Residency · Residency · Medical Genetics Genomics

Lynch Syndrome: Diagnosis, Surveillance, and Immunotherapy Implications

Molecular Basis

Mismatch Repair (MMR) System

The mismatch repair system corrects single-base mismatches and small insertion/deletion loops that arise during DNA replication. The key proteins are MLH1, MSH2, MSH6, and PMS2, which function as heterodimers: MutS-alpha (MSH2-MSH6) and MutL-alpha (MLH1-PMS2). MSH2-MSH6 recognizes the mismatch, after which MLH1-PMS2 is recruited to coordinate excision and resynthesis of the affected DNA strand. MSH2-MSH3 (MutS-beta) recognizes larger insertion/deletion loops. When MMR function is lost, mutations accumulate at microsatellite repeats and throughout the genome, driving carcinogenesis.

Genetic Basis of Lynch Syndrome

Lynch syndrome follows autosomal dominant inheritance of germline pathogenic variants in MMR genes. The distribution of pathogenic variants across genes is approximately 40% in MLH1, 34% in MSH2, 18% in MSH6, and 8% in PMS2. EPCAM deletions account for 1 to 3% of Lynch syndrome; deletions at the 3-prime end of EPCAM cause epigenetic silencing of the adjacent MSH2 gene through promoter hypermethylation, with risk primarily for colorectal and endometrial cancer. Lynch syndrome follows the two-hit model: a germline monoallelic mutation in one allele is followed by somatic loss of the remaining allele through loss of heterozygosity, somatic mutation, or promoter methylation.

Microsatellite Instability (MSI)

Microsatellites are short tandem repeat sequences of 1 to 6 base pair units scattered throughout the genome. Microsatellite instability is the hallmark of deficient mismatch repair (dMMR). MSI testing uses a panel of microsatellite markers (the Bethesda panel or newer pentaplex/mononucleotide panels). A tumor is classified as MSI-High (MSI-H) when 2 or more of 5 markers are unstable (or 30% or more of markers in expanded panels), and as MSI-Low or microsatellite stable (MSS) when fewer than 2 markers are unstable. PCR-based MSI testing and immunohistochemistry (IHC) for MMR proteins are complementary diagnostic approaches.

Cancer Risks

Colorectal Cancer (CRC)

Lifetime colorectal cancer risk varies by gene: MLH1 and MSH2 carriers face approximately 40 to 80% risk, while MSH6 carriers face approximately 10 to 20% and PMS2 carriers approximately 15 to 20%. The mean age of CRC diagnosis ranges from 44 to 61 years, with MSH6 and PMS2 associated with later onset. Lynch-associated CRC is predominantly right-sided and proximal. Histologic features include mucinous differentiation, abundant tumor-infiltrating lymphocytes, medullary-type morphology, and Crohn-like lymphocytic reaction. Despite these aggressive-appearing features, Lynch CRC has a better stage-for-stage prognosis than sporadic microsatellite stable CRC.

Endometrial Cancer

Lifetime endometrial cancer risk is approximately 40 to 60% for MLH1/MSH2 carriers, 16 to 26% for MSH6, and approximately 15% for PMS2. Endometrial cancer may be the sentinel cancer in up to 50% of female Lynch syndrome patients, preceding a colorectal cancer diagnosis. Location in the lower uterine segment is suggestive of Lynch-associated endometrial cancer.

Other Associated Cancers

Ovarian cancer risk is 6 to 12% for MLH1/MSH2 carriers, with lower risk for MSH6 and PMS2. Gastric cancer risk is 5 to 10%, higher in Asian populations and in MLH1/MSH2 carriers. Urinary tract cancers (renal pelvis and ureter) occur in 1 to 12%, with higher risk in MSH2 carriers. Small bowel cancer risk is 3 to 6%, and hepatobiliary and pancreatic cancer risks are 1 to 4%. Brain tumors, particularly glioblastoma, in combination with CRC constitute Turcot syndrome. Sebaceous neoplasms define the Muir-Torre syndrome variant.

Diagnostic Approach

Universal Tumor Screening

NCCN and multiple organizations recommend universal (reflexive) screening of all colorectal and endometrial cancers for Lynch syndrome. Two approaches are both acceptable as first-tier tests: immunohistochemistry for MMR proteins (MLH1, MSH2, MSH6, PMS2), where loss of protein expression identifies the deficient component, and MSI testing by PCR, which identifies MSI-H tumors requiring further workup. When IHC shows loss of MLH1/PMS2, reflex testing for MLH1 promoter hypermethylation and/or BRAF V600E mutation distinguishes sporadic hypermethylation (which accounts for approximately 15% of CRC) from Lynch syndrome. BRAF V600E is present in roughly 60% of sporadic MLH1-methylated CRC but is virtually absent in Lynch-associated CRC. If BRAF is negative and MLH1 is methylated, germline MLH1 testing should still be considered, as constitutional MLH1 epimutation is rare but has been reported.

