KMT2D/MLL2 inactivation is associated with recurrence in adult-type granulosa cell tumors of the ovary

Abstract

Adult-type granulosa cell tumors of the ovary (aGCTs) are rare gynecologic malignancies that exhibit a high frequency of somatic FOXL2 c.C402G (p.Cys134Trp) mutation. Treatment of relapsed aGCT remains a significant clinical challenge. Here we show, using whole-exome and cancer gene panel sequencing of 79 aGCTs from two independent cohorts, that truncating mutation of the histone lysine methyltransferase gene KMT2D (also known as MLL2) is a recurrent somatic event in aGCT. Mono-allelic KMT2D-truncating mutations are more frequent in recurrent (10/44, 23%) compared with primary (1/35, 3%) aGCTs (p = 0.02, two-sided Fisher's exact test). IHC detects additional non-KMT2D-mutated aGCTs with loss of nuclear KMT2D expression, suggesting that non-genetic KMT2D inactivation may occur in this tumor type. These findings identify KMT2D inactivation as a novel driver event in aGCTs and suggest that mutation of this gene may increase the risk of disease recurrence.

Fig. 1

Mutational landscape of primary and recurrent aGCTs. a Somatic mutation rate per megabase (Mb) for primary (n = 8) and recurrent (n = 16) aGCTs. Gray bars indicate samples with no matched normal tissue, for which the mutation rate may be inflated by the inclusion of rare SNPs. b Time in years between diagnosis, first recurrence (blue arrow), and sample collection (red circle). The receipt of cytotoxic chemotherapy at any time between diagnosis and sample collection is indicated by an orange box. c Significantly mutated genes in aGCT. d Significantly recurrent focal CNVs. e Recurrent arm-level CNVs. Heat map indicates log CN ratio for CNV event. Mb: megabases, CN: copy number

Fig. 2

Truncating KMT2D mutations are associated with aGCT recurrence. a Overview of all somatic KMT2D mutations (non-synonymous SNVs + indels) detected in the combined cohorts. A frameshift indel detected in the KGN cell line is also indicated. b Rate of truncating KMT2D mutations identified in exploratory cryopreserved tissue cohort (n = 24) and validation FFPE tissue cohort (n = 55). P value from two-sided Fisher’s exact test. WES: whole-exome sequencing, FFPE: formalin-fixed paraffin-embedded

Fig. 3

Nuclear KMT2D expression in primary and recurrent aGCTs. a Representative stained sections from tumors with positive (GCT004) and negative (GCT017) nuclear KMT2D expression. Scale bar = 200 μm. b Density plot of per nucleus mean KMT2D staining by KMT2D mutation status. Plots were derived from measurements made from individual nuclei in KMT2D wt/trunc (n = 1,964,133 nuclei) and KMT2D wt/wt (n = 12,121,768) tumors. Dotted line indicates numerical cutoff to distinguish “negative” from “positive” nuclei (see Methods). c Relationship between mono-allelic KMT2D-truncating mutation and loss of KMT2D protein expression by tumor type. fs: frameshift mutation, trunc: truncating mutation (any class)