Saskia Haupt

PURPOSE: Microsatellite instability (MSI) arises from mismatch repair-deficiency (MMR-d) and is a predictor of immune checkpoint blockade (ICB) therapy response. Although MSI diagnostics typically yield a binary classification (MSI or microsatellite stable), the molecular phenotype likely represents a continuum. We explored whether MSI follows a quantitative spectrum, reflecting the extent and severity of microsatellite alterations, and whether it holds clinical significance. METHODS: To quantitatively assess MSI, we evaluated the length of MSI peak shifts from polymerase chain reaction-based fragment length data in two cohorts (combined N = 237) of hereditary (Lynch syndrome) and sporadic MMR-d colorectal carcinomas (CRCs). We examined whether MSI peak shift lengths in diagnostic markers BAT25, CAT25, BAT26, and BAT40 correlate with specific MMR defects, histologic and clinical features, and coding microsatellite (cMS) mutations, potentially reflecting antigen load. RESULTS: MSI peak shift lengths varied among MMR-d CRCs and were influenced by the specific underlying MMR defect, such as germline mutations in MLH1 , MSH2 , MSH6 , or PMS2 , or somatic MLH1 promotor hypermethylation. Hereditary MSH6-deficient CRCs exhibited shorter peak shifts compared with hereditary MLH1-deficient and MSH2-deficient CRCs. Longer MSI peak shifts were associated with larger tumor sizes (odds ratio of 1.3 for every 1-cm increase in tumor diameter) and number of cMS mutations per tumor ( P = 8.73e-09). CONCLUSION: Our findings demonstrate that (1) MSI peak shift lengths differ among MMR-d CRCs, (2) this variation is influenced by the specific MMR defect, and (3) this variation correlates with tumor size and number of cMS mutations. These findings suggest that a quantitative MSI classification could enhance clinical utility, with potential, for instance, in predicting disease progression and ICB therapy response.

Lynch syndrome (LS), the most common inherited colorectal cancer (CRC) syndrome, increases the cancer risk in affected individuals. LS is caused by pathogenic germline variants in one of the DNA mismatch repair (MMR) genes, complete inactivation of which causes numerous mutations in affected cells. As CRC is believed to originate in colonic crypts, understanding the intra‐crypt dynamics caused by mutational processes is essential for a complete picture of LS CRC and may have significant implications for cancer prevention.We propose a computational model describing the evolution of colonic crypts during LS carcinogenesis. Extending existing modeling approaches for the non‐Lynch scenario, we incorporated MMR deficiency and implemented recent experimental data demonstrating that somaticCTNNB1mutations are common drivers of LS‐associated CRCs, if affecting both alleles of the gene. Further, we simulated the effect of different mutations on the entire crypt, distinguishing non‐transforming and transforming mutations.As an example, we analyzed the spread of mutations in the genesAPCandCTNNB1, which are frequently mutated in LS tumors, as well as of MMR deficiency itself. We quantified each mutation's potential for monoclonal conversion and investigated the influence of the cell location and of stem cell dynamics on mutation spread.Thein silicoexperiments underline the importance of stem cell dynamics for the overall crypt evolution. Further, simulating different mutational processes is essential in LS since mutations without survival advantages (the MMR deficiency‐inducing second hit) play a key role. The effect of other mutations can be simulated with the proposed model. Our results provide first mathematical clues towards more effective surveillance protocols for LS carriers.

Like many other types of cancer, colorectal cancer (CRC) develops through multiple pathways of carcinogenesis. This is also true for colorectal carcinogenesis in Lynch syndrome (LS), the most common inherited CRC syndrome. However, a comprehensive understanding of the distribution of these pathways of carcinogenesis, which allows for tailored clinical treatment and even prevention, is still lacking. We suggest a linear dynamical system modeling the evolution of different pathways of colorectal carcinogenesis based on the involved driver mutations. The model consists of different components accounting for independent and dependent mutational processes. We define the driver gene mutation graphs and combine them using the Cartesian graph product. This leads to matrix components built by the Kronecker sum and product of the adjacency matrices of the gene mutation graphs enabling a thorough mathematical analysis and medical interpretation. Using the Kronecker structure, we developed a mathematical model which we applied exemplarily to the three pathways of colorectal carcinogenesis in LS. Beside a pathogenic germline variant in one of the DNA mismatch repair (MMR) genes, driver mutations in APC, CTNNB1, KRAS and TP53 are considered. We exemplarily incorporate mutational dependencies, such as increased point mutation rates after MMR deficiency, and based on recent experimental data, biallelic somatic CTNNB1 mutations as common drivers of LS-associated CRCs. With the model and parameter choice, we obtained simulation results that are in concordance with clinical observations. These include the evolution of MMR-deficient crypts as early precursors in LS carcinogenesis and the influence of variants in MMR genes thereon. The proportions of MMR-deficient and MMR-proficient APC-inactivated crypts as first measure for the distribution among the pathways in LS-associated colorectal carcinogenesis are compatible with clinical observations. The approach provides a modular framework for modeling multiple pathways of carcinogenesis yielding promising results in concordance with clinical observations in LS CRCs.

