Abstract
Background/Objectives: The National Zero Childhood Cancer (ZERO) program, the most innovative child cancer research program in Australia, aims to assess the feasibility of a comprehensive ...precision medicine approach to improve outcomes for patients with high-risk pediatric cancer.
Design/Methods: ZERO combines comprehensive molecular profiling analysis (whole-genome sequencing tumor, germline DNA, deep sequencing of a 386-cancer associated gene panel, whole-transcriptome RNASeq, DNA methylation profiling Epic 850K array) with in vitro high-throughput drug screening (124-compound library, single agent) and patient-derived xenograft (PDX) drug efficacy testing. Results are curated and recommendations made through a national Multidisciplinary Tumor Board (MTB). Recommendations consist of targeted therapy, change of diagnosis, or genetics referral for a germline cancer predisposition gene mutation.
Results: The ZERO national trial (PRISM), which opened in September 2017 at all 8 pediatric centers in Australia, has enrolled 213 patients in the first 20 months (36% central nervous system tumors, 29% sarcoma, 15% leukemias/lymphomas, 7% neuroblastoma, 13% other rare or unknown cancers). The unique ZERO testing platform has resulted in at least one recommendation being issued for 70% of patients. 12% of patients have a reportable germline mutation. We have developed an integrated analytical pipeline to interrogate and cross-validate the full range of variants, structural abnormalities, and mutational signatures identified in pediatric cancers, and incorporate the molecular data with in vitro and in vivo drug sensitivity data where possible. The highest yield of reportable variants is derived from the integrated analysis of WGS and RNASeq. The most highly mutated genes/pathways include TP53, MAPK pathway, CDK/cyclin family, and PI3K/mTOR pathway. Mutation signatures and tumor mutation burden assessment support targeted treatment recommendations (e.g., PARP inhibitors or immunotherapy) and contribute to assessment of pathogenicity of some germline variants. Early experience with drug efficacy studies suggests these data may corroborate genomic therapeutic recommendations and may also identify unanticipated drug “vulnerabilities.” Of the first 21 patients who received an MTB-recommended therapy not usually used in the treatment of the respective tumors generally, 33% have a partial or complete response, 24% have stable disease, and 43% have progressive disease.
Conclusion: ZERO demonstrates the feasibility of a comprehensive precision medicine platform to identify treatment recommendations in high-risk pediatric cancer patients. ZERO is also partnering nationally and internationally to conduct parallel research studies in immunoprofiling, liquid biopsy, cancer predisposition, proteomics, health economics, health implementation, psychosocial impact of precision medicine, and improving access to molecularly targeted therapeutic clinical trials.
Citation Format: Paulette Barahona, Jamie Fletcher, Noemi Fuentes-Bolanos, Marie-Emilie Gauthier, Michelle Haber, Richard B. Lock, Glenn M. Marshall, Chelsea Mayoh, Emily Mould, Sumanth Nagabushan, Murray Norris, Tracey O’Brien, Alexandra Sherstyuk, David Thomas, Toby Trahair, Katherine Tucker, Meera Warby, Marie Wong, David S. Ziegler, Vanessa J. Tyrrell, Paul Ekert, Mark J. Cowley, Loretta Lau, Dong-Anh Khuong Quang, Zero Childhood Cancer Program National Consortium. Zero Childhood Cancer (ZERO): A comprehensive precision medicine platform for children with high-risk cancer abstract. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A52.
Abstract
Introduction: Zero Childhood Cancer’s National Precision Medicine for Children with Cancer Study (PRISM) utilizes novel technologies to guide individualized management of children with ...high-risk cancer (expected overall survival less than 30%). Germline DNA is utilized to distinguish cancer-specific somatic variants from constitutional variants or polymorphisms, allowing identification of clinically relevant germline mutations. The prevalence of cancer predisposition syndromes in pediatric cancer may range from 8.5% to as high as 33%. Method PRISM combines molecular genomic analysis (WGS and RNASeq) with in vitro high-throughput drug screening and patient-derived xenograft drug efficacy testing. A Molecular Tumour Board (MTB) of Oncology and Genetics professionals convenes to determine the significance of genomic analysis as curated by bioinformaticians, molecular scientists, and clinicians.
Results: Between September 2017 and June 2019, 218 children aged under 21 years have been recruited in PRISM (37% with central nervous system tumors, 47% with non-CNS solid tumors, and 16% with hematologic malignancies), and results are available for 208 after discussion at MTB meeting. Forty-two reportable germline variants were detected in 35 participants (detection rate: 16.8%), comprising 28 pathogenic and 14 likely pathogenic variants, across 22 cancer predisposition genes. The most frequently affected gene was CHEK2 (n=7), followed by SMARCB1 (n=5) and BRCA2 (n=3) and NF1 (3). In one out of three participants with germline mutations, somatic analysis revealed a double hit in the same gene altered in the germline. Distributions of participants with germline mutation per group were 16% of patients with CNS tumors (12/77), 19% of patients with non-CNS solid tumors (18/96), and 15% of patients with hematologic malignancies (5/34).
