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Figure 1.
Treehouse Workflow
Treehouse Workflow

The components in brown are performed by the University of California, Santa Cruz bioinformatics team, while the components in gray are performed by the clinical partners. Calculation of gene-level expression profiles can occur at the University of California, Santa Cruz or at a partner site through the use of portable software. Both the University of California, Santa Cruz and clinical partners participate in research discussions about cases. RNA-Seq indicates RNA sequencing.

Figure 2.
Actionable Gene Expression Outliers Identified Through Comparative RNA Sequencing Analysis of the Cohort
Actionable Gene Expression Outliers Identified Through Comparative RNA Sequencing Analysis of the Cohort

The details of findings in each sample are listed in eTable 3 in the Supplement. BCR indicates B-cell receptor; CNS, central nervous system tumors; HEME, hematopoietic tumors; HSP, heat-shock proteins; JAK/STAT, Janus kinase and signal transducer and activator of transcription signaling pathway; NBL, neuroblastomas; PI3K/AKT/mTOR, phosphatidylinositol-3-kinase (PI3K)/AKT and the mammalian target of rapamycin (mTOR) signaling pathway; RAS/RAF/MEK, mitogen-activated protein kinase RAS/RAF/MEK/ERK pathway; RTK, receptor tyrosine kinases; SHH, sonic hedgehog; and SRC, sarcomas.

Figure 3.
Recurrent Actionable Gene Expression Outliers
Recurrent Actionable Gene Expression Outliers

Recurrent actionable gene expression outliers (y-axis), colored by gene sets as in Figure 2B, organized by disease (x-axis). Filled black squares denote outliers identified using the pan-cancer analysis approach, while unfilled white squares denote outliers identified by the pan-disease analysis approach. CNS indicates central nervous system tumors; HEME, hematopoietic tumors; NBL, neuroblastoma; and SRC, sarcoma.

Figure 4.
Comparison of DNA and RNA Analysis Results
Comparison of DNA and RNA Analysis Results

DNA and RNA analysis results were reviewed for 74 samples with both types of data available.

Figure 5.
Utility of RNA Sequencing (RNA-Seq) Analysis
Utility of RNA Sequencing (RNA-Seq) Analysis

A, RNA-Seq analysis can be used as additional support for DNA aberrations when a single mutated gene is itself highly expressed or downstream genes are highly expressed as a result of the mutation. B, With multiple mutated genes, RNA-Seq analysis can be used to prioritize among them based on high expression of the mutated gene itself or downstream targets. C, If DNA aberration is not expressed, nor are downstream genes, RNA-Seq analysis can be used to deprioritize DNA abnormalities with no evidence of effectiveness at the level of RNA. D, RNA-Seq analysis can reveal an abnormality in the absence of DNA mutation.

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    Original Investigation
    Genetics and Genomics
    October 25, 2019

    Comparative Tumor RNA Sequencing Analysis for Difficult-to-Treat Pediatric and Young Adult Patients With Cancer

    Author Affiliations
    • 1Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz
    • 2University of California, Santa Cruz Genomics Institute, Santa Cruz
    • 3Howard Hughes Medical Institute, University of California, Santa Cruz
    • 4Division of Hematology and Oncology, Department of Pediatrics, University of California, San Francisco
    • 5Integrated Cancer Genomics Division, Translational Genomics Research Institute (TGen), Phoenix, Arizona
    • 6Cancer and Cell Biology Division, TGen, Phoenix, Arizona
    • 7Center for Data Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
    • 8Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
    • 9CHOC Children’s Hospital, Hyundai Cancer Institute, Orange, California
    • 10British Columbia Children’s Hospital Research Institute, British Columbia Children’s Hospital, Vancouver, British Columbia, Canada
    • 11BC Cancer, Vancouver, British Columbia, Canada
    • 12Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
    • 13Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
    • 14Department of Neurology, University of California, San Francisco
    • 15Department of Neurosurgery, University of California, San Francisco
    • 16Department of Pediatrics, University of California, San Francisco
    • 17Now with Anthem, Inc, Palo Alto, California
    JAMA Netw Open. 2019;2(10):e1913968. doi:10.1001/jamanetworkopen.2019.13968
    Key Points español 中文 (chinese)

    Question  Is it feasible and useful to compare the tumor RNA sequencing data of a child or young adult with the tumor RNA sequencing data of thousands of other patients (of all ages) in a research setting?

    Findings  Among 144 tumor samples from children and young adults, comparative RNA sequencing analysis, conducted across 4 precision medicine studies in the United States and Canada, was feasible and potentially useful for 99 of 144 pediatric and young adult cancer samples. In contrast, DNA mutation information was potentially useful for only 34 of 74 samples.

    Meaning  This study’s findings suggest that open sharing and combined analysis of tumor RNA sequencing data from pediatric and young adult patients treated on different clinical trials may represent a feasible approach and may produce useful clinical and biological information for individual patients.

