Comprehensive molecular characterization of brain metastases (BM) from colorectal cancer (CRC)


Francesca Battaglin, Joanne Xiu, Yasmine Baca, Richard M. Goldberg, Axel Grothey, Anthony F. Shields, Andreas Seeber, Mohamed E. Salem, Alberto Puccini, Ryuma Tokunaga, Madiha Naseem, Hiroyuki Arai, Jingyuan Wang, Martin D. Berger, Wu Zhang, Philip A. Philip, John L. Marshall, W. Michael Korn and Heinz-Josef Lenz


  • Development of brain metastases (BM) is a leading cause of morbidity and mortality among cancer patients with advanced disease, and prognosis remains poor despite multimodal treatments and advances in systemic therapies, including immunotherapy and targeted agents.
  • The incidence of BM in patients with CRC is estimated to range from 0.6 to 3.2% and more frequently associated with young age, a rectal primary and presence of lung metastases. 1,2 Although relatively rare, the incidence of BM is increasing due to the improvement in metastatic CRC treatment and longer patients’ survival. BM are associated with an extremely poor prognosis with median survival times reported between
    3-6 months.
  • Recent advances in genomic analyses have revealed abnormalities in several genes, including KRAS, BRAF, PIK3CA and NRAS, which may play a role in the metastatic patterns of CRC. While there is no evidence to suggest the presence of a specific mechanism linking RAS mutations to the development of BM, recent studies show that RAS-mutant mCRCs exhibit a significantly higher cumulative incidence of lung, bone, and brain metastasis (with higher prevalence of KRAS G12D in BM).3-5 HER2 amplification, a well-known driver of oncogenesis associated with an increased risk of BM in breast cancer, is also currently emerging as a relatively frequent alteration in BM from CRC. 6,7
  • Overall, available evidence calls for a more extensive characterization of the molecular profile and driver mutations of CRC-derived BM to enhance our understanding of BM susceptibility and to identify novel therapeutic targets for CRC patients with BM. Hence, we designed our study evaluating the results from an extensive NGS panel in a large cohort of BM from CRC patients and a comparison between the molecular characteristics of BM, primary tumor (PT) samples and other distant metastases (OM).


  • NGS was performed on genomic DNA isolated from FFPE tumor samples using the NextSeq (592-genes) or TruSeq platform (45-gene) (Illumina, Inc., San Diego, CA). All variants were detected with > 99% confidence based on allele frequency and amplicon coverage, with an average sequencing depth of coverage > 500 and an analytic sensitivity of 5%.
  • Microsatellite instability (MSI) was evaluated based on the number of microsatellite loci that were altered by somatic insertion or deletion counted for each sample. The threshold to determine MSI by NGS was determined to be 46 or more loci with insertions or deletions to generate a sensitivity > 95% and a specificity > 99%.
  • Tumor mutational burden (TMB) was estimated by counting all nonsynonymous missense mutations found per tumor that had not been previously described as germline alterations (TMB-high ≥ 17 mt/MB).
  • IHC was performed on FFPE sections of glass slides. PD-L1 testing was performed using the SP142 anti-PD-L1 clone (Ventana, Tucson, AZ).
  • Chi-square and t-tests were used for comparative analyses

Download Publication