Germline Testing

Confirmatory germline testing using a multigene panel that includes MLH1, MSH2, MSH6, PMS2, and EPCAM is indicated when tumor screening suggests Lynch syndrome. It is also indicated based on personal or family history meeting clinical criteria, even without tumor testing. Direct germline testing without prior tumor screening is increasingly accepted, especially with the availability of multigene panels.

Clinical Criteria (Historical)

The Amsterdam II criteria require three or more relatives with Lynch-associated cancer spanning two or more generations, with at least one diagnosed before age 50, one being a first-degree relative of the other two, and FAP excluded. The revised Bethesda guidelines are broader criteria for identifying individuals who should undergo tumor MSI testing. However, these clinical criteria miss approximately 50% of Lynch syndrome cases, which supports universal tumor screening.

Surveillance Protocols

Colorectal Cancer Surveillance

Colonoscopy every 1 to 2 years should begin at age 20 to 25, or 2 to 5 years before the youngest CRC diagnosis in the family. For MLH1/MSH2 carriers, annual colonoscopy is recommended, while MSH6 and PMS2 carriers may undergo colonoscopy every 1 to 2 years, with some guidelines allowing longer intervals. The accelerated adenoma-to-carcinoma progression in Lynch syndrome (approximately 2 to 3 years compared to roughly 10 years in sporadic cases) justifies these short surveillance intervals. Aspirin chemoprevention, studied at 600 mg daily in the CAPP2 trial (with lower doses under investigation in CAPP3), reduces CRC risk by approximately 35 to 40% after 2 or more years of use.

Endometrial and Ovarian Cancer Surveillance

No proven effective screening strategy exists for gynecologic cancers in Lynch syndrome. Endometrial sampling every 1 to 2 years starting at age 30 to 35 may be considered based on expert opinion, though evidence is limited. Transvaginal ultrasound is not recommended as a primary screening tool due to low sensitivity. Risk-reducing hysterectomy and bilateral salpingo-oophorectomy after completion of childbearing, typically at age 35 to 40, is the recommended preventive strategy.

Other Cancer Surveillance

Upper endoscopy (EGD) every 2 to 3 years starting at age 30 to 35 is recommended for gastric and small bowel cancer risk, along with Helicobacter pylori testing and treatment. Annual urinalysis is recommended particularly for MSH2 carriers to screen for urothelial cancer. Annual skin examination screens for sebaceous neoplasms. Brain MRI is not routinely recommended but should be considered if there is a family history of CNS tumors.

Immunotherapy Implications

MSI-H/dMMR and Immune Checkpoint Inhibitors

MSI-H/dMMR tumors have a high tumor mutational burden due to accumulated frameshift mutations. These frameshift mutations generate neoantigens that are recognized by the immune system. Although dMMR tumors develop dense immune infiltration with tumor-infiltrating lymphocytes, they also upregulate PD-L1 to evade immune destruction. Immune checkpoint inhibitors (anti-PD-1/PD-L1 antibodies) remove this immune evasion mechanism, unleashing anti-tumor immunity.

Landmark Clinical Evidence

Pembrolizumab received FDA approval for all MSI-H/dMMR solid tumors regardless of tissue origin, making it the first tissue-agnostic approval in 2017. The GARNET trial of dostarlimab demonstrated a complete clinical response in 100% (12 of 12) of dMMR rectal cancers treated with neoadjuvant dostarlimab, as reported by Cercek et al. in the New England Journal of Medicine in 2022, with the study continuing with expanded enrollment. CheckMate 142 showed durable responses to nivolumab plus ipilimumab in MSI-H metastatic CRC. Response rates to checkpoint inhibitors in MSI-H CRC are approximately 30 to 50% with monotherapy and 55 to 70% with combination therapy.

Clinical Implications

MSI/MMR testing is now standard of care for all CRC at diagnosis, serving dual purposes of Lynch syndrome screening and treatment selection. Importantly, dMMR CRC does not benefit from 5-FU adjuvant chemotherapy in stage II disease, making this a critical treatment decision. Neoadjuvant immunotherapy may enable organ preservation in dMMR rectal cancer. Lynch syndrome patients who develop cancer may have superior outcomes with immunotherapy compared to surgery-first approaches in select settings.

Constitutional Mismatch Repair Deficiency (CMMRD)

Constitutional mismatch repair deficiency results from biallelic germline MMR gene mutations following autosomal recessive inheritance. It manifests as a childhood cancer predisposition syndrome with brain tumors (glioblastoma, astrocytoma), hematologic malignancies (lymphoma, leukemia), and early-onset CRC among other cancers. Affected children often present with cafe-au-lait macules resembling neurofibromatosis type 1, but NF1 testing is negative. Tumors display extremely high tumor mutational burden, suggesting potential responsiveness to immunotherapy. Diagnosis involves functional MMR testing, MSI testing in non-neoplastic tissue, and germline sequencing. Aggressive surveillance protocols are required from early childhood.