Lynch syndrome (LS), the most common inherited colorectal cancer (CRC) syndrome, increases the cancer risk in affected individuals. LS is caused by pathogenic germline variants in one of the DNA mismatch repair (MMR) genes, complete inactivation of which causes numerous mutations in affected cells. As CRC is believed to originate in colonic crypts, understanding the intra-crypt dynamics caused by mutational processes is essential for a complete picture of LS CRC and may have significant implications for cancer prevention. We propose a computational model describing the evolution of colonic crypts during LS carcinogenesis. Extending existing modeling approaches for the non-Lynch scenario, we incorporated MMR deficiency and implemented recent experimental data demonstrating that somatic CTNNB1 mutations are common drivers of LS-associated CRCs, if affecting both alleles of the gene. Further, we simulated the effect of different mutations on the entire crypt, distinguishing non-transforming and transforming mutations. As an example, we analyzed the spread of mutations in the genes APC and CTNNB1 , which are frequently mutated in LS tumors, as well as of MMR deficiency itself. We quantified each mutation’s potential for monoclonal conversion and investigated the influence of the cell location and of stem cell dynamics on mutation spread. The in silico experiments underline the importance of stem cell dynamics for the overall crypt evolution. Further, simulating different mutational processes is essential in LS since mutations without survival advantages (the MMR deficiency-inducing second hit) play a key role. The effect of other mutations can be simulated with the proposed model. Our results provide first mathematical clues towards more effective surveillance protocols for LS carriers.

The immune system can recognize and attack cancer cells, especially those with a high load of mutation-induced neoantigens. Such neoantigens are abundant in DNA mismatch repair (MMR)-deficient, microsatellite-unstable (MSI) cancers. MMR deficiency leads to insertion/deletion (indel) mutations at coding microsatellites (cMS) and to neoantigen-inducing translational frameshifts. Here, we develop a tool to quantify frameshift mutations in MSI colorectal and endometrial cancer. Our results show that frameshift mutation frequency is negatively correlated to the predicted immunogenicity of the resulting peptides, suggesting counterselection of cell clones with highly immunogenic frameshift peptides. This correlation is absent in tumors with Beta-2-microglobulin mutations, and HLA-A*02:01 status is related to cMS mutation patterns. Importantly, certain outlier mutations are common in MSI cancers despite being related to frameshift peptides with functionally confirmed immunogenicity, suggesting a possible driver role during MSI tumor evolution. Neoantigens resulting from shared mutations represent promising vaccine candidates for prevention of MSI cancers.

BRAF V600E mutations have been reported as a marker of sporadic microsatellite instability (MSI) colorectal cancer (CRC). Current international diagnostic guidelines recommend BRAF mutation testing in MSI CRC patients to predict low risk of Lynch syndrome (LS). We evaluated the age‐specific performance of BRAF testing in LS diagnostics. We systematically compared the prevalence of BRAF mutations in LS‐associated CRCs and unselected MSI CRCs in different age groups as available from published studies, databases and population‐based patient cohorts. Sensitivity/specificity analysis of BRAF testing for exclusion of LS and cost calculations were performed. Among 969 MSI CRCs from LS carriers in the literature and German HNPCC Consortium, 15 (1.6%) harbored BRAF mutations. Six of seven LS patients with BRAF‐mutant CRC and reported age were BRAF mutations were detected in patients BRAF testing led to high risk of missing LS patients and increased costs at age BRAF testing in patients BRAF testing.

