Distribution of microsatellite instability (MSI), tumor mutational load (TML) and PD-L1 status in molecularly profiled invasive breast cancer


Elias Obeid, Angela Ellerbrock, Elizabeth Handorf, Lori Goldstein, Zoran Gatalica, Sandra M. Swain, Claudine Isaacs, Jeff Vacirca, David Arguello, Antoinette Tan, Lee Schwartzberg


  • Recent data indicate a promising response to immune check point blockade (ICB) in patients with breast cancer (BC).
  • Pembrolizumab, a monoclonal antibody against programmed death 1 (PD-1) receptor and one of several ICB agents in development, received FDA approval for all MSI (microsatellite instability)-high solid tumors.
  • MSI incidence in breast cancer is not fully elucidated. Other biomarkers being explored in possible relationship to ICB activity include PD-1 ligand (PD-L1) status and tumor mutational load (TML).
  • In this study, we aimed to explore the incidence of these biomarkers in invasive breast cancers.


  • A retrospective data analysis of breast cancer patients profiled by commercial next-generation sequencing (NGS) at Caris Life Sciences was performed.
  • MSI was calculated by comparing repeat-insertions or deletions across over 7,000 microsatellite sequences in the patient sample to the hg19 reference genome.
  • Samples with repeat variances in more than 45 microsatellites were classified as MSI-High.
  • PD-L1 expression was evaluated using immunohistochemical analysis (IHC), with clone SP-142 (Roche Diagnostics). A sample was considered positive (PD-L1+) if there was >5% membranous staining of tumor cells.
  • TML (tumor mutation load) was calculated as a total number of non-synonymous somatic mutations identified per megabase of genome coding area with high being greater than or equal to 17.


  • A total of 9,627 BC cases were queried from Caris Life Sciences database.
  • 5,202 tested for PD-L1 status (354 PD-L1+, 6.8%, CI 6.2-7.5%).
  • Of all queried cases, 1,952 tumors were tested for all three biomarkers of interest in ICB: PD-L1, MSI status, and TML: Details are presented next.


  • PD-L1-positivity, MSI-H, or TML-H was present in 189 cases (9.7%). At least one of the three aforementioned biomarker results was present in 7.3% of ER/PR+ cases, 10% of HER2+ , and 13% of TNBC . The majority of this was PD-L1+ and TML-H (6.1% and 3.7%), while low MSI-H distribution (0.6%).
  • We observed statistically significant differences in PD-L1 and TML distributions based on molecular subtype, specimen site, distant metastatic site, and age. This was not observed with MSI.
  • No differences in distribution were observed based on AR status in TNBC cases.
  • PD-L1 distribution was higher in TNBC cases, while TML was higher in ER/PR+ cases. • TML-H in lobular breast cancer (13.7%) was noted, warranting further research .
  • Future research is needed to show the clinical utility of these biomarkers in response to ICB and should be considered in designing prospective clinical trials.

Download Publication