Microsatellite instability (MSI) is a condition of genetic hypermutability focusing on microsatellites, which are short, repetitive DNA sequences scattered throughout the genome. Normally, the length of these sequences remains stable during cell division. MSI is defined by the rapid change in length, typically through the insertion or deletion of repeat units. This instability is a direct consequence of a failure in the cell’s natural DNA repair mechanisms.
The Role of the Mismatch Repair System
MSI is fundamentally caused by a breakdown in the Mismatch Repair (MMR) system, which functions as the cell’s primary genetic “spellchecker.” This system scans newly synthesized DNA strands and corrects errors that spontaneously occur during replication, such as single-base mismatches or small insertion-deletion loops.
The MMR system involves proteins that identify the error, excise the faulty segment, and insert the correct sequence. When the genes encoding these MMR proteins are inactivated, the repair function is compromised. Since microsatellite regions are highly repetitive, the failure to correct replication errors leads to a high frequency of length alterations, creating a hypermutable state known as the MSI phenotype.
Defining the Categories of MSI Status
The status of microsatellite instability is classified into three standardized categories for clinical reporting, based on the number or percentage of microsatellite markers showing length changes compared to normal tissue.
Microsatellite Instability-High (MSI-H)
MSI-H is defined by instability in two or more of the five standard markers tested, or instability in 30% or more of the markers analyzed.
Microsatellite Stable (MSS)
MSS means that no instability is detected in any of the markers examined.
Microsatellite Instability-Low (MSI-L)
MSI-L is defined as instability in only one of the five standard markers, or in fewer than 30% of the loci studied. For most clinical purposes, MSI-H tumors are grouped as “MSI-positive,” while MSI-L tumors are generally considered to behave similarly to MSS tumors.
Clinical Relevance in Cancer Treatment
Testing for MSI status is a standard procedure because it has significant prognostic and predictive implications for cancer patients. The status helps identify individuals who may have an inherited predisposition to cancer, such as Lynch syndrome. This hereditary condition, caused by germline mutations in MMR genes, is associated with a high lifetime risk of developing several types of cancer, including colorectal, endometrial, and gastric cancers.
For patients with an MSI-H tumor, the prognosis in early-stage disease is often more favorable compared to those with an MSS tumor. The MSI status is particularly relevant because it predicts the tumor’s response to modern therapies. The hypermutability of MSI-H tumors results in the creation of many novel proteins, known as neoantigens, which the immune system can recognize.
This high number of neoantigens makes the tumor appear highly foreign to the body’s immune defenses. This increased visibility translates into a strong response to immune checkpoint inhibitors (ICI). The success of these therapies has led to the approval of ICI treatments for any solid tumor classified as MSI-H, regardless of where the tumor originated.
Methods for Detecting MSI Status
MSI status can be determined clinically using two main laboratory methods that provide complementary information.
Polymerase Chain Reaction (PCR)
PCR analysis directly measures the length changes in microsatellite markers. This technique involves amplifying specific DNA sequences from both the tumor sample and a matched normal tissue sample. Comparing the fragment lengths between the two samples reveals instability, with new, different-sized fragments in the tumor indicating MSI status.
Immunohistochemistry (IHC)
IHC indirectly assesses the MMR system’s function by staining for the presence or absence of the MMR proteins themselves. Loss of staining for one or more of the MMR proteins indicates a deficient mismatch repair (dMMR) system, which strongly suggests an MSI-H status.
Both methods have a high concordance rate. The PCR method is considered the gold standard for directly measuring instability, while IHC is often used first due to its convenience and lower cost. These testing strategies provide the molecular data necessary to classify the tumor and guide treatment decisions.