Molecular Profiling of Hard-to-Treat Childhood and Adolescent Cancers

Abstract

Importance: Little progress in pediatric cancer treatment has been noted in the past decade, urging the development of novel therapeutic strategies for adolescents and children with hard-to-treat cancers. Use of comprehensive molecular profiling in the clinical management of children and adolescents with cancer appears a suitable approach to improve patient care and outcomes, particularly for hard-to-treat cases.

Objective: To assess the feasibility of identifying potentially actionable mutations using next-generation sequencing-based assays in a clinically relevant time frame.

Design, setting, and participants: This diagnostic study reports the results of the TRICEPS study, a prospective genome sequencing study conducted in Québec, Canada. Participants, aged 18 years or younger at diagnosis, with refractory or relapsed childhood and adolescent cancers were enrolled from April 2014 through January 2018. Whole-exome sequencing (WES) of matched tumor normal samples and RNA sequencing of tumor were performed to identify single-nucleotide variants, fusion transcripts, differential gene expression, and copy number alterations. Results reviewed by a team of experts were further annotated, synthesized into a report, and subsequently discussed in a multidisciplinary molecular tumor board.

Main outcomes and measures: Molecular profiling of pediatric patients with hard-to-treat cancer, identification of actionable and targetable alteration needed for the management of these patients, and proposition of targeted and personalized novel therapeutic strategies.

Results: A total of 84 patients with hard-to-treat cancers were included in the analysis. These patients had a mean (range) age of 10.1 (1-21) years and a similar proportion of male (45 [54%]) and female (39 [46%]). Sixty-two patients (74%) had suitable tissues for multimodal molecular profiling (WES and RNA sequencing). The process from DNA or RNA isolation to genomic sequencing and data analysis steps took a median (range) of 24 (4-41) days. Potentially actionable alterations were identified in 54 of 62 patients (87%). Actions were taken in 22 of 54 patients (41%), and 18 (33%) either were on a second or third line of treatment, were in remission, or had stable disease and thus no actions were taken.

Conclusions and relevance: Incorporating genomic sequencing into the management of hard-to-treat childhood and adolescent cancers appeared feasible; molecular profiling may enable the identification of potentially actionable alterations with clinical implications for most patients, including targeted therapy and clinically relevant information of diagnostic, prognostic, and monitoring significance.

Figure 1.. Enrollment Overview and Distribution of Potentially Actionable Alterations

MRD indicates minimal residual disease.

Figure 2.. Tumor Mutation Burden for 62 Patients

Distribution of the somatic tumor mutation burden is defined as the number of nonsynonymous coding mutations per megabase. Each bar indicates the mutation number in each sample. The blue line indicates the median of the TMB in the cohort (1.09), and the orange line indicates pediatric high threshold, as determined by Gröbner et al. Solid tumors are labeled in tan, brain tumors in orange, and hematological malignant neoplasms in blue. ALL indicates acute lymphoblastic leukemia; AML, acute myeloid leukemia; ETP, early T-cell precursor; NET, neuroendocrine tumors; NUT, nuclear protein of the testis.

Figure 3.. Summary of the Molecular Profiling of Patients in Oncogene Gene Category

Data were derived from all 62 patients with completed whole-exome sequencing as well as RNA sequencing of tumors and whole-exome sequencing of germline DNA. The presence of specific mutations, insertion/deletions (indels), amplification/deletions, and genes fusions are indicated by colored circles for hematological malignant neoplasms and solid tumors. Only sequencing findings with biological significance are included. Somatic type included somatic single-nucleotide variants or indels. Sarcoma included rhabdomyosarcoma, Ewing sarcoma, osteosarcoma, round cell sarcoma. Brain type included pilocytic astrocytoma medulloblastoma. Other types included malignant rhaboid tumor, adrenal gland carcinoma, hepatoblastoma, paraganglioma, Wilms tumor, sinus carcinoma, hepatocarcinoma, pleuropulmonary blastoma, NUT midline carcinoma, epithelial tumor, and gastric NET. ALL indicates acute lymphoblastic leukemia; AML, acute myeloid leukemia; LOH, loss of heterozygosity; NB, neuroblastoma; NET, neuroendocrine tumors; NUT, nuclear protein of the testis.

Figure 4.. Summary of the Molecular Profiling of Patients in Fusion, Other, and Tumor Suppression Gene Category

Data were derived from all 62 patients with completed whole-exome sequencing as well as RNA sequencing of tumors and whole-exome sequencing of germline DNA. The presence of specific mutations, insertion/deletions (indels), amplification/deletions, and genes fusions are indicated by colored circles for hematological malignant neoplasms and solid tumors. Only sequencing findings with biological significance are included. See the caption to Figure 3 for the types included in each neoplasm/tumor category and for the color key.