Presence of Pathogenic Variants Provide Rationale for Germline Sequencing in Pediatric Rhabdomyosarcoma

Pathogenic germline variants identified among children and young adults with rhabdomyosarcoma (RMS) suggest that all children with RMS should undergo germline sequencing to utilize available surveillance guidelines and inform potential gene-specific therapy options, according to findings from an analysis of 2 study cohorts published in JCO Precision Oncology.

Specifically, 7.7% of patients in the discovery cohort (n = 273) and 6.6% of patients in the secondary cohort (n = 121) with RMS were found to harbor pathogenic or likely pathogenic (P/LP) germline variants within dominant-acting cancer susceptibility genes (CSG).

Moreover, among patients with alveolar RMS who were FOXO1 fusion negative, 15.5% and 12.5% of patients in the discovery (n = 18) and secondary (n = 5) cohorts, respectively, had P/LP variants. When stratified to evaluate dominant-acting CSG, the frequency of P/LP was 9.8% and 8.3%, respectively.

“Children with RMS should have germline sequencing. Those who have a germline P/LP variant in a CSG should have genetic counseling and cascade testing for other family members, especially for [the American College of Medical Genetics and Genomics] Secondary Findings genes and/or those with gene-specific surveillance guidelines,” wrote lead study author Jung Kim, PhD, a staff scientist at the National Cancer Institute, and co-investigators.

RMS is the most common soft-tissue sarcoma subtype among pediatric patients and accounts for about 3% of all pediatric cancers. The World Health Organization classification categorizes RMS into 4 subcategories: alveolar, embryonal, pleomorphic, and sclerosing/spindle cell. Each subgroup confers a different presentation and is commonly driven by various genetic mutations.

Currently, a multidisciplinary approach to treatment, including surgery, radiation therapy, and chemotherapy, is used for patients with RMS irrespective of risk group. Patients who are in remission can develop long-term morbidities, including treatment-related secondary malignancies.

Around 10% to 12% of children with cancer will harbor a pathogenic germline variant. RMS is associated with hereditary cancer disorders, such as Li-Fraumeni, Lynch, neurofibromatosis type 1, Noonan, Costello, DICER1, and Beckwith-Wiedemann syndromes. Additionally, NRAS, KRAS, HRAS, FGFR4, PIK3CA, CTNNB1, FBXW7, BCOR, and MYOD1 mutations are associated with RMS.

Given these disease characteristics, investigators sought to determine the prevalence of P/LP variants in known CSG within younger patients with RMS.

In the discovery cohort, DNA samples were collected from patients with intermediate-risk RMS who were enrolled on the phase 3 ARST0531 trial. In the secondary cohort, DNA samples were collected from the Cooperative Human Tissue Network (n = 31), Children’s Oncology Group (n = 69), Children’s Hospital at Westmead (n = 19), and the 10-C-0086 clinical trial (n = 2).

Overall, the majority of patients had embryonal (n = 192) or alveolar (n = 161) histology followed by mixed alveolar/embryonal (n = 6), embryonal/botryoid (n = 1), botryoid (n = 13), embryonal ectomesenchymoma (n = 1), spindle cell (n = 3), other (n = 12), and unknown (n = 5).

In both cohorts, the majority of patients were male (discovery, 53.5%; secondary, 53.7%), were White (discovery, 74.0%; secondary; 66.1%), and had a median age at the time of enrollment of approximately 7.5 years (discovery, 7.5; secondary, 7.6)

The majority of patients with alveolar RMS harbored a FOXO1 fusion (discovery, 55.4%; secondary, 67.3%).

Additionally, the majority of patients in the discovery cohort had intermediate-risk RMS (n = 256; 93.8%), whereas the majority of patients in the secondary cohort had unknown risk (n = 52; 43.0%). In the secondary cohort, 14 patients (11.6%) had low-risk disease, 32 patients (26.4%) had intermediate-risk disease, and 23 patients (19.0%) had high-risk disease.

The analysis by exome and genome sequencing focused on 130 CSG with various modes of inheritance, including autosomal dominant (n = 76), autosomal recessive (n = 28), both autosomal dominant and recessive (n = 16), X-linked (n = 5), Y-linked (n = 1), and unknown (n = 4).

Additional results revealed that 7 heterozygous variants observed at the variant-specific level occurred in both cohorts in genes with dominant TP53 and recessive MUTYH, GBA, SBDS, and ERCC2 inheritance modes. At the gene-specific level, P/LP variants occurred in 8 genes with dominant DICER1 and TP53, dominant and recessive ATM and COL7A1, and recessive ERCC2, GBA, MUTYH, and SBDS inheritance patterns in both patient cohorts. Finally, at the pathway-specific level, MSH2 and MSH6 gene variants that are associated with Lynch syndrome were observed in both cohorts.

Notably, beyond these genes that are associated with RMS, P/LP variants were identified in dominant-acting genes that have never or rarely been reported in RMS. Such genes included BRCA2, CBL, CHEK2, FH, RET, and SMARCA4.

No significant correlation was observed between sex of patients and risk of P/LP in both cohorts (Fisher’s exact test, discovery, P = .87; secondary, P = .59). Additionally, no correlation between overall survival or event-free survival and germline variants was observed; however, a univariate analysis did show a statistically significant correlation with an earlier age of tumor onset and dominant-acting genes (P = .01).

“Larger studies are needed to quantify the risk of RMS from germline pathogenic variants. This study of predominantly intermediate-risk and unselected RMS may not be generalizable to all RMS-risk groups,” the study authors concluded.

Reference

1. Kim J, Light N, Subasri V, et al. Pathogenic germline variants in cancer susceptibility genes in children and young adults with rhabdomyosarcoma. JCO Precis Oncol. 2021;5:75-87. doi:10.1200/PO.20.00218