Like many other tumors, colorectal cancers develop through multiple pathways containing different driver mutations. This is also true for colorectal carcinogenesis in Lynch syndrome, the most common inherited colorectal cancer syndrome. However, a comprehensive understanding of Lynch syndrome tumor evolution which allows for tailored clinical treatment and even prevention is still lacking. We suggest a linear autonomous dynamical system modeling the evolution of the different pathways. Starting with the gene mutation graphs of the driver genes, we formulate three key assumptions about how these different mutations might be combined. This approach leads to a dynamical system that is built by the Kronecker sum of the adjacency matrices of the gene mutation graphs. This Kronecker structure makes the dynamical system amenable to a thorough mathematical analysis and medical interpretation, even if the number of incorporated genes or possible mutation states is increased. For the case that some of the mathematical key assumptions are not satisfied, we explain possible extensions to our model. Additionally, improved bio-medical measurements or novel medical insights can be integrated into the model in a straightforward manner, as all parameters in the model have a biological interpretation. Modifications of the model are able to account for other forms of colorectal carcinogenesis, such as Lynch-like and familial adenomatous polyposis cases. Graphical From the Medical Hypothesis Over the Modeling Approach To the Mathematical Structure.: The medical hypothesis of multiple pathways in carcinogenesis is widely known for various types of cancer. Left: We present a model for this phenomenon at the example of Lynch syndrome, the most common inherited colorectal cancer syndrome, with specific key driver events in the MMR genes, CTNNB1 , APC , KRAS and TP53 . Middle: This current medical understanding of carcinogenesis is translated into a mathematical model using a specific dynamical system, which can be represented by a graph structure, where each vertex in the graph represents a genotypic state and the edges correspond to the transition probabilities between those states. Starting with all colonic crypts in the state of all genes being wild-type and a single MMR germline mutation due to Lynch syndrome, we are interested in the distribution of the crypts among the graph at different ages of the patient in order to obtain estimates for the number of crypts in specific states, e.g. adenomatous or cancerous states. Right: The underlying matrix of the dynamical system makes use of the Kronecker sum and product. It is a sparse upper triangular matrix accounting for the assumption that mutations cannot be reverted. This allows fast numerical solving by using the matrix exponential. Each nonzero entry of the matrix represents a connection between genotypic states in the graph.

Background and aims: BRAF V600E mutations have been reported to be associated with sporadic microsatellite-unstable (MSI) colorectal cancer (CRC), while rarely detected in CRCs of Lynch syndrome (LS) patients. Therefore, current international diagnostic guidelines recommend somatic BRAF mutation testing in MLH1-deficient MSI CRC patients to exclude LS. As sporadic BRAF -mutant MSI CRC is a disease of the elderly, while LS-associated CRC usually occurs at younger age, we hypothesized that the efficacy of BRAF testing in LS diagnostics may be age-dependent. Methods: We systematically compared the prevalence of BRAF V600E mutations in LS-associated CRCs and MSI CRCs from population-based cohorts in different age groups as available from published studies, databases, and population-based patient cohorts. Cost calculations and sensitivity analysis of the BRAF testing for exclusion of LS was performed. Results: Among 969 MSI CRCs from LS mutation carriers from the literature and German HNPCC Consortium, 15 (1.6%, 95% CI: 0.9-2.6%) harbored BRAF mutations. 6/7 LS patients with BRAF -mutant CRC and reported age were 60 years. In MSI CRC patients BRAF mutations were detected only in 0.6% (2/339), and the inclusion of BRAF testing led to increased costs and higher risk of missing LS patients (1.2%) compared to other age groups. Conclusion: BRAF testing in patients BRAF testing.

The immune system can recognize and attack cancer cells, especially those with a high load of mutation-induced neo antigens. Such neo antigens are particularly abundant in DNA mismatch repair (MMR)-deficient, microsatellite-unstable (MSI) cancers. MMR deficiency leads to insertion/deletion (indel) mutations at coding microsatellites (cMS) and to neo antigen-inducing translational frameshifts. The abundance of mutational neo antigens renders MSI cancers sensitive to immune checkpoint blockade. However, the neoantigen landscape of MMR-deficient cancers has not yet been systematically mapped. In the present study, we used a novel tool to monitor neo antigen-inducing indel mutations in MSI colorectal and endometrial cancer. Our results show that MSI cancers share several highly immunogenic neo antigens that result from specific, recurrent indel mutation events. Notably, the frequency of such indel mutations was negatively correlated to the predicted immunogenicity of the resulting neo antigens. These observations suggest continuous immunoediting of emerging MMR-deficient cells during tumor evolution. One sentence summary: Quantitative indel mutation analysis reveals evidence of immune selection in mismatch repair-deficient cancers