DNA Mismatch Repair and Lynch Syndrome

Mismatch Repair Mechanism and MSI-High Phenotype

DNA replication introduces approximately one misincorporation per 10^9 base pairs copied due to DNA polymerase error rate and slippage at repetitive microsatellite sequences. The mismatch repair (MMR) pathway corrects these errors: MutSα (MSH2–MSH6) or MutSβ (MSH2–MSH3) heterodimers recognise the mismatch, recruit MutLα (MLH1–PMS2), which nicks the newly synthesised strand and coordinates excision and re-synthesis using the template strand. This reduces the replication error rate by 1,000-fold.

When MMR is deficient — through biallelic gene mutation, promoter methylation (MLH1 is epigenetically silenced in ~15% of sporadic colorectal cancers), or germline mutation — replication errors at microsatellite repeats accumulate as insertions/deletions. These accumulated errors create the MSI-high phenotype: frameshift mutations at hundreds of microsatellites throughout the genome, detectable by PCR (length variability at 5 standard microsatellite markers) or NGS. Frameshift mutations in coding microsatellites generate novel protein sequences (frameshifted peptides) that are uniquely recognised as foreign neoantigens by T cells.

Lynch Syndrome: Clinical Genetics and Cancer Spectrum

Lynch syndrome is caused by germline heterozygous mutations in MLH1, MSH2, MSH6, or PMS2 (or deletions in EPCAM affecting MSH2 expression), following autosomal dominant inheritance. The lifetime colorectal cancer risk ranges from 25–80% depending on the gene (highest for MLH1/MSH2, lower for MSH6/PMS2). Lynch syndrome also elevates risk for endometrial (~40–60% for MLH1/MSH2), ovarian (~10–15%), gastric, urinary tract, and small bowel cancers.

Universal MMR/MSI tumour testing of all colorectal and endometrial cancers (regardless of age) is now recommended to identify Lynch syndrome probands. Germline confirmation by multigene panel testing allows cascade testing of first-degree relatives. Colonoscopic surveillance every 1–2 years from age 25 detects colorectal adenomas at an early, curable stage. The MSI-high tumour status identified in Lynch syndrome patients also predicts excellent response to adjuvant pembrolizumab in early-stage colon cancer and front-line PD-1 blockade in metastatic disease.

MLH1 Epigenetic Silencing in Sporadic MSI-High Colorectal Cancer

Approximately 15% of all sporadic colorectal cancers are MSI-high, yet most of these are not Lynch syndrome — they arise through somatic MLH1 promoter CpG island hypermethylation rather than germline mutation. This epigenetic silencing mimics biallelic MLH1 inactivation without DNA sequence change, eliminating MMR function and generating the MSI-high phenotype through accumulated microsatellite frameshift mutations. Importantly, sporadic MLH1-methylated MSI-high CRCs are frequently associated with concurrent BRAF V600E mutation (~40–50% co-occurrence), a pattern essentially never seen in Lynch syndrome germline carriers — providing a diagnostic tool to distinguish the two.

Clinical algorithms for Lynch syndrome identification from tumour MMR testing therefore include reflex BRAF V600E testing and/or MLH1 promoter methylation analysis in MMR-deficient tumours with MLH1 loss, as BRAF mutation or MLH1 methylation indicates sporadic origin. Patients with MMR-deficient, BRAF-wild-type, MLH1-unmethylated tumours should proceed to germline testing. This reflex algorithm identifies Lynch syndrome in approximately 3–5% of all colorectal cancers while avoiding unnecessary germline testing in sporadic cases — a critical efficiency improvement in universal MMR testing programmes.

Pembrolizumab in MSI-High Cancer: Clinical Evidence

Pembrolizumab (anti-PD-1) became the first tumour-agnostic cancer treatment in FDA history when approved in 2017 for any MSI-high or dMMR solid tumour, regardless of tissue of origin — a landmark in biomarker-driven oncology. The KEYNOTE-158 basket trial demonstrated 40.6% ORR across 10 different MSI-H solid tumour types, with particularly high response rates in colorectal cancer, endometrial cancer, and gastric cancer. Durability of responses is a defining feature: in KEYNOTE-158, the majority of responses lasted >2 years, with some patients maintaining complete remission beyond 5 years — a pattern of durable benefit fundamentally different from chemotherapy.

In metastatic MSI-H/dMMR colorectal cancer, KEYNOTE-177 established pembrolizumab as the preferred first-line treatment over chemotherapy (12.0 vs 5.4 months PFS; HR 0.60), with a substantially longer median duration of response (NR vs 10.6 months). Nivolumab plus ipilimumab (CheckMate-142) also demonstrated 65% ORR in previously treated MSI-H CRC, and nivolumab monotherapy is approved as a second-line option. These approvals collectively establish MSI-high/dMMR status as the most actionable pan-tumour immunotherapy biomarker currently available.

Key Takeaways

• ·Mismatch repair (MMR) reduces the replication error rate 1,000-fold; loss of MMR through MLH1/MSH2/MSH6/PMS2 mutation or methylation generates the MSI-high phenotype with frameshift mutations at hundreds of microsatellite repeats.
• ·Lynch syndrome (germline MMR mutation) is the most common hereditary CRC syndrome (~1 in 300 people), conferring 25–80% lifetime colorectal cancer risk depending on gene — highest for MLH1/MSH2.
• ·Sporadic MSI-high CRC (~15% of all CRC) arises through somatic MLH1 promoter hypermethylation, frequently co-occurring with BRAF V600E — a pattern absent in Lynch syndrome, enabling algorithmic distinction.
• ·Pembrolizumab received the first tumour-agnostic FDA approval (2017) for MSI-high/dMMR solid tumours, achieving ~40% ORR pan-tumour with highly durable responses lasting years in complete responders.
• ·Universal tumour MMR testing in all colorectal and endometrial cancers is recommended to identify Lynch syndrome probands, guide immunotherapy eligibility, and enable cascade genetic testing of first-degree relatives.