    Abstract

    Importance  Pediatric cancers are epigenetic diseases; therefore, considering tumor gene expression information is necessary for a complete understanding of the tumorigenic processes.

    Objective  To evaluate the feasibility and utility of incorporating comparative gene expression information into the precision medicine framework for difficult-to-treat pediatric and young adult patients with cancer.

    Design, Setting, and Participants  This cohort study was conducted as a consortium between the University of California, Santa Cruz (UCSC) Treehouse Childhood Cancer Initiative and clinical genomic trials. RNA sequencing (RNA-Seq) data were obtained from the following 4 clinical sites and analyzed at UCSC: British Columbia Children’s Hospital (n = 31), Lucile Packard Children’s Hospital at Stanford University (n = 80), CHOC Children’s Hospital and Hyundai Cancer Institute (n = 46), and the Pacific Pediatric Neuro-Oncology Consortium (n = 24). The study dates were January 1, 2016, to March 22, 2017.

    Exposures  Participants underwent tumor RNA-Seq profiling as part of 4 separate clinical trials at partner hospitals. The UCSC either downloaded RNA-Seq data from a partner institution for analysis in the cloud or provided a Docker pipeline that performed the same analysis at a partner institution. The UCSC then compared each participant’s tumor RNA-Seq profile with more than 11 000 uniformly analyzed tumor profiles from pediatric and young adult patients with cancer, downloaded from public data repositories. These comparisons were used to identify genes and pathways that are significantly overexpressed in each patient’s tumor. Results of the UCSC analysis were presented to clinical partners.

    Main Outcomes and Measures  Feasibility of a third-party institution (UCSC Treehouse Childhood Cancer Initiative) to obtain tumor RNA-Seq data from patients, conduct comparative analysis, and present analysis results to clinicians; and proportion of patients for whom comparative tumor gene expression analysis provided useful clinical and biological information.

    Results  Among 144 samples from children and young adults (median age at diagnosis, 9 years; range, 0-26 years; 72 of 118 [61.0%] male [26 patients sex unknown]) with a relapsed, refractory, or rare cancer treated on precision medicine protocols, RNA-Seq–derived gene expression was potentially useful for 99 of 144 samples (68.8%) compared with DNA mutation information that was potentially useful for only 34 of 74 samples (45.9%).

    Conclusions and Relevance  This study’s findings suggest that tumor RNA-Seq comparisons may be feasible and highlight the potential clinical utility of incorporating such comparisons into the clinical genomic interpretation framework for difficult-to-treat pediatric and young adult patients with cancer. The study also highlights for the first time to date the potential clinical utility of harmonized publicly available genomic data sets.

    Introduction

    We present a framework for comparative RNA sequencing (RNA-Seq) analysis of pediatric tumors across multiple precision medicine studies. Our framework uses public genomic data sets of more than 11 000 tumor RNA-Seq samples that we consolidated and released to the community. We describe an application of our framework and the data compendium to the analysis of 144 tumors from children and young adults with a relapsed, refractory, or rare cancer, studied on 4 separate precision medicine trials in the United States and Canada.

    While genomic profiling of tumors is becoming the standard of care in oncology, many tumors, especially in children, do not harbor actionable DNA aberrations. Tumor gene expression information may increase the number of actionable aberrations detected in tumors, and its utility is being evaluated in adults (eg, the WINTHER trial1). Results of several studies suggested the possible clinical utility of RNA-Seq for children. The Michigan Oncology Sequencing Center's Peds-MiOncoSeq study2 evaluated 92 patients with relapsed or refractory tumors using a combination of whole-exome sequencing (WES) and RNA-Seq and reported that 46% of samples had actionable findings, including 36% of this subset that had gene fusions with a known or suspected role in tumorigenesis identified through RNA-Seq analysis. In another study3 of 59 children, most with relapsed or refractory cancers, analysis revealed actionable findings, including RNA fusions, in 51% of cases. The Individualized Therapy for Relapsed Malignancies in Childhood (INFORM) consortium4 studied 57 patients with WES, low-coverage whole-genome sequencing, RNA-Seq, methylation, and gene expression microarrays and reported a 50% rate of actionable findings that included overexpression of druggable oncogenes. Several patients whose tumors exhibited oncogene overexpression were placed on targeted therapies against these alterations.4 Finally, the Precision in Pediatric Sequencing (PIPseq) program5 profiled 65 patients using a combination of tumor or normal WES and tumor RNA-Seq. Tumor RNA-Seq identified therapeutic targets in 23% of the patients; these targets included overexpression of druggable oncogenes, defined based on comparisons of tumor RNA-Seq expression with the RNA-Seq expression levels in a panel of normal tissues. While results of these studies suggested that RNA-Seq expression may be clinically beneficial, they did not provide reproducible methods that could be applied across different precision medicine trials.

