2018) PMID: 29695279
Pleguezuelos-Manzano et al., Nature 580:269-273 (2020) PMID: 32106218

Strategy 2: Retrospective lineage tracing of childhood leukemia and lymphoma
Why do children get cancer? For certain cancer types, such as leukemia, young children show a higher incidence compared to young adolescents. This phenomenon represents an apparent paradox, as young cells should have less somatic (oncogenic) mutations than adult cells. Therefore, the etiology of pediatric cancers may differ from cancer in the elderly. We aim to determine the rate-limiting steps underlying the genesis of childhood cancer by studying mutation accumulation and clonal lineages in blood of children with leukemia or lymphoma. For this, we study the processes that contribute to the development of childhood leukemia/lymphoma by comparing somatic mutation patterns between cancerous and patient-matched normal hematopoietic cells. Secondly, we aim to pinpoint the clonal origin of childhood leukemia during the development of the hematopoietic system by retrospective lineage tracing.

Publications:
Brandsma et al., Blood Cancer Discov DOI: 10.1158/2643-3230.BCD-21-0010