Lynch syndrome, molecular mechanisms and variant classification

Abstract

Patients with the heritable cancer disease, Lynch syndrome, carry germline variants in the MLH1, MSH2, MSH6 and PMS2 genes, encoding the central components of the DNA mismatch repair system. Loss-of-function variants disrupt the DNA mismatch repair system and give rise to a detrimental increase in the cellular mutational burden and cancer development. The treatment prospects for Lynch syndrome rely heavily on early diagnosis; however, accurate diagnosis is inextricably linked to correct clinical interpretation of individual variants. Protein variant classification traditionally relies on cumulative information from occurrence in patients, as well as experimental testing of the individual variants. The complexity of variant classification is due to (1) that variants of unknown significance are rare in the population and phenotypic information on the specific variants is missing, and (2) that individual variant testing is challenging, costly and slow. Here, we summarise recent developments in high-throughput technologies and computational prediction tools for the assessment of variants of unknown significance in Lynch syndrome. These approaches may vastly increase the number of interpretable variants and could also provide important mechanistic insights into the disease. These insights may in turn pave the road towards developing personalised treatment approaches for Lynch syndrome.

Fig. 1. The human DNA mismatch repair (MMR) system.

a The MSH2 protein forms dimers with MSH6 (MutSα) and MSH3 (MutSβ). The MLH1 protein forms dimers with PMS2 (MutLα), PMS1 (MutLβ) and MLH3 (MutLγ). Heterodimer functions are listed. IDL, insertion/deletion loop. b A schematic illustration of the 5’ to 3’ MMR pathway. EXO1 binds a nick in the newly synthesised DNA strand 5’ to the mismatch. MutSα recognises the mismatch and undergoes an ATP-dependent conformational change, which locks the complex around the DNA to form a sliding clamp. MutSα moves along the DNA strand and interacts with MutLα, which further binds the DNA. MutSα/MutLα binds EXO1 and moves in the 5’ to 3’ direction allowing for the excision of the mismatch by EXO1. RPA protects the unpaired strand until the DNA polymerase bound to PCNA repairs the strand, after which the DNA ligase seals off any remaining nicks (not shown).

Fig. 2. Proteasomal degradation of misfolded proteins.

a Overview of the ubiquitin–proteasome system (UPS). A ubiquitin moiety is activated by an E1 enzyme and transferred to an E2 enzyme. From here, the ubiquitin is transferred to the target protein by the means of an E3 ubiquitin-protein ligase. Ubiquitination promotes binding at the proteasome and subsequent degradation of the target protein. b A wild-type protein (left) mainly exists in the functional native structure that is not degraded. Mutations affect the protein structure to mild (centre) or more severe (right) degrees and may obstruct the protein function. Both mildly and severely misfolded proteins risk undergoing proteasomal degradation.

Fig. 3. Overview of tools used for testing individual variant effects.

a Low-throughput lab-based experimental tools, i.e., individual variant testing. b Computational prediction tools, i.e., FoldX, GEMME, etc. c High-throughput lab-based experimental tools, i.e., MAVEs. Created with BioRender.com.