Comparative genomics of high grade neuroendocrine carcinoma of the cervix

Abstract

In order to improve treatment selection for high grade neuroendocrine carcinomas of the cervix (NECC), we performed a comparative genomic analysis between this rare tumor type and other cervical cancer types, as well as extra-cervical neuroendocrine small cell carcinomas of the lung and bladder. We performed whole exome sequencing on fresh-frozen tissue from 15 NECCs and matched normal tissue. We then identified mutations and copy number variants using standard analysis pipelines. Published mutation tables from cervical cancers and extra-cervical small cell carcinomas were used for comparative analysis. Descriptive statistical methods were used and a two-sided threshold of P < .05 was used for significance. In the NECC cohort, we detected a median of 1.7 somatic mutations per megabase (range 1.0-20.9). PIK3CA p.E545K mutations were the most frequency observed oncogenic mutation (4/15 tumors, 27%). Activating MAPK pathway mutations in KRAS (p.G12D) and GNAS (p.R201C) co-occurred in two tumors (13%). In total we identified PI3-kinase or MAPK pathway activating mutations in 67% of NECC. When compared to NECC, lung and bladder small cell carcinomas exhibited a statistically significant higher rate of coding mutations (P < .001 for lung; P = .001 for bladder). Mutation of TP53 was uncommon in NECC (13%) and was more frequent in both lung (103 of 110 tumors [94%], P < .001) and bladder (18 of 19 tumors [95%], P < .001) small cell carcinoma. These comparative genomics data suggest that NECC may be genetically more similar to common cervical cancer subtypes than to extra-cervical small cell neuroendocrine carcinomas of the lung and bladder. These results may have implications for the selection of cytotoxic and targeted therapy regimens for this rare disease.

Fig 1. Somatic mutational landscape of high grade neuroendocrine carcinoma of the cervix.

(A) NECC somatic mutation burden expressed as somatic mutations per Mb. Gray color indicates sample with no available matched normal tissue. (B) Genes in COSMIC Cancer Gene Census with recurrent (>1) non-silent somatic mutations. (C) Copy number alterations in PI3-kinase pathway members PIK3CA and PTEN, as well as BCL2L11 which was identified as recurrently deleted in NECC (q = .04). NECC = small cell neuroendocrine carcinoma of the cervix, Mb = megabase.

Fig 2. Gene-adjacent HPV integration events in high grade neuroendocrine carcinoma of the cervix.

(A) Fraction of genome altered by copy number alterations (.3 > log CN ratio > -.3) as a function of tumor ploidy. Red, HPV genome detected; Blue, HPV genome not detected. (B) The presence of HPV is associated with polyploid karyotype in NECC. *, p < .05. (C) Map of gene-adjacent HPV integration events identified in NECC. Yellow, HPV16; Purple, HPV18.

Fig 3. Comparison of somatic mutation rate among cervical carcinomas and extra-cervical small cell carcinomas of the lung and bladder.

(A) Coding mutation burden by tumor type. Statistical comparisons were performed between NECC and each other tumor type using a two-sided Wilcoxon rank-sum test. (B) Fraction of mutated samples by tumor type for frequently mutated genes. For each gene, statistical comparisons were performed between the mutation rate of NECC and each other tumor type using a two-sided Fisher’s exact test. ***, p < .001; **, p < .01; *, p < .05; n.s. = not significant. SNV = single nucleotide variant, indel = small insertion/deletion, SCCB = small cell carcinoma of the bladder, SCLC = small cell lung carcinoma, NECC = small cell neuroendocrine carcinoma of the cervix, SCC = squamous carcinoma of the cervix, ACC = endocervical adenocarcinoma.

Fig 4. Mutational signature contribution across tumor types.

(A) SNV mutational signature contribution by NECC sample. (B) Unsupervised hierarchical clustering of SNV mutational signature contributions by sample across tumor types. (C) Relative cluster membership of sample by tumor type. SNV = single nucleotide variant, SCCB = small cell carcinoma of the bladder, SCLC = small cell lung carcinoma, NECC = small cell neuroendocrine carcinoma of the cervix, SCC = squamous carcinoma of the cervix, ACC = endocervical adenocarcinoma.