<image>A diagnostic algorithm for universal Lynch syndrome screening. Starting with a newly diagnosed colorectal or endometrial cancer, the flowchart shows two parallel first-tier tests: IHC for MMR proteins and MSI by PCR. For IHC showing loss of MLH1/PMS2: reflex to MLH1 promoter methylation and BRAF V600E testing. If BRAF positive or MLH1 methylated: likely sporadic (no germline testing). If BRAF negative and MLH1 unmethylated: proceed to germline MLH1 testing. For IHC showing loss of MSH2/MSH6: proceed directly to germline MSH2/MSH6/EPCAM testing. For IHC showing isolated PMS2 or MSH6 loss: proceed to germline testing of the respective gene. All paths converge on confirmatory germline multigene panel testing and cascade testing of relatives if positive.</image>

<image>A schematic showing the mechanism of immunotherapy response in MSI-H tumors. Panel 1: Normal MMR system correcting a replication error (mismatch) in DNA. Panel 2: dMMR tumor cell accumulating hundreds of frameshift mutations, generating neoantigen peptides displayed on MHC class I molecules on the tumor cell surface. Panel 3: T cells recognizing neoantigens but being inhibited by PD-1/PD-L1 interaction (immune evasion). Panel 4: Anti-PD-1 antibody (pembrolizumab/dostarlimab) blocking the PD-1/PD-L1 interaction, allowing T cell-mediated tumor killing. The high tumor mutational burden (TMB) and dense tumor-infiltrating lymphocyte (TIL) infiltrate characteristic of dMMR tumors are annotated.</image>

<image>A surveillance timeline for a Lynch syndrome patient with MSH2 pathogenic variant. Starting at age 20: begin colonoscopy every 1-2 years. Age 25: add annual urinalysis. Age 30-35: add upper endoscopy every 2-3 years, consider endometrial sampling for females, annual skin examination. Age 35-40: discuss risk-reducing hysterectomy/BSO for females. Aspirin chemoprevention is shown as a continuous bar starting at diagnosis. Cancer risk curves for CRC, endometrial, ovarian, and urothelial cancers are overlaid on the timeline, showing increasing cumulative risk with age. Management decision points are highlighted at each surveillance milestone.</image>

Clinical Pearls

Universal tumor screening with IHC and/or MSI of all colorectal and endometrial cancers is recommended regardless of age or family history, as clinical criteria miss approximately 50% of Lynch syndrome cases. BRAF V600E mutation in a CRC with MLH1 loss effectively excludes Lynch syndrome with greater than 99% specificity and indicates sporadic MLH1 promoter hypermethylation, avoiding unnecessary germline testing. Lynch syndrome CRC has an accelerated adenoma-to-carcinoma progression of approximately 2 to 3 years versus roughly 10 years for sporadic CRC, justifying colonoscopy intervals of 1 to 2 years rather than the standard 10-year screening interval. Aspirin chemoprevention reduces CRC risk in Lynch syndrome by approximately 35 to 40%, with optimal dosing being clarified by the CAPP3 trial. MSI-H/dMMR status is now as important for treatment selection (immunotherapy eligibility) as it is for Lynch syndrome diagnosis, and all CRC should be tested at diagnosis for both purposes. Stage II dMMR CRC does not benefit from 5-FU-based adjuvant chemotherapy, making this a critical treatment decision informed by MSI/MMR testing. EPCAM deletions should be included in Lynch syndrome testing panels, as they account for 1 to 3% of Lynch syndrome and cause MSH2 silencing through promoter hypermethylation.

References

• Vasen HFA et al. Revised guidelines for the clinical management of Lynch syndrome. Gut. 2013;62(6):812-823.
• Le DT et al. PD-1 blockade in tumors with mismatch-repair deficiency. N Engl J Med. 2015;372(26):2509-2520.
• Cercek A et al. PD-1 blockade in mismatch repair-deficient, locally advanced rectal cancer. N Engl J Med. 2022;386(25):2363-2376.
• Burn J et al. Cancer prevention with aspirin in hereditary colorectal cancer (Lynch syndrome): 10-year follow-up of the CAPP2 randomised controlled trial. Lancet. 2020;395(10240):1855-1863.
• Hampel H et al. Screening for Lynch syndrome (hereditary nonpolyposis colorectal cancer). N Engl J Med. 2005;352(18):1851-1860.
• NCCN Clinical Practice Guidelines: Genetic/Familial High-Risk Assessment: Colorectal. Version 2.2025.

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