Tumor analysis of MMR genes in Lynch-like syndrome: Challenges associated with results interpretation

Abstract

Background: Up to 70% of suspected Lynch syndrome patients harboring MMR deficient tumors lack identifiable germline pathogenic variants in MMR genes, being referred to as Lynch-like syndrome (LLS). Previous studies have reported biallelic somatic MMR inactivation in a variable range of LLS-associated tumors. Moreover, translating tumor testing results into patient management remains controversial. Our aim is to assess the challenges associated with the implementation of tumoral MMR gene testing in routine workflows.

Methods: Here, we present the clinical characterization of 229 LLS patients. MMR gene testing was performed in 39 available tumors, and results were analyzed using two variant allele frequency (VAF) thresholds (≥5% and ≥10%).

Results and discussion: More biallelic somatic events were identified at VAF ≥ 5% than ≥10% (35.9% vs. 25.6%), although the rate of nonconcordant results regarding immunohistochemical pattern increased (30.8% vs. 20.5%). Interpretation difficulties question the current utility of the identification of MMR somatic hits in the diagnostic algorithm of suspected LS cases.

Keywords: Lynch syndrome; Lynch‐like syndrome; clinical management; mismatch repair genes; mismatch repair‐deficiency; tumor testing.

FIGURE 1

Summary of results from tumor analyses in the somatic testing cohort. (A) Pie charts displaying the interpretation of somatic testing results according to immunohistochemical staining of tumors of 39 LLS individuals using two different VAF thresholds: ≥5% and ≥10%. (B) Sankey diagram showing the divergences in the interpretation of somatic testing results in 39 LLS individuals using two different VAF thresholds. Scaled arcs are used to display flows in the interpretation from VAF ≥5% scenario to VAF ≥10% scenario. (C) Scatter plot displaying somatic MMR hits identified in 39 LLS individuals. Cases are represented in the Y axis, VAFs are indicated in the X axis, and MMR hits concordant with immunohistochemical staining of tumors are plotted as blue dots. Two vertical discontinuous lines delimitate MMR hits identified at VAFs ranging from 5% to 10%, in order to highlight somatic MMR hits lost when raising the VAF threshold from ≥5% to ≥10%. LLS, Lynch‐like syndrome; VAF, variant allele frequency.

FIGURE 2

Details from a Lynch syndrome patient identified through tumor testing (Case 198). (A) Pedigree from Case 198. A black arrowhead is used to indicate the proband, and a red plus symbol to display carrier status of MLH1 c.113A > G pathogenic variant. A quarter of an individual's symbol shadowed represents individuals diagnosed with cancer. The current age of each individual is displayed below their symbol, followed by their cancer type and age of onset. (B) Immunohistochemistry screening of mismatch repair genes MLH1, MSH2, MSH6 and PMS2. Results indicate loss of PMS2 expression. (C) Blood testing by Sanger sequencing in patient 198 confirms the presence of MLH1 c.113A > G as a constitutional variant previously missed. CRC, colorectal cancer; IHC, immunohistochemistry; MSI+, microsatellite instability positive (high); NEG, negative IHC pattern (loss of expression).