CDKN2C-Null Leiomyosarcoma: A Novel, Genomically Distinct Class of TP53/RB1–Wild-Type Tumor With Frequent CIC Genomic Alterations and 1p/19q-Codeletion

Abstract

PURPOSE Leiomyosarcoma (LMS) harbors frequent mutations in TP53 and RB1 but few actionable genomic alterations. Here, we searched for recurrent actionable genomic alterations in LMS that occur in the absence of common untreatable oncogenic drivers. METHODS Tissues from 276,645 unique advanced cancers, including 2,570 uterine and soft tissue LMS, were sequenced by hybrid-capture–based next-generation DNA and RNA sequencing/comprehensive genomic profiling of up to 406 genes. We characterized clinicopathologic features of relevant patient cases. RESULTS Overall, 77 LMS exhibited homozygous copy loss of CDKN2C at chromosome 1p32.3 (3.0% of LMS). Genomic alterations (GAs) in TP53, RB1, and ATRX were rare compared with the remainder of the LMS cohort (11.7% v 73.4%, 0% v 54.5%, 2.6% v 24.5%, respectively; all P < .0001). CDKN2C-null LMS patient cases were significantly enriched for GAs in CIC (40.3% v 1.4%) at 19q13.2, CDKN2A (46.8% v 7.0%), and RAD51B (16.9% v 1.7%; all P < .0001). Chromosome arm-level aneuploidy analysis of available LMS patient cases (n = 1,284) found that 81% (58 of 72) of CDKN2C-null LMS exhibited 1p/19q-codeletion, a significant enrichment compared with 5.1% in the remainder of the LMS cohort ( P < .0001). In total, 99% of CDKN2C-null LMS were in women; the median age was 61 years at surgery (range, 36-81 years). Fifty-five patient cases were uterine primary, four were nonuterine, and the remaining 18 were of uncertain primary site. Sixty percent of cases showed at least focal epithelioid variant histology. Most patients had advanced-stage disease, with 62% of confirmed uterine primary LMS at International Federation of Gynecology and Obstetrics stage IVB. We further validated our findings in two publicly available datasets: The Cancer Genome Atlas and the Project GENIE initiative. CONCLUSION CDKN2C-null LMS defines a genomically distinct tumor that may have prognostic and/or therapeutic clinical implications, including possible use of specific cyclin-dependent kinase inhibitors.

Novel Driver Strength Index highlights important cancer genes in TCGA PanCanAtlas patients

“…CIC is located on 19q. Recently, 1p/19q co-deletion and CIC mutation have been discovered as characteristic features of CDKN2C-null leiomyosarcoma (62). NDSI shows that gains of 17p and 19p arms are the strongest cancer-promoting chromosome arm gains.…”

High-Level MYCN-Amplified RB1-Proficient Retinoblastoma Tumors Retain Distinct Molecular Signatures

“…CDKN2C repression has been reported in multiple cancers including melanoma, oesophageal squamous cell carcinoma and pituitary adenomas [28][29][30] . Furthermore, a recent genomic study in leiomyosarcoma-characterized by frequent RB1/TP53 mutations identified a distinct class featuring wild type TP53/RB1 and homozygous deletion of CDKN2C 31 .…”

A computational and structural analysis of germline and somatic variants affecting the DDR mechanism, and their impact on human diseases

“…Other studies found that 11.8% (82/692) of patients with mCRPC had at least one germline variant in a gene involved in DNA repair 9 . These and other mCRPC-based studies 8 – 14 highlighted BRCA2 as the most frequently involved, and also found that a high proportion of those patients presented a second “hit” somatic aberration in either of two forms: loss-of-function mutation or a gene-copy-loss 9 , 15 , 16 . The same authors suggested that only half of the patients could be detected by germline variants in DDR genes.…”