Conclusion: Germline mutation detection rate in cancer predisposition genes was higher than expected, 16.8%; however, it may result from selection bias (i.e., cohort of high-risk cancers). Although genomic sequencing has expanded our understanding of pediatric cancer predisposition and presented opportunities for genetics-mediated care, identifying underlying germline mutations with potential clinical implications remains a clinical challenge for pediatric oncologists.
Citation Format: Paulette Barahona, Alexandra Sherstyuk, Mark Cowley, Paul Ekert, Judy Kirk, Dong-Anh Khuong-Quang, Amit Kumar, Loretta Lau, Chelsea Mayoh, Glenn Marshall, Emily Moud, Tracey O’Brien, Mark Pinese, David Thomas, Vanessa Tyrell, David Ziegler, Michelle Haber, Katherine Tucker, Noemi Auxiliadora Fuentes-Bolanos, Meera Warby. Prevalence and spectrum of germline mutations in children with high-risk cancer abstract. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A03.
Abstract
Molecular genomics analyses aim to identify subsets of patients harboring actionable aberrations as a pathway to improved targeted treatment selection. However, recent pan-cancer analyses of ...the molecular landscape of pediatric cancers1,2 have emphasized the stark contrast with adult cancers, with low mutation rates, distinct mutated genes and a prevalence of structural rearrangements suggesting that genomic analyses alone have limitations for translation into clinical benefit. The Zero Childhood Cancer (ZCC) program aims to assess the feasibility of precision medicine to identify targeted therapeutic agents for patients with high-risk (HR) pediatric malignancies (expected survival <30%). We combine comprehensive molecular profiling analysis whole genome sequencing (tumor, germline DNA), deep sequencing of a 386 cancer associated gene panel, whole transcriptome (RNASeq), methylation profiling with in vitro high-throughput drug screening (124 compound library, single agent) and patient-derived xenograft (PDX) drug efficacy testing. Results are curated and recommendations made by a national Multidisciplinary Tumor Board. Recommendations consist of targeted therapy, change of diagnosis or genetics referral for a germline cancer predisposition gene mutation. The national multicenter prospective trial (PRISM) opened in September 2017 at all 8 pediatric oncology centers around Australia, following the successful completion of a 2-year pilot feasibility study. PRISM has enrolled 131 patients to date (35% central nervous system tumors, 29% sarcoma, 13% leukemias/lymphomas, 6% neuroblastoma, 17% other rare or unknown cancers). The unique ZCC testing platform has resulted in at least one recommendation being issued for 67% of patients. Fifteen % of patients have a reportable germline cancer predisposition. We have developed an analytical pipeline to interrogate and cross-validate the full range of variants, structural abnormalities and mutational signatures identified in pediatric cancers and incorporate the molecular data with in vitro and in vivo drug sensitivity data where possible. The highest yield of reportable variants is derived from the integrated analysis of WGS and RNASeq; unique to ZCC compared to other pediatric precision medicine programs internationally. ZCC demonstrates the feasibility of a comprehensive precision medicine platform to identify treatment recommendations in HR pediatric cancer patients. The national trial is planned to run for 3 years, recruiting ~400 patients. In addition, ZCC is partnering nationally and internationally to conduct parallel research studies in immunoprofiling, liquid biopsy, psychosocial impact of precision medicine, health economics and health implementation. 1. Gröbner et al. Nature. 2018; 555(7696):321-327. 2. Ma et al. Nature. 2018; 555(7696):371-376.
Citation Format: Emily V. Mould, Loretta Lau, Greg Arndt, Paulette Barahona, Mark J. Cowley, Paul Ekert, Tim Failes, Jamie Fletcher, Andrew Gifford, Dylan Grebert-Wade, Michelle Haber, Alvin Kamili, Amit Kumar, Richard B. Lock, Glenn M. Marshall, Chelsea Mayoh, Murray Norris, Tracey O'Brien, Dong Anh Khuong Quang, Patrick Strong, Alexandra Sherstyuk, Toby Trahair, Maria Tsoli, Katherine Tucker, Meera Warby, Marie Wong, Jinhan Xie, David S. Ziegler, Vanessa Tyrrell. Zero Childhood Cancer: A comprehensive precision medicine platform for children with high-risk cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3111.
Prompt recognition of a child with a cancer predisposition syndrome (CPS) has implications for cancer management, surveillance, genetic counseling, and cascade testing of relatives. Diagnosis of CPS ...requires practitioner expertise, access to genetic testing, and test result interpretation. This diagnostic process is not accessible in all institutions worldwide, leading to missed CPS diagnoses. Advances in electronic health technology can facilitate CPS risk assessment.
