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Pediatric Cancer Program Uses Comprehensive Molecular Profiling to Match Patients to Therapies

NEW YORK – Researchers from the precision medicine Zero Childhood Cancer Program in Australia said they were able to use tumor and germline whole-genome sequencing (WGS), RNA sequencing, and methylome analysis to elucidate the molecular basis of tumors from high-risk pediatric patients, leading to some patients being able to receive targeted therapies.

A major challenge of using a comprehensive profiling approach for precision medicine is separating pathogenic from non-pathogenic molecular changes within a tumor, the researchers noted. The Zero Childhood Cancer Program is Australia's first national pediatric cancer precision medicine program, and is focused on real-time recruitment and analysis of patients with high-risk pediatric cancer. In a study published on Monday in Nature Medicine, the researchers presented the program's first systematic evaluation of the utility and early clinical effects of a comprehensive molecular profiling platform to identify clinically significant variants relevant to the biology of the tumor, diagnosis, clinical management, or prognosis.

They analyzed 252 tumors from high-risk pediatric patients with cancer. These patients typically have aggressive tumors, but have few treatment options, or relapsed or refractory disease despite having undergone standard therapy. The analysis identified 968 reportable molecular aberrations — 39.9 percent through WGS and RNA-seq, 35.1 percent through WGS only, and 25 percent through RNA-seq.

Of these patients, 93.7 percent had at least one germline or somatic aberration, 71.4 percent had molecular aberrations that could be treated with a targeted therapy, and 5.2 percent had a change in diagnosis. The researchers also noted that WGS identified pathogenic cancer-predisposing variants in 16.2 percent of the patients. When they conducted methylome analysis in 76 central nervous system tumors, diagnosis was confirmed in 71.1 percent of patients and contributed to a change of diagnosis in two patients.

"To date, 43 patients have received a recommended therapy, 38 of whom could be evaluated, with 31 percent showing objective evidence of clinical benefit," the authors wrote. "Comprehensive molecular profiling resolved the molecular basis of virtually all high-risk cancers, leading to clinical benefit in some patients."

In their analysis, the researchers found that common SNV mutations affected epigenetic regulation, DNA maintenance, cell cycle, and kinase signaling pathway genes, consistent with the cancer subtypes in the cohort and previous studies. Frequent CNVs included homozygous deletions of tumor suppressor genes and epigenetic modifiers, and gene amplifications involving transcriptional regulators, receptor tyrosine kinases, or the cyclin-dependent kinase CDK4. Chromosome 1q gains were the most common whole chromosome arm gain in all tumor types, but whole chromosome arm gains or losses were uncommon compared to segmental CNVs, unlike in adult tumors.

The researchers sought to identify non-coding driver variants linked to unexplained gene expression changes, and identified 67 established or novel driver fusions using integrated WGS and RNA-seq. The most frequent were EWSR1 rearrangements, PAX3-FOXO1, and ASPCR1-TFE3 in Ewing's sarcoma, alveolar rhabdomyosarcoma, and alveolar soft part sarcoma, respectively. They noted that there were 15 likely kinase-activating fusions, including six NTRK fusions, and that other fusions highlighted new tumor biology.

WGS with RNA-seq also identified an additional 34 intragenic CNVs or other structural variants that either activated oncogenes or inactivated tumor suppressor genes. These arose from deletions, duplications, inversions, or translocations throughout the genome, frequently expressed as out-of-frame fusions in RNA-seq data.

When the investigators looked for therapeutically actionable SNVs, CNVs, and structural variants, they found them clustered most frequently in RTK signaling, MAP kinase signaling, and PI3K-mTOR signaling pathways. RTKs were activated by point mutations, high copy number gains, or fusions. PI3K-mTOR variants included known activating PIK3CA mutations or loss-of-function mutations and deletions affecting PTEN, PTPN11, PIK3R1, PIK3R2, MTORC1, and MTORC2. The researchers also recurrently observed potentially targetable variants in epigenetic regulation genes and in the chromatin-remodeling gene PBRM1.

Notably, they added, many common oncodrivers such as MYC or MYCN amplifications and TP53 deletions or mutations, remained undruggable and wouldn't be considered actionable even though they are pathogenic.

"To maximize the number of potential treatment recommendations, multiple platforms corroborating a variant reduces the need for additional validation tests, particularly for novel mutations, which would otherwise be required at least in all instances where a clinical action might result," the authors concluded.

They further noted that the rate of pathogenic germline variants — 16.2 percent of the cohort — was higher than anticipated based on studies in other populations. "This is the first estimate of the prevalence of germline mutations driving high-risk pediatric cancer in the Australian population based on tumor-germline WGS," the researchers wrote. "WGS was critical for the assignment of pathogenicity to several variants, notably where somatic features, such as mutation signatures, TMB and second-hit mutations, were instrumental in identifying the underlying germline mutation(s)."