    Our group recently developed a reproducible and scalable approach for performing outlier analysis for pediatric patients with cancer by using large publicly available cancer RNA-Seq data sets.6 The objective of the present study was to evaluate the feasibility and potential utility of our approach for cancer samples collected prospectively from multiple precision medicine trials in difficult-to-treat pediatric and young adult patients with cancer.

    Methods
    Study Design

    Among 144 tumors from children and young adults, this cohort study was conducted as a consortium of the following 4 clinical sites: British Columbia Children’s Hospital (BCCH), Vancouver, British Columbia, Canada; Lucile Packard Children’s Hospital at Stanford University (LPCH), Stanford, California; CHOC Children’s Hospital and Hyundai Cancer Institute, Orange, California; and the Pacific Pediatric Neuro-Oncology Consortium (PNOC), San Francisco, California. During the period from January 1, 2016, to March 22, 2017, the University of California, Santa Cruz (UCSC) obtained and processed tumor RNA-Seq data, as well as deidentified clinical and molecular information, for 181 tumors from 161 children and young adults with a relapsed, refractory, or rare cancer treated on precision medicine protocols. Tumor RNA-Seq data were obtained from the following 4 clinical sites: BCCH (n = 31), LPCH (n = 80), CHOC (n = 46), and PNOC (n = 24). Each clinical site had its own precision medicine protocol in place, and UCSC Treehouse Childhood Cancer Initiative served as a third-party institution conducting secondary analysis of each site’s tumor RNA-Seq data. This study followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guideline.

    The BCCH study was approved by the University of British Columbia Research Ethics Committee. The LPCH protocol “Clinical Implementation of Genomic Analysis in Pediatric Malignancies” was approved by the Stanford University Institutional Review Board. The CHOC study “Pilot Project: Molecular Profiles of Newly Diagnosed, Refractory and Recurrent Childhood, Adolescent, and Young Adult Cancers” was approved by the CHOC Children’s Hospital and Hyundai Cancer Institute Institutional Review Board. The PNOC-003 protocol has been previously described.7 The UCSC Treehouse Childhood Cancer Initiative protocol was approved by the UCSC Institutional Review Board.

    Because this study involved the sharing of deidentified data, UCSC was not required by our institutional review board to obtain informed consent from study participants; however, clinical partners obtained written informed consent from their participants as per their individual study protocols. All study participants were informed that their deidentified data would be shared with research partners, including UCSC.

    Statistical Analysis
    Comparative RNA-Seq Analysis

    All RNA-Seq data (11 340 compendium samples and 144 samples from clinical partners) were first uniformly processed using the RNA-Seq pipeline version 3.2 developed by the UCSC Computational Genomics Lab8 (eMethods in the Supplement). The UCSC either downloaded RNA-Seq data from a partner institution for analysis in the cloud or provided a Docker pipeline composed of gene-level expression calculation, which was run at the partner institution; gene expression outlier analysis and identification of druggable genes and pathways was then run on each of the 144 samples at UCSC.

    Gene Expression Outlier Analysis

    Gene-level transcript per million data were used to perform gene expression outlier analysis9 to identify transcripts significantly enriched in each patient’s tumor compared with either all 11 340 tumors or tumor types identified as most similar (pan-disease analysis). For pan-cancer analysis, we used the filtered set of 27 084 genes; for pan-disease analysis, we used the unfiltered set of 58 581 unique GENCODE Human Release 23 genes (eMethods in the Supplement) to make sure we did not miss genes whose expression is specific to certain tumor subtypes.

    Identification of Druggable Overexpressed Genes and Gene Sets

    We obtained the following 3 lists of overexpressed genes: one list from pan-disease outlier analysis, a second list from pan-cancer outlier analysis, and a third list from overlapping genes in pan-disease and pan-cancer lists. For each list, we identified potential druggable genes and statistically enriched pathways.

    Drug-Gene Interaction Analysis

    We used the Drug-Gene Interaction Database to assess which of the overexpressed genes can be considered actionable by available therapies.10 The database programmatically searches through publications and other curated databases for reported associations between human genes and available inhibitors. To refine our findings to only existing cancer therapies, we set the Drug-Gene Interaction Database to query for drug-gene interactions among the following 4 curated cancer databases (all part of the Drug-Gene Interaction Database10): CIViC, Cancer Commons, My Cancer Genome, and My Cancer Genome Clinical Trial. The Drug-Gene Interaction Database does not contain all known drug-gene interactions, nor does it guarantee a gene’s druggability. As a result, we performed additional literature searches and consulted published clinical cancer genomic studies. We prioritized studies, such as INFORM,4 in which gene expression information was considered in assessing the actionability of each gene. The 92 genes for which overexpression was considered directly or indirectly actionable in this study are listed in eTable 1 in the Supplement.

