Discordant dMMR/IHC Status Correlates With Improved Treatment Outcomes in CRC and Endometrial Cancer


Patients with mismatch repair–deficient, immunohistochemistry-intact colorectal cancer or endometrial cancer benefit from immune checkpoint inhibitors.

Elias J. Bou Farhat, MD

Elias J. Bou Farhat, MD

Patients with mismatch repair–deficient (dMMR), immunohistochemistry (IHC)–intact colorectal cancer (CRC) or endometrial cancer achieved survival benefits when treated with immune checkpoint inhibitors vs those with mismatch repair–proficient (pMMR), IHC-intact disease, according to findings from a retrospective analysis comparing next-generation sequencing (NGS) and IHC MRR results published in Cancer Cell.1

Notably, patients with discordant NGS and IHC results, defined as NGS dMMR/IHC-intact (NGSd/IHC+) who received immune checkpoint inhibitors experienced significantly longer median overall survival (OS) and time to treatment failure (TTF) compared with patients with concordant NGS pMMR/IHC-intact (NGSp/IHC+) results. The median OS was not reached (NR; 95% CI, 10 months–NR) vs 14.9 months (95% CI, 7.3-25) in the NGSd/IHC+ and NGSp/IHC+ groups, respectively (P = .003). The median TTF in these respective groups was 44.4 months (95% CI, 10-NR) and 5.0 months (95% CI, 3.2-7.3; P = .001).

The most common dMMR cancer types are CRC and endometrial cancer. The National Comprehensive Cancer Network recommends universal MMR testing by IHC for all newly diagnosed patients with CRC, regardless of stage.2 Furthermore, several global treatment guidelines recommend IHC as the preferred MMR testing method for patients with CRC or endometrial cancer.1

Previously, a study assessing microsatellite instability (MSI) and MMR status by IHC in 38 patients with metastatic CRC (mCRC) enrolled in trials investigating immune checkpoint inhibitors found that misdiagnoses of MSI or MMR status by IHC caused 3 out of 5 cases of primary resistance to immune checkpoint inhibitors.3

“Accurate assessment of MMR status is critical for treatment decision making, as a false negative can erroneously limit immune checkpoint inhibitor use, reducing clinical benefit,” lead study author Elias J. Bou Farhat, MD, a postdoctoral research fellow at Brigham and Women’s Hospital in Boston, Massachusetts, and coauthors, wrote in the paper.1 “In turn, a false positive result will drive immune checkpoint inhibitor use in microsatellite-stable tumors where a lack of benefit has been demonstrated, while other therapeutic strategies may have greater efficacy.”

Bou Farhat and coinvestigators noted that NGS is capable of high-throughput genotyping of several genomic regions and can thus detect DNA replication errors caused by dMMR. Conversely, IHC genotypes are based on the tumor epitope, which may result in differing germline or somatic missense mutations in MMR genes that may express nonfunctioning MMR proteins with preserved antibody-binding capacity. IHC sensitivity may also decrease with ambiguous subclonal staining interpretation. Thus, investigators hypothesized that tumor-only NGS not paired with normal sequencing may be more sensitive than MMR IHC testing, which could improve decision making regarding immune checkpoint inhibitors.

This study used a clinically validated, standardized, tumor-only NGS mutation signature pipeline at Dana-Farber Cancer Institute in Boston to compare MMR determination by NGS vs IHC. Investigators also evaluated a subset of patients who received immune checkpoint inhibitors to determine the clinical implications of this study’s findings.

Investigators performed IHC and NGS on the same 1655 tumor specimens, which were taken from patients with CRC or endometrial cancer who had both tumor-only NGS by Oncopanel and MMR IHC. An NGS-based mutation signature classified tumors as NGS dMMR or pMMR. NGS dMMR tumor samples were defined as those having more than 1 single nucleotide deletion or insertion adjacent to a homopolymer site of at least 2 mononucleotide repeats. NGS pMMR tumor samples were defined as those that did not meet these criteria. Investigators also classified tumor samples as IHC absent or intact per standard clinical scoring criteria.

