A paper and visual abstract on microsatellite instability by Gloria Zaffaroni, Miguel Cunha and Gabriela Möslein.

Gloria Zaffaroni, Miguel Cunha and Gabriela Möslein

MSI Visual Abstract - links to PDF version

What is microsatellite instability?

Microsatellite instability (MSI) is the spontaneous alteration (insertion or deletion) of nucleotides from repetitive DNA tracs and it is recognised as one of the major carcinogenetic pathways of colorectal cancer (CRC), accounting for approximately 20% of unselected CRC cases.

Microsatellites are short tandem repeat DNA sequences of one to tetra base pairs distributed throughout the genome. Owing to their repeated structure, microsatellites are prone to replications errors.

The mismatch repair (MMR) system normally corrects spontaneous mutation in repetitive DNA sequences. MMR is a very highly conserved cellular process, involving many proteins that identify and repair mismatched bases in DNA (arisen during replication, genetic recombination or chemical or physical damage). Small DNA mismatches errors are detected by MSH2/MSH6 and MSH2/MSH3 heterodimers and are corrected by MLH1/PSM2 heterodimers. Both complex are required for MMR.

MSI manifests as novel alleles of varying length that can arise from impairments in the MMR system. This genomic hypermutability is the diagnostic hallmark of MSI as a molecular tumour phenotype.

MSI-positive (MSI+) cancers exhibit clinical, pathological and molecular characteristics that distinguish them from MSI-negative (MSI-) irrespective of hereditary or sporadic origins. In particular, MSI causes accumulation of frameshift mutations in repeated sequences of target tumor suppressor genes. Thus, MSI+ cancers show specific patterns of gene regulation and often have aberrant alterations such as hypermethylation of various gene, including the MMR gene, most frequently MLH1.

There are three different type of MSI:

  • caused by an inherited germline mutation in one allele of MMR, followed by somatic inactivation of the wild-type allele, as in hereditary nonpolyposis colorectal cancer (HNPCC), known as Lynch syndrome (LS)
  • caused by somatic inactivation of both alleles, detected in 15% of sporadic colorectal cancers.

In Lynch syndrome a germ line mutation in MMR genes (MLH1, MSH2, MSH6 PMS2) predispose individual to an increased lifetime risk of developing a variety of cancers. It requires a biallelic 'two hits' inactivation of responsible MMR genes, and the somatic inactivation in the wild-type allele can occur through loss of heterozygosis, somatic mutation or promoter methylation. Recently these genes have been subdivided into the much more penetrant genes MSH2 and MLH1 and the less penetrant, but quite frequent MSH6 and PMS2 genes. The individual gene and gender relate to substantially different cancer risks. These have now led to a revision of the previous European expert guidelines in a joint effort of ESCP and EHTG and will be published in BJS open access shortly for further reference.

Sporadic MSI+ cancers are often associated with hypermethylation of the MLH1 gene.

MSI is categorised as three different subtypes:

  • High level of MSI (MSI-H): two or more microsatellite with mutation
  • Low level of MSI (MSI-L): one mutated
  • Stable microsatellite (MSS).

CRCs with defective DNA-MMR have unique molecular and clinical presentations:

  • MSI+
  • Poor differentiation
  • Abundant mucin secretion
  • Marked lymphocytic infiltration
  • Preferential localisation in proximal colon.

MSI role in the decision making and future perspectives

MSI status will be important for the decision-making process for several reason:

  • Defining the prognoses: Cancer with MSI+ has been associated with favorable prognoses. MMR deficiency generates multiple aberrant proteins that are truncated by frameshift mutations, providing a source of abnormal peptides that can be presented to cytotoxic T lymphocytes (CTLs). In MSI+ there is an activated immune response because of an upregulation of immunomodulatory genes, such proinflammatory cytokines and cytotoxic mediators.
  • Defining the chemotherapy regimen: Several studies supporting MSI-H as a predictive factor for improved response to irinotecan-based chemotherapy. On the other hand, numerous studies seem to suggest a lack of benefit of 5-FU chemotherapy in patients with MSI.
  • Defining treatment targets: MSI+ CRCs show highly upregulated expression of multiple immune checkpoint proteins, that are potentially targetable with inhibitors.
  • Defining the hereditary status: There are evidence showing that presence of MSI-H is predictive of LS and supporting a germline assessment for HNPCC, with cascade testing of at-risk relatives, given clinical implications for increased cancer surveillance and potential risk-reducing surgeries in addition to the option of administering Aspirin, which has proven to reduce the CRC cancer burden by approximately 50%.

At present, many frameshift peptides vaccines have been artificially synthesized and successfully applied in basic research and clinical therapy. It could have a great significance for preventing and treating malignancies.


In conclusion, the identification of MSI-H as a biomarker for response to immune checkpoint blockade represents a breakthrough in the treatment of individuals with advanced solid tumours.

Identification of MSI CRC is important, as MSI may serve as a screening tool for detecting LS, a prognostic marker for patient outcome, and a predictive marker for response to chemotherapy and to immunotherapy. Based on the evidence available, all CRC tumors should be systematically tested for MSI either by Immunohistochemistry or PCR-based methods.


  • De' Angelis, Gian Luigi et al. "Microsatellite instability in colorectal cancer." Acta bio-medica : Atenei Parmensis vol. 89,9-S 97-101. 17 Dec. 2018, doi:10.23750/abm.v89i9-S.7960
  • Hause, Ronald J et al. "Classification and characterization of microsatellite instability across 18 cancer types." Nature medicine vol. 22,11 (2016): 1342-1350. doi:10.1038/nm.4191
  • Yang, Guang et al. "Correlations between microsatellite instability and the biological behaviour of tumours." Journal of cancer research and clinical oncology vol. 145,12 (2019): 2891-2899. doi:10.1007/s00432-019-03053-4
  • Latham, Alicia et al. "Microsatellite Instability Is Associated With the Presence of Lynch Syndrome Pan-Cancer." Journal of clinical oncology: official journal of the American Society of Clinical Oncology vol. 37,4 (2019): 286-295. doi:10.1200/JCO.18.00283
  • Engel, Christoph et al. "Associations of Pathogenic Variants in MLH1, MSH2, and MSH6 With Risk of Colorectal Adenomas and Tumors and With Somatic Mutations in Patients With Lynch Syndrome." Gastroenterology vol. 158,5 (2020): 1326-1333. doi:10.1053/j.gastro.2019.12.032
  • Ahadova, Aysel et al. "Three molecular pathways model colorectal carcinogenesis in Lynch syndrome." International journal of cancer vol. 143,1 (2018): 139-150. doi:10.1002/ijc.31300
  • Seppälä, Toni T et al. "Prospective observational data informs understanding and future management of Lynch syndrome: insights from the Prospective Lynch Syndrome Database (PLSD)." Familial cancer, 10.1007/s10689-020-00193-2. 8 Jun. 2020, doi:10.1007/s10689-020-00193-2
  • Burn, John et al. "Long-term effect of aspirin on cancer risk in carriers of hereditary colorectal cancer: an analysis from the CAPP2 randomised controlled trial." Lancet (London, England) vol. 378,9809 (2011): 2081-7. doi:10.1016/S0140-6736(11)61049-0
  • The Role of Epigenetic Factors for Preventing Colorectal Cancer - interview with Sir John Burn
  • Insights from the Prospective Lynch Syndrome Database: an Introduction by Dr Toni Seppälä
ESCP Affiliates