    Gene Set Overlap Analysis

    In parallel to identifying druggable genes, we used the Molecular Signature Database11 to identify overexpressed cancer pathways in the tumor sample. Gene set overlap analysis computes statistically significant pathways by evaluating the overlap between the input gene list of overexpressed genes and the gene sets from the Molecular Signature Database11 collections “Hallmark Gene Sets” and “Canonical Pathways.” In this analysis, for each input gene list, we looked at the first 100 reported gene sets that have the false discovery rate (false discovery rate q value) below 0.05.

    DNA Mutation Analysis

    DNA mutation data were obtained from the following platforms: Foundation Medicine gene panel (LPCH), whole-genome sequencing as part of the Personalized Onco-Genomics Program (POG) (BCCH), NantOmics whole-genome sequencing (CHOC), or Ashion Analytics whole-exome sequencing (PNOC). We used the National Cancer Institute (NCI) Pediatric Molecular Analysis for Therapeutic Choice (hereinafter the NCI Pediatric MATCH) considerations to curate the mutation data reported by the DNA platforms and to classify samples into treatment arms based on the DNA aberrations.12

    Results
    Patient Characteristics

    To evaluate the feasibility of comparative RNA-Seq analysis across multiple precision medicine studies, we obtained RNA-Seq data from 181 samples from 161 pediatric and young adult patients (age range, 0-29 years; 65 of 108 [60.2%] male) with a relapsed, refractory, or rare cancer treated at the following 4 clinical sites: BCCH (n = 31), LPCH (n = 80), CHOC (n = 46), and PNOC (n = 24). The age at diagnosis was available for 126 individuals: the median age at diagnosis was 9 years, and the range was 0 to 26 years. Among 144 tumor samples, 46 were from female patients, while 72 were male patients; sex was not reported for 26 samples. RNA sequencing quality control analysis (eMethods in the Supplement) was applied to all 181 samples; of these, 144 samples from 128 patients were of sufficient quality for further analysis. For each case, gene-level transcript per million measurements were computed8 from tumor RNA-Seq data, which were used in 2 types of analyses to identify expression features of potential clinical relevance (Figure 1).

    Reference Compendium for Tumor Comparisons

    To provide a robust reference for tumor comparisons and gene expression outlier detection, we assembled a compendium of 11 340 uniformly analyzed adult, pediatric, and young adult tumor profiles (eTable 2 and eFigure 1 in the Supplement). Of 11 340 samples in the compendium, 1859 (16.4%) were from pediatric, adolescent, and young adult patients with cancer who were younger than 30 years.

    Gene Expression Outlier Analysis

    Gene expression outlier analysis is a promising method for identifying druggable overexpressed oncogenes in adult tumors.9,13 We performed gene expression outlier analysis against similar tumors (pan-disease analysis) and against all cancers in our compendium (pan-cancer analysis) (eMethods in the Supplement).

    The gene expression outliers were analyzed for the presence of genes whose products could be targeted by small molecules directly or indirectly by targeting the downstream signaling pathway (eTable 1 in the Supplement). This list is based on a similar list prepared by the INFORM study4 and contains 37 genes whose protein products can be targeted directly and 55 genes whose products cannot be targeted but that function in a pathway that can be targeted by a therapy. We hypothesized that aberrant gene dosage of these directly or indirectly actionable genes could be detected by gene expression outlier analysis. We also sought to assess whether multiple members of the same pathways were highly expressed in concert in the same tumor.

    Of 144 high-quality RNA-Seq data sets, 99 (68.8%) harbored outlier gene expression of 1 of 92 actionable genes. In 75 samples, both an actionable gene and the corresponding pathway were overexpressed using outlier analysis. The most common gene expression outlier was FLT3 (OMIM 136351), overexpressed in 16 samples, all from hematopoietic tumors. This was followed by BTK (OMIM 300300) and CDK6 (OMIM 603368), overexpressed in 14 samples each. While BTK was overexpressed in 14 hematopoietic tumors, CDK6 was overexpressed in both hematopoietic and nonhematopoietic tumors, including neuroblastoma and glioma. The most common gene expression outlier in nonhematopoietic tumors was PTCH1 (OMIM 601309), overexpressed in 11 samples from craniopharyngioma, neurofibroma, sarcoma, glioma, medulloblastoma, and osteosarcoma. The most common overrepresented gene set was receptor tyrosine kinases, overexpressed in 55 samples from all diagnostic categories (Figure 2). Among these, FLT3 was most commonly overexpressed, followed by FGFR1 (OMIM 136350) and PDGFRA (OMIM 173490). While FGFR1 was overexpressed in a variety of nonhematopoietic tumor types, PDGFRA was exclusively overexpressed in brain tumors, and FLT3 was exclusively overexpressed in acute leukemias. Of the 92 actionable genes, 47 were overexpressed in 2 or more samples (Figure 3). For the remaining 45 of the 144 samples (31.3%), our comparative RNA-Seq analysis did not identify any actionable outliers (eTable 3 in the Supplement). An example of Treehouse analysis is provided in eFigure 2 in the Supplement.

