Genetic Analysis of Biopsy Tissues from Colorectal Tumors in Patients with Ulcerative Colitis

Abstract

Background/objectives: Colorectal neoplasia developing from ulcerative colitis mucosa (CRNUC) can be divided into ulcerative colitis-associated neoplasia (UCAN) and non-UCAN; however, it is often difficult to distinguish UCAN from non-UCAN during a biopsy diagnosis. We investigated whether a genomic analysis could improve the diagnostic accuracy of UCAN using biopsy specimens.

Methods: In step 1, 14 CRNUCs were used to examine whether the genomic landscape of biopsy and resection specimens matched. In step 2, we investigated the relationship between the genomic landscapes and the pathological diagnosis of 26 CRNUCs. The cancer genome was analyzed by deep sequencing using a custom panel of 27 genes found to be mutated in our previous CRNUC analysis.

Results: In step 1, of the 27 candidate genes, 14 were mutated. The concordance rate of the pathogenic mutations in these 14 genes between the biopsy and resection specimens was 29% (4/14), while that of the pathogenic mutations in TP53 and KRAS was 79% (11/14). In step 2, the pathological diagnosis of biopsy specimens using only hematoxylin and eosin (HE) staining had a sensitivity of 33% and an accuracy of 38% for UCAN diagnosis. On the other hand, the combination of the HE pathology and p53 immunohistochemical staining had a sensitivity of 73% and an accuracy of 85% for UCAN diagnosis, while the combination of HE staining and a TP53 mutation had a sensitivity of 87% and an accuracy of 88% for UCAN diagnosis.

Conclusions: An evaluation of TP53 mutations in biopsy specimens may be useful for diagnosing UCAN. However, further studies with larger sample sizes are required before this can be applied in clinical practice.

Keywords: TP53 mutation; biopsy; sporadic neoplasia; ulcerative colitis; ulcerative colitis-associated neoplasia.

Figure 1

Flow chart of enrolled lesions. In step 1, preoperative biopsy specimens were used from resected specimens of colorectal neoplasia developing from ulcerative colitis of mucosa (CRNUC) that were previously identified through endoscopic or surgical resection, and whose genomic landscape was determined in earlier research. In step 2, preoperative biopsy specimens, different from those used in step 1 and obtained through endoscopic or surgical resection, were utilized as independent samples.

Figure 2

The genomic landscapes of the resected and biopsy specimens of the 14 CRNUC cases in step 1. The panel contains the mutation patterns of 14 genes from the 14 CRNUCs in step 1. The pink, yellow, orange, green, and black cells indicate nonsense mutations, splice site mutations, frameshift insertions/deletions, missense mutations, and multiple hits, respectively. The upward triangles represent mutations in the resection specimens. The downward triangles represent mutations in the biopsy specimens. The cells framed by red rectangles indicate that the mutation sites match in the resected and biopsy specimens. In total, 29% (4/14) of the CRNUC cases had the same mutation status for all the detected genes in the resected and biopsy specimens. Furthermore, 79% (11/14) of the CRNUC cases had the same mutation status for TP53 and KRAS in the resected and biopsy specimens. CRNUC, colorectal neoplasia developing from ulcerative colitis mucosa.

Figure 3

The pathological diagnosis and genomic landscapes of the 26 CRNUC cases in Step 2. (Upper panel) The p53 staining status of the biopsy or resected specimens. The red and gray cells indicate strongly positive and weakly positive/negative p53 staining status, respectively. (Middle panel) The pathological diagnosis of the biopsy and resected specimens. The pathological diagnosis of the biopsy specimens in this figure refers to the pathological diagnosis by hematoxylin and eosin (HE) staining only, and the pathological diagnosis of the resection specimens refers to the pathological diagnosis by HE staining with a p53 and Ki67 immunostaining assessment. The brown and light-blue cells indicate a UCAN and non-UCAN diagnosis, respectively. The asterisks in the cells indicate CRNUCs with serrated changes. (Lower panel) The mutation patterns of 12 genes from the 26 CRNUCs in step 2. The pink, yellow, orange, green, and black cells indicate nonsense mutations, splice site mutations, frameshift insertions/deletions, missense mutations, and multiple hits, respectively. The bar graph on the right shows the frequency of mutations in each gene. CRNUC, colorectal neoplasia developing from ulcerative colitis mucosa; UCAN, ulcerative colitis-associated neoplasia.