Multiomic Characterization and Molecular Profiling of Nuclear Protein in Testis Carcinoma

Abstract

Purpose: Nuclear protein in testis carcinoma (NC) is an underdiagnosed and aggressive squamous/poorly differentiated cancer characterized by rearrangement of the gene NUTM1 on chromosome 15q14. Co-occurring alternations have not been fully characterized.

Methods: We analyzed the genomic and immune landscape of 54 cases of NC that underwent DNA- and RNA-based NGS sequencing (Caris).

Results: While NC is driven by NUTM1 fusion oncoproteins, co-occurring DNA mutations in epigenetic or cell cycle pathways were observed in 26% of cases. There was no significant difference between the fusion partner of NUTM1 and co-occurring gene mutations. RNA sequencing analysis showed increased MYC pathway activity in NC compared with head and neck squamous cell carcinoma (HNSCC) and lung squamous cell carcinoma (LUSC), which is consistent with the known pathophysiology of NC. Characterization of the NC tumor microenvironment using RNA sequencing revealed significantly lower immune cell infiltration compared with HNSCC and LUSC. NC was 10× higher in patients with HNSCC and LUSC younger than 50 years than in those older than 70 years.

Conclusion: To our knowledge, this is the first series of NC profiled broadly at the DNA and RNA level. We observed fewer intratumoral immune cells by RNA sequencing, which may be associated with anecdotal data of lack of immunotherapy benefit in NC. High MYC pathway activity in NC supports ongoing trials targeting MYC suppression. The incidence of NC among patients younger than 50 years with LUSC/HNSCC supports testing for NC in these patients. The prognosis of NCs remains dismal, and future studies should focus on improving the response to immunotherapy and targeting MYC.

FIG 1.

Detected NUTM1 fusions involving BRD4, BRD3, and NSD3 (WHSC1L1). The genes are illustrated at the genomic and protein transcript level with depiction of the various fusion products, including pertinent subdomains. Red boxes correspond to breakpoints. Asterisks represent the most frequently identified fusions per partner gene. aa, amino acid; ex, exon.

FIG 2.

Oncoprint diagram with baseline characteristics and genomic coalterations, categorized by NUTM1 fusion partner. DDR, DNA damage response; IHC, immunohistochemistry; mut/Mb, mutation/megabase; TMB, tumor mutational burden.

FIG 3.

RNA expression of the NC cohort. (A) Differences in inferred immune cell populations in individual tumor samples by RNA sequencing in NC compared with HNSCC (nonNC) and LUSC (nonNC). Cell fraction represents % of all immune cells. (B) Differences in inferred immune cell populations in NC on the basis of primary tumor sites. (C) Fold change of immune-related genes in NC relative to HNSCC (non-NC) and LUSC (non-NC), with significance shown on each bar. HN, head and neck; HNSCC, head and neck squamous cell carcinoma; LUSC, lung squamous cell carcinoma; NC, nuclear protein in testis carcinoma. *P < .05; **P < .0001.

FIG 4.

OS in chemotherapy-treated versus no chemotherapy–treated NC. NC, nuclear protein in testis carcinoma; OS, overall survival.

FIG 5.

Rate of NC among squamous cell carcinomas of lungs and head and neck by age in those profiled by Caris. HN, head and neck; NC, nuclear protein in testis carcinoma; SCC, squamous cell cancer.

FIG A1.

Pathway analysis comparing NC versus HNSCC (non-NC) versus LUSC (non-NC) sorted by NUT versus LUSC (non-NC). Shading represents the normalized enrichment score from GSEA between the cohorts, whereas pathways that are statistically significant are marked with asterisks. GSEA, Gene Set Enrichment Analysis; HNSCC, head and neck squamous cell carcinoma; LUSC, lung squamous cell carcinoma; NC, nuclear protein in testis carcinoma; NUT, nuclear protein in testis.

FIG A2.

Gene Set Enrichment Analysis results of NC with primary lung versus primary head and neck cancer. (A) Bar plot showing the distribution of the normalized enrichment score between cohorts. (B) GSEA plot of MYC target V2 between cohorts. (C). Distribution of gene expression levels between cohorts. Shading represents the normalized enrichment score from GSEA between cohorts, whereas the P value represents the significance of enrichment. GSEA, Gene Set Enrichment Analysis; HN, head and neck; NC, nuclear protein in testis carcinoma; NES, normalized enrichment score; TPM, transcripts per million.

FIG A3.

OS in chemo-treated versus chemo-IO–treated NC. chemo-IO, chemoimmunotherapy; Inf, infinite; NC, nuclear protein in testis carcinoma; OS, overall survival.

FIG A4.

OS compared among different NUTM1 partners from biopsy to last contact. NR, survival not reached; OS, overall survival.

FIG A5.

Incidence rate calculation for NUT carcinoma. HN, head and neck; NC, nuclear protein in testis carcinoma; NUT, nuclear protein in testis; SC, squamous cell; SCC, squamous cell cancer. ^aCaris has no pediatric practice contracts. ^bApproximately 33% of NC is observed in patients older than 40 years, and approximately 40% of NC is squamous per Luo the study by et al.