The integrity of the human genome relies on complex DNA repair mechanisms. Although Deoxyribonucleic acid (DNA) is replicated with remarkable accuracy, mistakes inevitably occur during this copying process. The Mismatch Repair (MMR) system functions as a highly specialized quality control mechanism to catch and fix these errors. This ability to proofread the newly synthesized DNA strand safeguards against the accumulation of mutations that can lead to disease.
The Role of Mismatch Repair
DNA polymerase, the primary enzyme responsible for copying the genome, has its own proofreading capability, but a small number of mismatched bases or small insertion-deletion loops still slip through. The MMR system is tasked with correcting these remaining replication errors, increasing the fidelity of DNA replication. It acts like a spell-checker that scans the newly created DNA strand immediately following the initial copying process.
The MMR system involves a coordinated molecular machinery composed primarily of four proteins: MLH1, MSH2, MSH6, and PMS2. These proteins work together in functional pairs called heterodimers. The MSH2/MSH6 complex, often referred to as MutSα, is responsible for recognizing the error—specifically, a single base-pair mismatch or a small insertion or deletion.
Once the MSH2/MSH6 complex recognizes the error, it recruits the MLH1/PMS2 complex, or MutLα, to the site. This larger complex then coordinates the excision of the segment of DNA containing the error from the newly synthesized strand. Following excision, DNA polymerase fills the gap with the correct nucleotides, and DNA ligase seals the strand, completing the repair. This intricate process corrects thousands of errors per cell division, maintaining genomic stability.
Defining the Deficiency and Microsatellite Instability
Mismatch Repair Deficiency (MMRD) occurs when one or more components of the repair system become non-functional, leading to a failure to correct replication errors. When the MMR machinery is broken, the cell loses its spell-checking capability, resulting in an accumulation of uncorrected mutations throughout the genome. This condition is characterized as a hypermutator phenotype.
The most measurable and distinct consequence of MMRD is Microsatellite Instability (MSI). Microsatellites are specific regions of DNA composed of short, repetitive sequences, typically one to six base pairs in length, that are repeated multiple times. These repetitive tracts are particularly prone to slippage errors during DNA replication, where the DNA polymerase adds or deletes a small number of repeat units.
In a cell with a functioning MMR system, these slippage errors are quickly detected and repaired, keeping the microsatellite length consistent. Without functional MMR proteins, however, these replication errors remain uncorrected, causing the length of the microsatellite sequences to fluctuate. This change in length defines Microsatellite Instability.
Tumors are classified as Microsatellite Instability-High (MSI-H) when a significant proportion of these repetitive markers show altered lengths. MSI-H is the direct molecular signature confirming the MMR system is deficient. The high number of mutations accumulating in these regions can disrupt the function of genes controlling cell growth, contributing to cancer development.
Causes and Associated Conditions
Mismatch Repair Deficiency can arise through two distinct pathways: hereditary (inherited) or sporadic (acquired). The inherited form is most commonly associated with Lynch Syndrome, also known as hereditary non-polyposis colorectal cancer (HNPCC). Lynch Syndrome is an autosomal dominant condition caused by a germline mutation in one of the MMR genes, typically MLH1, MSH2, MSH6, or PMS2.
A person with Lynch Syndrome inherits one defective copy of an MMR gene. The second, healthy copy must also become inactivated through a somatic mutation later in life for the MMR system to fail and for cancer to develop. This inherited predisposition significantly elevates the lifetime risk for several cancer types, most notably colorectal cancer, which accounts for up to 3% of all cases.
Lynch Syndrome also increases the risk for extracolonic cancers. The specific gene that is mutated often influences the spectrum of cancers seen, which can include:
- Endometrial (uterine) cancer, which is the most common cancer in female carriers.
- Ovarian cancer.
- Stomach cancer.
- Small intestine cancer.
- Urinary tract cancers.
The sporadic, or acquired, form of MMRD accounts for the majority of MMR-deficient tumors, particularly in colorectal and endometrial cancers diagnosed later in life. In this scenario, the MMR genes are not defective in the germline, but they become inactivated in a somatic cell. The most frequent cause of sporadic MMRD is the epigenetic silencing of the MLH1 gene.
Epigenetic silencing occurs through a process called hypermethylation, where chemical groups are added to the promoter region of the MLH1 gene. This chemical modification acts like a lock, preventing the cell’s machinery from “reading” the gene and producing the MLH1 protein, leading to a complete loss of function. Unlike Lynch Syndrome, which carries a broad cancer risk, sporadic MMRD is confined to the tumor tissue and is not passed down to offspring.
Identification and Therapeutic Implications
Identifying MMR status is a standard and necessary step in the clinical management of several cancers, most frequently colorectal and endometrial cancers. The two primary methods for determining MMR status are complementary and widely used in pathology labs.
The first method is Immunohistochemistry (IHC), which uses antibodies to visualize the presence or absence of the four core MMR proteins (MLH1, MSH2, MSH6, and PMS2) in the tumor tissue. If a protein is present and functional, the cell nuclei will stain positive; if the protein is absent, the tissue is classified as deficient. Because the proteins work in pairs, the loss of one often leads to the degradation of its partner, creating predictable patterns, such as the simultaneous loss of MLH1 and PMS2 staining.
The second method is molecular testing for Microsatellite Instability (MSI). This is performed using Polymerase Chain Reaction (PCR) or Next-Generation Sequencing (NGS) to compare the length of specific microsatellite markers in the tumor DNA versus normal DNA. A tumor is classified as MSI-High (MSI-H) if a high percentage of the markers show length changes, confirming the biological consequence of MMRD.
The MMR/MSI status is important because it serves as a predictive biomarker for immune checkpoint inhibitors (ICIs), such as PD-1 blockers. MMR-deficient tumors accumulate a high number of mutations, resulting in a high Tumor Mutational Burden (TMB). Many of these mutations occur in protein-coding regions, leading to the creation of abnormal, non-self proteins called neoantigens.
These numerous neoantigens act as molecular flags, making the MMR-deficient tumor recognizable and “visible” to the body’s immune system. The immune system often attempts to attack these mutated cells, but the tumor protects itself by upregulating checkpoint proteins like PD-L1, which effectively place “brakes” on the attacking immune T-cells.
Immune checkpoint inhibitors work by blocking these inhibitory signals, releasing the T-cells to mount a directed attack against the neoantigenic tumor. This mechanism results in a strong response rate in MSI-H/MMR-deficient tumors, regardless of the tumor’s location—a concept known as tumor-agnostic treatment. The status of the MMR system has shifted from being merely a diagnostic feature to being a significant predictor of successful personalized oncology treatment.