    Comparison of RNA-Seq Findings With DNA Mutation Analysis

    A small number of childhood tumors contain DNA alterations that may forecast response to molecularly targeted therapies.14 Children’s Oncology Group NCI Pediatric MATCH12 is a nationwide basket trial for children and adolescents with relapsed or refractory solid tumors evaluating the use of DNA analysis to match patients to therapies. We had mutation data available for 74 of the 144 samples in our cohort; 52 of 74 were solid tumors.

    Of 74 solid tumor and leukemia samples, 34 (45.9%) had an actionable abnormality as defined by the NCI Pediatric MATCH study12 detected by DNA analysis. Fifty-five of 74 samples (74.3%) had an actionable gene expression outlier (eTable 3 in the Supplement) detected by RNA-Seq, 28 (37.8%) had abnormalities detected by both DNA and RNA analysis, 6 (8.1%) had only DNA abnormalities, and 13 (17.6%) had no DNA or RNA abnormalities. Remarkably, 27 samples (36.5%) had only a gene expression dosage abnormality, highlighting the potential utility of comparative RNA-Seq for nominating molecular targets for patients with no DNA findings (Figure 4 and Figure 5).

    To assess the consistency of DNA and RNA findings, we reviewed 28 samples that had both types of findings. In 11 of 28 samples, at least 1 of the genes with a targetable DNA mutation was identified as a gene expression outlier, suggesting that actionable DNA mutations are often associated with the overexpression of the mutated gene. In 17 of 28 samples, however, none of the genes with a targetable DNA abnormality were identified as a gene expression outlier. Because we do not necessarily expect all mutant genes to be abnormally expressed themselves, we then reviewed the 17 samples to see if there was expression support of the DNA abnormality downstream of the mutated gene.

    DNA analysis of 2 acute lymphoblastic leukemia samples (TH01_0122_S01 and TH01_0130_S01) revealed a PAX5 (OMIM 167414)–JAK2 (OMIM 147796) fusion, which was previously shown to activate Janus kinase and signal transducer and activator of transcription (JAK/STAT) signaling and promote a progenitor phenotype in leukemia cells.15 Our comparative gene expression analysis did not reveal the overexpression of the JAK/STAT pathway in these tumors but instead identified overexpression of phosphatidylinositol-3-kinase (PI3K)/AKT and the mammalian target of rapamycin (mTOR) (PI3K/AKT/mTOR) signaling pathway and B-cell receptor signaling pathways in both tumors and overexpression of FLT3 in TH01_0130_S01. The overexpression of PI3K/AKT/mTOR and B-cell receptor signaling pathway genes may be indicative of a progenitor B-cell state assumed by the leukemia cells.16 Similarly, another acute lymphoblastic leukemia sample (TH01_0129_S01) harbored a BCRABL (OMIM 151410) fusion. RNA sequencing revealed outlier expression of PI3K/AKT/mTOR and B-cell receptor signaling pathways; PI3K/AKT/mTOR activation is known to be downstream of the BCR-ABL fusion signaling,17 suggesting that this overexpression is consistent with the DNA finding of the gene fusion. DNA analysis of 5 leukemia samples (TH01_0124_S01, TH01_0134_S01, TH03_0010_S01, TH03_0010_S02, and TH03_0011_S01) identified an activating mutation in NRAS (OMIM 164790). Activation of NRAS has been associated with proliferation and self-renewal in leukemia via the activation of MEK and mTOR signaling pathways.18 Our RNA-Seq analysis revealed overexpression of cell cycle or BCL2 (OMIM 603167)–MDM2 (OMIM 164785) pathways in TH01_0134_S01, TH03_0010_S01, TH03_0010_S02, and TH03_0011_S01; these pathways are downstream of activated RAS signaling, and their overexpression is thus consistent with the activating NRAS mutation. Notably, TH01_0124_S01 harbored subclonal activating mutations in both KRAS (OMIM 190070) and NRAS (20.6% and 29.1% mutant allele frequency based on RNA-Seq, respectively). While gene expression analysis revealed overexpression of FLT3, outlier expression associated with pathways downstream of activated RAS signaling was not found. These findings may represent either discordance between the DNA and RNA analysis or intratumor heterogeneity in this leukemia sample, already suspected based on the presence of 2 subclonal RAS mutations.

    DNA analysis of a diffuse intrinsic pontine glioma (DIPG), TH02_0092_S01, revealed copy number gains of KDR (OMIM 191306), KIT (OMIM 164920), and PDGFRA, located on 4q12. Notably, while KIT and PDGFRA were highly expressed but not meeting the outlier threshold (84th and 93rd percentiles in the compendium), KDR was expressed at a much lower level, in the 54th percentile. Therefore, considering expression information alongside the copy number information may be useful for prioritizing druggable targets within copy number amplicons.19 In another DIPG sample, TH02_0091_S01 with a BRAF (OMIM 164757) p.V600E mutation, gene expression analysis revealed outlier expression of CSF1R (OMIM 164770). Recent work in melanoma showed that overexpression of CSF1R can occur in melanomas with activating BRAF or MAPK mutations and is associated with resistance to BRAF inhibitors.20 Because the interaction of these 2 pathways in DIPG is not known, we did not consider these concordant DNA and RNA findings.

