Contributed by: Kyle Knickelbein, MD, PhD, and Tanner Freeman, MD, PhD
Clinical History
A young adult female patient presented to the hospital with a case of ruptured appendicitis and was managed non-operatively. A colonoscopy and appendectomy were recommended, but the patient was lost to follow-up. The patient later presented to the hospital complaining of abdominal pain. A CT scan of the abdomen and pelvis revealed cecal mucosal thickening and regional lymphadenopathy with concerns for an abscess. A colonoscopy was again recommended, but she was unable to complete the screening. A subsequent CT scan several months later demonstrated peri-enteric inflammatory stranding with continued lymphadenopathy.
The patient again presented to the hospital with complaints of severe abdominal pain and lightheadedness. She further reported a strong family history of colorectal cancer, notably in her father who was diagnosed in his fifties and in her paternal aunt. A CT scan demonstrated cecal distension with mucosal thickening. A colonoscopy was also performed which revealed deep cecal ulcerations, and a surgical resection was recommended and subsequently performed.
Final Surgical Pathology Report
The resection specimen demonstrated an invasive poorly-differentiated adenocarcinoma with spread to peri-colonic lymph nodes. Due to the patient’s family history in addition to presenting with colorectal cancer at a young age, additional testing for a work-up of suspected Lynch syndrome was warranted. Lynch syndrome is an inherited condition caused by a germline mutation in one of the key mismatch repair (MMR) genes which include MLH1, PMS2, MSH2, and MSH6. Their protein products dimerize, MLH1 to PMS2 and MSH2 to MSH6, and function to maintain genomic integrity. Their function ensures that mismatched bases, or insertions or deletions at microsatellite regions, during the process of DNA replication are repaired. Germline mutations within one allele of one of the MMR proteins in non-tumor tissue are diagnostic of Lynch syndrome. These mutations lead to microsatellite instability when a somatic, or second-hit, mutation is acquired. To assess the status of these proteins, immunohistochemical stains were used to visualize the pattern of expression in the patient’s primary tumor (Figures 1 and 2).
Molecular Testing Results
Molecular testing was performed on the patient’s primary tumor utilizing the Oncomine Pan-Cancer Mutation Panel next-generation sequencing assay. The results reveal several pathogenic variants in KRAS, PIK3CA, CREBBP, and two within MSH2. The MSH2 variants demonstrated one at 49.9% variant allele frequency, suggestive of a germline origin, and a second mutation at 35.6% variant allele frequency, suggestive of a somatic alteration.
Tumor mutational burden (TMB) and microsatellite instability (MSI) are two clinical biomarkers that are also assessed in the Oncomine panel. TMB is calculated bioinformatically and is defined as the number of somatic mutations per megabase of genomic DNA, and it serves as a predictive marker to immunotherapy regimens. The TMB is calculated as 45 mutations per megabase (Mut/Mb) and ranks at a high percentile (82) when compared to the Memorial Sloan Kettering Cancer Center (MSKCC) dataset. MSI is analyzed by PCR-based testing that interrogates specific microsatellite markers that contain one, two, or four nucleotide repeat sequences. For the mono-nucleotide markers, the size of the PCR products should be normally distributed and fall within a narrow, pre-set range. One of the mono-nucleotide markers analyzed, BAT40, shows a non-normal distribution of the PCR products with several amplified products at sizes below the pre-set range (Figure 3). All interrogated markers demonstrated a pattern compatible with MSI; thus, the tumor is denoted as MSI-High.