When MMR status was determined independently via NGS and IHC, patients were stratified into 3 categories:

  • Discordant NGS dMMR/IHC-intact (NGSd/IHC+)
  • Concordant NGS pMMR/IHC-intact (NGSp/IHC+)
  • Concordant NGS dMMR/IHC-absent (NGSd/IHC)

Furthermore, the NGS MMR mutation signature determined an additional 1% of patients with dMMR CRC and 5.9% of those with dMMR endometrial cancer that had been deemed MMR intact per IHC.

The incidence of NGSd/IHC+ results was similar across different racial populations with CRC at approximately 1%. After accounting for tumor type and prior lines of therapy, patients with NGSd/IHC+ mCRC and/or metastatic endometrial cancer who received immune checkpoint inhibitor­–based regimens had similar OS and TTF outcomes vs those with NGSd/IHC results.

When treatment outcomes were stratified by cancer type, patients with CRC achieved similar OS and TTF results as those in the entire study population. Although the numbers in the NGSd/IHC+ endometrial cancer population were too small to detect a difference between outcomes in the overall study population, investigators observed similar trends in this cohort.

Furthermore, a subgroup analysis of patients with NGSd/IHC+ results—regardless of systemic therapy—demonstrated that patients with NGSd/IHC+ CRC or endometrial cancer who received immune checkpoint inhibitor–based regimens achieved longer survival outcomes than those who were immune checkpoint inhibitor–naive and received other systemic treatment options.

“Even if MMR discordance is low between NGS and IHC, using an NGS mutation signature approach that is more sensitive could qualify many more patients for life-extending immunotherapy,” the authors emphasized. In 2022, 65,950 new cases of endometrial cancer and 151,030 new cases of CRC were diagnosed. Using the NGS mutational signature to complement IHC results would aid in the diagnosis of approximately 3891 additional patients with dMMR endometrial cancer cases and 1510 additional patients with dMMR CRC each year.

“NGS mutation signature serves as a backstop to identify these false negatives who are eligible for first-line immune checkpoint inhibitor therapy,” the authors explained.

Investigators also noted that these study findings support guideline recommendation revisions for MMR diagnostic testing per IHC that incorporate MMR testing via targeted NGS tumor panels that use sensitive and specific mutation-signature–calling algorithms. Moreover, since NGS is more commonly used in routine clinical care than IHC, NGS MMR testing should be shifted earlier in the diagnostic pipeline to detect false negative dMMR cases per IHC. This shift may shorten testing turnaround times and improve clinical decision making for patients with cancers for which immune checkpoint inhibitors continue to gain regulatory approval in earlier-stage settings.

Bou Farhat and colleagues concluded that these findings warrant further investigation and confirmation in larger prospective studies of patients with metastatic endometrial cancer and mCRC who have received treatment with immune checkpoint inhibitors, as well as in patients with other tumor types. They added that further study implementing deep-learning approaches is also needed.


  1. Bou Farhat E, Adib E, Daou M, et al. Benchmarking mismatch repair testing for patients with cancer receiving immunotherapy. Cancer Cell. 2024;42(1):6-7. doi:10.1016/j.ccell.2023.12.001
  2. Ajani JA, D’Amico TA, Bentrem DJ, et al. Gastric cancer, version 2.2022, NCCN Clinical Practice Guidelines in Oncology. J Natl Compr Canc Netw. 2022;20(2):167-192. doi:10.6004/jnccn.2022.0008
  3. Cohen R, Hain E, Buhard O, et al. Association of primary resistance to immune checkpoint inhibitors in metastatic colorectal cancer with misdiagnosis of microsatellite instability or mismatch repair deficiency status. JAMA Oncol. 2019;5(4):551-555. doi:10.1001/jamaoncol.2018.4942
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