    An atypical teratoid rhabdoid tumor (TH03_0016_S01) and myoepithelial carcinoma (TH03_0113_S01) harbored loss of SMARCB1 (OMIM 601607) (INI1) through a frameshift mutation or protein loss of unknown mechanism detected by immunohistochemistry, respectively. Comparative gene expression analysis of both tumors revealed outlier expression of FGFR1, a promising target in rhabdoid tumors deficient in SMARCB1 (INI1).21 Gene expression analysis of DIPG tumor TH02_0087_S01 with a loss-of-function mutation of PIK3R1 (OMIM 171833) activating the PI3K/AKT/mTOR pathway revealed overexpression of the JAK/STAT pathway. While it is unknown whether PI3K/AKT/mTOR and JAK/STAT pathways interact in DIPG, these pathways may be coactivated as a result of PI3K mutations in meningiomas.22 Because the interaction of these 2 pathways in DIPG is not known, we did not count this sample as having concordant DNA and RNA findings. Comparative gene expression analysis of a malignant peripheral nerve sheath tumor TH06_0645_S01 and neurofibroma TH06_0646_S01 with loss of NF1 (OMIM 162200) revealed overexpression of sonic hedgehog signaling present in this tumor type.23 We also identified overexpression of receptor tyrosine kinases ERBB3 (OMIM 190151) and EGFR (OMIM 131550) in these tumors.

    Finally, in a glioma TH03_0290_S01 with a BRAF p.V600E mutation, the mutation was not expressed in the RNA. In an additional case (TH01_0131_S01), an activating JAK2 mutation was supported by only a few reads, with more than 100 total read coverage in both the DNA and RNA, suggesting that the mutation may represent a subclonal event or a technical artifact.

    Overall, our review of 17 samples with mutated genes not themselves overexpressed by RNA-Seq analysis revealed that in 12 of the 17 samples the overexpressed genes and pathways were consistent with the detected DNA mutations, even though the mutant genes themselves were not overexpressed. In the remaining 5 samples, outlier expression was not consistent with an activating mutation detected in the sample (including the lack of a BRAF p.V600E mutant allele in the RNA in TH03_0290_S01; ambiguous evidence in TH02_0087_S01, TH01_0124_S01, and TH02_0091_S01; and possible technical issues in TH01_0131_S01).

    Discussion

    DNA sequencing is increasingly integrated in clinical trials to identify new molecular targets for children with incurable cancers. However, molecular targets are found for only a small number of patients, and the yield is much lower than that of similar adult cancer trials.24 Studies focusing on pediatric cancers have shown that the percentage of patients with potentially actionable findings increases to 40% to 50% when RNA-Seq data are considered alongside DNA mutation information.4 Herein, we described a framework for including RNA-Seq–derived gene expression information into precision medicine studies. Most notably, we show for the first time to date that such a framework can be used consistently across separate precision medicine clinical trials.

    To our knowledge, our work represents the first report of a translational cancer genomic analysis in which prospective patient data are analyzed by a third-party computational group, with results returned to clinicians and researchers. We found that this comparative analysis is feasible and can produce new information of potential clinical relevance in 68.8% of samples. In 36.5% of samples (27 of 74), druggable overexpressed genes and pathways were identified based on RNA analysis alone and were not apparent in the tumor DNA analysis. Our work suggests that direct investigations of the clinical utility and effectiveness of tumor RNA-Seq–derived gene expression information will be valuable, and the next phase of our project will focus on defining the incremental benefit of this approach. The findings from our work also suggest that open sharing of cancer genomic data can benefit each pediatric and young adult patient with cancer so that every family’s struggle contributes to the advancement of clinical care for the families that follow.

