MSI and dMMR in Cancer: Microsatellite Instability Explained

Every time a cell divides, its DNA must be copied, and small errors inevitably creep in, especially in short repeated DNA sequences called microsatellites. Healthy cells have a quality-control system called the DNA mismatch repair (MMR) pathway, built around four proteins — MLH1, MSH2, MSH6 and PMS2 — that work in pairs to detect and correct these copying mistakes. When one of these proteins is missing or non-functional, the repair system fails, and errors in microsatellites accumulate over time. This instability in the length of microsatellite sequences is what pathologists call microsatellite instability, or MSI.

MSI and mismatch repair deficiency (dMMR) describe the same underlying biological problem but are measured in different ways. dMMR is assessed directly, by staining tumour tissue for the four repair proteins with immunohistochemistry (IHC) and checking whether each one is present. MSI is assessed indirectly, by comparing the length of specific microsatellite DNA markers in tumour tissue against normal tissue from the same patient, typically using PCR or NGS. A tumour that is dMMR is expected to be MSI-high (MSI-H), and vice versa, so the two results are usually — though not always perfectly — interchangeable in clinical practice.

Most MSI-H/dMMR cancers arise sporadically, most often because the MLH1 gene has been silenced by a chemical process called promoter hypermethylation rather than by an inherited mutation. A minority arise from Lynch syndrome, an inherited condition in which a person is born with one non-functioning copy of one of the four mismatch repair genes in every cell of their body, making it much more likely that the second copy will also be lost inside a developing tumour.

If your tumour is reported as MSI-H or dMMR, it means your cancer's immune environment is often more visible to the immune system than a typical microsatellite-stable (MSS) tumour, and this is the biological reason why checkpoint inhibitor immunotherapy tends to work particularly well in this group. Depending on your cancer type and stage, this may mean immunotherapy is considered earlier in your treatment course than it otherwise would be, sometimes even before surgery.

If you have stage II colon cancer and your tumour is MSI-H, your oncologist may specifically advise against single-agent fluoropyrimidine chemotherapy (such as 5-FU alone), because evidence suggests this particular chemotherapy does not add benefit, and may even be less effective, in MSI-H stage II disease; this is a good example of a biomarker being used to withhold rather than add a treatment.

A dMMR or MSI-H result should also prompt a conversation about genetic counselling and germline testing for Lynch syndrome, particularly if you were diagnosed before age 50, have had more than one Lynch-associated cancer, or have relatives with colorectal, endometrial, ovarian, gastric or urinary tract cancers. If Lynch syndrome is confirmed, first-degree relatives (parents, siblings, children) have roughly a 50% chance of carrying the same gene variant, and those who test positive are typically offered earlier and more frequent colonoscopies, and sometimes gynaecological surveillance or risk-reducing surgery discussions, well before any cancer develops.

MSI/dMMR status does not diagnose cancer itself; it is a biomarker layered onto an existing tissue diagnosis, most often obtained from the same biopsy or surgical specimen used to confirm and stage the cancer. In colorectal and endometrial cancer, current guidelines from bodies including NCCN and ESMO recommend universal testing of all newly diagnosed tumours, regardless of age or family history, because relying on clinical features alone misses a meaningful proportion of Lynch syndrome cases. When dMMR is found without a clear sporadic explanation (such as MLH1 methylation or a BRAF mutation), referral to genetic counselling for germline testing is the recommended next diagnostic step, since only germline sequencing of the mismatch repair genes and EPCAM can definitively confirm or exclude Lynch syndrome.

MSI/dMMR testing is usually performed on the tumour tissue obtained at biopsy or surgery, most often as one of the first tests ordered at diagnosis of colorectal or endometrial cancer, and it is increasingly checked in many other cancer types either routinely or when standard treatments have been exhausted.

Immunohistochemistry (IHC) is the most widely used method. A pathologist stains thin slices of tumour tissue with antibodies against MLH1, MSH2, MSH6 and PMS2 and examines whether each protein is present in the tumour cell nuclei. Loss of staining for one or more proteins indicates dMMR; a specific pattern of loss (for example, MLH1 and PMS2 lost together, since PMS2 depends on MLH1 to be stable) can point toward the most likely underlying cause.

PCR-based MSI testing uses a standard panel of microsatellite markers (often the Bethesda panel) and compares their length in tumour DNA against normal tissue DNA from the same person; instability at two or more markers is classified as MSI-H, instability at one marker as MSI-low, and no instability as microsatellite-stable (MSS).

Next-generation sequencing (NGS) can calculate an MSI score computationally from broad genomic panels, alongside other information such as tumour mutational burden (TMB), and is increasingly used because it can be obtained from the same sample used for other biomarker testing. When MLH1 loss is found by IHC or PCR, an additional test for BRAF V600E mutation or MLH1 promoter methylation is usually performed, since a positive result strongly suggests a sporadic cause rather than Lynch syndrome and can appropriately reduce the urgency of germline testing.

MSI-H and dMMR are found most often in colorectal cancer, where they occur in roughly 15% of all cases, and in endometrial cancer, where they occur in a similar or slightly higher proportion, making these the two cancer types where universal testing is most firmly established in guidelines. Both cancer types are also the ones most classically associated with Lynch syndrome, alongside ovarian cancer, gastric cancer, small bowel cancer, and cancers of the urinary tract, brain and skin (sebaceous tumours), all of which form part of the Lynch syndrome tumour spectrum.

MSI-H/dMMR status also occurs, at lower frequency, in gastric, small intestinal, biliary tract, pancreatic, prostate and other cancers, and this is precisely why it has become a tumour-agnostic biomarker: regardless of where in the body a cancer starts, a tumour that is genuinely MSI-H or dMMR is considered eligible for immune checkpoint inhibitor treatment approaches once standard options have been considered. This tumour-agnostic approach was one of the earliest examples in oncology of a treatment being approved based on a shared molecular feature rather than the organ of origin, alongside other biomarkers discussed elsewhere in this Knowledge Center such as MSI's related concept, tumour mutational burden.

For advanced or metastatic MSI-H/dMMR cancers, immune checkpoint inhibitors targeting the PD-1/PD-L1 pathway are the treatment approach most directly supported by this biomarker and may be used earlier in the treatment sequence than chemotherapy, sometimes as first-line therapy. For localised colorectal or gastric cancer confirmed as dMMR, some centres now offer immunotherapy before surgery within clinical trials or established practice, an approach studied specifically because dMMR tumours respond unusually well to this strategy.

For early-stage colon cancer, treatment options are guided by combining MSI status with stage, tumour grade and other pathology features: MSI-H stage II disease often leads to a recommendation of observation or a different chemotherapy approach rather than single-agent fluoropyrimidine. If Lynch syndrome is confirmed, treatment options extend beyond the current cancer to long-term surveillance colonoscopy, discussion of risk-reducing gynaecological surgery once childbearing is complete, and consideration of chemoprevention strategies such as regular aspirin use, which should always be discussed individually with your care team. Enrolment in clinical trials is also frequently available for MSI-H/dMMR tumours, since this biomarker is widely used as an eligibility criterion across many modern immunotherapy studies.