    Clinical Implications

    Although this study was not designed to assess clinical consequences, we noted associations of comparative RNA-Seq analysis findings and clinical features. For example, our analysis of a high-risk neuroblastoma sample revealed outlier expression of the ALK (OMIM 105590) kinase and CDK6 kinase (eFigure 2 in the Supplement). The outlier expression of CDK6, as well as several other cell cycle genes, was consistent with a known DNA amplification of CDK6 in this sample; however, the potential activation of ALK (OMIM 191175) was not evident before the RNA analysis. In another example, a 2-year-old boy with multifocal stage 4 hepatoblastoma metastatic to the lungs, was initially treated in the Childhood Liver Tumour Strategy Group of the International Society of Paediatric Oncology (SIOPEL-4) study,25 followed by surgery, 2 cycles of HEP0731 regimen T protocol, then salvage therapy with 3 cycles of vincristine, irinotecan, and temozolomide and 1 cycle of gemcitabine-oxaliplatin with bevacizumab. The patient had disease progression despite these therapies. Pathological analysis showed well and poorly differentiated hepatoblastoma with fetal and embryonal elements, and immunostaining showed retention of INI1 staining and diffuse nuclear and cytoplasmic β-catenin. Foundation Medicine testing revealed the p.G34V variant in CTNNB1, previously reported in hepatocellular carcinoma as an activating mutation.26 Comparative RNA-Seq analysis of the liver sample (TH03_0004_S04) uncovered gene expression similar to the proliferation subtype of hepatocellular carcinoma27,28 as well as outlier expression of HSP90B1, interleukin 6, and 4 other members of the JAK/STAT pathway. The overexpression of HSP90B was previously noted in hepatocellular carcinoma.29 The proliferative subtype of hepatocellular carcinoma is characterized by increased proliferation, high levels of serum α-fetoprotein (AFP), and chromosomal instability27; tumors with chromosomal instability are potentially sensitive to Aurora kinase inhibitors.30 Consistent with the similarity of the tumor to the proliferative subtype of hepatocellular carcinoma, the patient with the TH03_0004_S04 tumor had a response to the pan-kinase inhibitor pazopanib hydrochloride, with activity against Aurora kinase A.31 Based on the present study, after initiation of this treatment, the patient had a decline in his AFP levels from 14 036 to 1052 ng/mL at 7 weeks after initiation of the therapy (to convert AFP level to micrograms per liter, multiply by 1.0). At 10 weeks into this therapy, restaging studies showed progressive disease, and the patient was switched to therapy with ruxolitinib phosphate, without objective response by AFP levels or by imaging criteria.

    Limitations

    Our study has some limitations. The heterogeneous nature of the patients analyzed in this study (all types of relapsed, refractory, and rare cancers) made drawing general statements difficult. The study was not designed to directly evaluate clinical utility of comparative RNA-Seq analysis, and clinical follow-up data on these patients were not readily available.

    Conclusions

    Our experience suggests that it is feasible to include RNA-Seq–derived gene expression analysis in precision medicine studies and that this analysis can be harmonized across studies. We showed that RNA-Seq–derived gene expression was potentially useful for 68.8% of 144 samples compared with DNA mutation information, which was potentially useful for only 45.9% of 74 samples. Our study also highlights for the first time to date the potential clinical utility of harmonized publicly available genomic data sets. Open sharing and combined analysis of tumor RNA-Seq data from pediatric and young adult patients treated on separate clinical trials represent a feasible approach and can produce useful clinical and biological information for individual patients.

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    Article Information

    Accepted for Publication: September 6, 2019.

    Published: October 25, 2019. doi:10.1001/jamanetworkopen.2019.13968

    Open Access: This is an open access article distributed under the terms of the CC-BY License. © 2019 Vaske OM et al. JAMA Network Open.

    Corresponding Author: Olena M. Vaske, PhD, Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, 1156 High St, Santa Cruz, CA 95060 (olena@ucsc.edu).

    Author Contributions: Drs Sender, Mueller, Sweet-Cordero, Goldstein, and Haussler are co–senior authors. Dr Vaske had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis.

    Concept and design: Vaske, Bjork, Salama, Pfeil, Newton, Resnick, Spunt, Deyell, Laskin, Mueller, Goldstein, Haussler.

    Acquisition, analysis, or interpretation of data: Vaske, Beale, Tayi Shah, Sanders, Lam, Learned, Durbin, Kephart, Currie, Swatloski, McColl, Vivian, Zhu, Lee, Leung, Spillinger, Liu, Liang, Byron, Berens, Resnick, Lacayo, Spunt, Rangaswami, Huynh, Torno, Plant, Kirov, Zabokrtsky, Rassekh, Deyell, Marra, Sender, Mueller, Sweet-Cordero, Goldstein.

    Drafting of the manuscript: Vaske, Bjork, Beale, Pfeil, Lam, Currie, Swatloski, Resnick, Lacayo, Torno, Zabokrtsky, Marra, Goldstein.

    Critical revision of the manuscript for important intellectual content: Vaske, Salama, Beale, Tayi Shah, Sanders, Pfeil, Learned, Durbin, Kephart, Newton, McColl, Vivian, Zhu, Lee, Leung, Spillinger, Liu, Liang, Byron, Berens, Lacayo, Spunt, Rangaswami, Huynh, Plant, Kirov, Rassekh, Deyell, Laskin, Sender, Mueller, Sweet-Cordero, Goldstein, Haussler.

    Statistical analysis: Vaske, Beale, Pfeil, Lam, Resnick, Goldstein.

    Obtained funding: Vaske, Bjork, Resnick, Spunt, Rassekh, Deyell, Laskin, Sender, Mueller, Goldstein, Haussler.

    Administrative, technical, or material support: Bjork, Sanders, Learned, Durbin, Kephart, Currie, Swatloski, McColl, Lee, Spillinger, Liu, Liang, Resnick, Spunt, Torno, Plant, Zabokrtsky, Rassekh, Deyell, Laskin, Sender, Sweet-Cordero, Goldstein.

    Supervision: Vaske, Bjork, Salama, Pfeil, Berens, Resnick, Lacayo, Laskin, Goldstein, Haussler.

    Conflict of Interest Disclosures: Drs Vaske, Beale, and Haussler, Mss Sanders, Lam, Learned, Durbin, and Kephart, and Mr Pfeil reported receiving grants from the State of California’s California Initiative to Advance Precision Medicine (CIAPM), St Baldrick’s Foundation, Alex’s Lemonade Stand Foundation, Unravel Pediatric Cancer, Team G Childhood Cancer Foundation, and Live for Others Foundation. Dr Vaske disclosed that her spouse is an employee of ImmunityBio Inc (formerly NantOmics) and has equity interests in NantHealth. Ms Bjork reported receiving grants from the CIAPM. Dr Newton reported receiving funding from ImmunityBio Inc (formerly NantOmics). Ms Swatloski reported receiving grants from the American Association for Cancer Research, California Initiative to Advance Precision Medicine, National Institutes of Health (NIH)/National Cancer Institute, NIH/National Heart, Lung, and Blood Institute, Prostate Cancer Foundation, and Northern California California Institute for Regenerative Medicine (CIRM) Genomics Center of Excellence. Drs Byron and Berens reported receiving grants from TGen Foundation. Dr Spunt reported receiving grants from University of California, Santa Cruz, F. Hoffman–La Roche & Co, Novartis, Alex’s Lemonade Stand Foundation, Cookies for Kids’ Cancer, Bayer HealthCare Pharmaceuticals, Sanofi US Services, Inc, Loxo Oncology, Incyte Corporation, Bristol-Myers Squibb, St Baldrick’s Foundation, and Pfizer. Ms Zabokrtsky reported being supported by grants from Hyundai Motor America/Hyundai Hope on Wheels. Dr Laskin reported receiving grants from Roche Canada and AstraZeneca and receiving honoraria for academic talks from Boehringer Ingelheim, Roche Canada, and Pfizer. Dr Marra reported receiving grants from British Columbia Cancer Foundation and Genome British Columbia. Dr Goldstein reported disclosing that this work was completed before he joined Anthem, Inc, while he was on the faculty of University of California, Santa Cruz. Dr Haussler reported receiving grants from Howard Hughes Medical Institute, having a patent to BAMBAM issued and a patent to PARADIGM issued, and disclosing that Five3 Genomics, LLC and NantOmics data were used in this article. No other disclosures were reported.

    Funding/Support: This study was funded by St Baldrick’s Foundation Consortium Award and Emily Beazley Kures for Kids Fund Hero Award, CIAPM, Alex’s Lemonade Stand Foundation for Childhood Cancer Research, Unravel Pediatric Cancer, Team G Childhood Cancer Foundation, and Live for Others Foundation. Dr Goldstein was supported by NIH grant U24 CA195858 from the National Cancer Institute Oncology Models Forum. Dr Haussler is a Howard Hughes Medical Institute Investigator. The Personalized Onco-Genomics (POG) team acknowledges the generous support of the British Columbia Cancer Foundation and Genome British Columbia (project B20POG), as well as contributions toward equipment and infrastructure from Genome Canada and Genome British Columbia (projects 202SEQ, 212SEQ, and 12002), Canada Foundation for Innovation (projects 20070, 30981, 30198, and 33408), and the B.C. Knowledge Development Fund.

    Role of the Funder/Sponsor: The funding sources had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

    Additional Contributions: Jacquelyn M. Roger, University of California, Santa Cruz, helped in evaluating the significance of outlier genes. A. Geoffrey Lyle, MSc, University of California, Santa Cruz, assisted in addressing editorial queries. They received no compensation for their contributions. We thank the patients and their parents for participating in this study.

    Additional Information: Dr Vaske holds the Colligan Presidential Chair in Pediatric Genomics. The Treehouse data compendium (eTable 2 in the Supplement) and processed RNA-Seq data from the 144 patient samples discussed in this study are publicly available (https://treehousegenomics.ucsc.edu/p/vaske-2019-comparative-tumor-RNA). A previously published case (https://www.ncbi.nlm.nih.gov/pubmed/31511612) was included in the cohort of 144 samples. The POG pediatrics program (https://www.personalizedoncogenomics.org/; poginfo@bcgsc.ca) does not consent for data release, as such raw data are not posted publicly. The CHOC raw data have not been consented for data release and are not posted publicly. Raw data from the Stanford trial are available through the European Genome-Phenome Archive (accession No. EGAS00001003900). Raw data from PNOC-003 are available on CAVATICA (https://cavatica.sbgenomics.com/p/datasets#cavatica/cbttc-mixed-pa-01).

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