To evaluate the diagnostic accuracy of a CPS prediction tool (McGill Interactive Pediatric OncoGenetic Guidelines MIPOGG) in identifying children with cancer who have a low or high likelihood of having a CPS.
In this international, multicenter diagnostic accuracy study, 1071 pediatric (<19 years of age) oncology patients who had a confirmed CPS (12 oncology referral centers) or who underwent germline DNA sequencing through precision medicine programs (6 centers) from January 1, 2000, to July 31, 2020, were studied.
Exposures were MIPOGG application in patients with cancer and a confirmed CPS (diagnosed through routine clinical care; n = 413) in phase 1 and MIPOGG application in patients with cancer who underwent germline DNA sequencing (n = 658) in phase 2. Study phases did not overlap. Data analysts were blinded to genetic test results.
The performance of MIPOGG in CPS recognition was compared with that of routine clinical care, including identifying a CPS earlier than practitioners. The tool's test characteristics were calculated using next-generation germline DNA sequencing as the comparator.
In phase 1, a total of 413 patients with cancer (median age, 3.0 years; range, 0-18 years) and a confirmed CPS were identified. MIPOGG correctly recognized 410 of 412 patients (99.5%) as requiring referral for CPS evaluation at the time of primary cancer diagnosis. Nine patients diagnosed with a CPS by a practitioner after their second malignant tumor were detected by MIPOGG using information available at the time of the first cancer. In phase 2, of 658 children with cancer (median age, 6.6 years; range, 0-18.8 years) who underwent comprehensive germline DNA sequencing, 636 had sufficient information for MIPOGG application. When compared with germline DNA sequencing for CPS detection, the MIPOGG test characteristics for pediatric-onset CPSs were as follows: sensitivity, 90.7%; specificity, 60.5%; positive predictive value, 17.6%; and negative predictive value, 98.6%. Tumor DNA sequencing data confirmed the MIPOGG recommendation for CPS evaluation in 20 of 22 patients with established cancer-CPS associations.
In this diagnostic study, MIPOGG exhibited a favorable accuracy profile for CPS screening and reduced time to CPS recognition. These findings suggest that MIPOGG implementation could standardize and rationalize recommendations for CPS evaluation in children with cancer.
Abstract
Molecular genomics analyses aim to identify the subset of patients harbouring actionable mutations as a pathway to better targeted treatment selection. Low mutation rates and the paucity of ...clinical data linking targeted treatments with mutations in paediatric cancer suggests genomic analysis alone has limitations for translation into clinical benefit. The Zero Childhood Cancer program aims to assess the feasibility of a precision medicine platform to identify targeted therapeutic agents for high-risk (HR) paediatric malignancies (expected survival <30%). We combine molecular genomic analysis (WGS (tumour, germline DNA), deep sequencing of a panel of cancer associated genes, and whole transcriptome (RNASeq)) with in vitro high-throughput drug screening, and patient-derived xenograft (PDX) drug efficacy testing, followed by assessment of and recommendations made by a national Multidisciplinary Tumour Board (MTB). The Pilot Feasibility Study enrolled 59 patients from June 2015 to October 2017 with a range of tumour types (47% central nervous system tumours, 20% sarcoma, 12% leukaemia, 9% neuroblastoma, 12% other rare cancers). The median age was 9 years (range 1-21 years) and 49% of patients were enrolled at diagnosis and 51% at relapse. In 54 curated cases, the complete molecular platform identified reportable somatic SNVs, fusions, and CNVs in 56%, 24% and 39% of patients, respectively. 5 patients had a reportable germline cancer predisposition variant and in 3 patients, the genomic findings changed the primary diagnosis. Fresh tissue collection in 48 of cases resulted in successful in vitro high-throughput drug screening (112 compound library single agent) in 23 cases and 23 successful patient-derived xenograft model engraftments. Overall, 57% of patients received a personalised medicine recommendation (targeted therapy, change in diagnosis, germline mutation referral), and 10 patients with a therapy recommendation went on to receive the recommended therapy. The Zero Childhood Cancer Pilot demonstrates the likelihood that oncologists will more frequently use a recommendation to benefit individual patients on the clinical trial who have typically exhausted other therapeutic approaches. Now, a national multicentre prospective study of the feasibility and clinical value of identifying therapeutic targets and recommending personalised treatment for children and adolescents with high-risk cancer (PRISM) opened in late 2017 for Australians up to 21 years with HR cancer.
Citation Format: Emily Mould, Loretta Lau, Greg Arndt, Paulette Barahona, Mark Cowley, Paul Ekert, Tim Failes, Jamie Fletcher, Andrew Gifford, Michelle Haber, Alvin Kamili, Amit Kumar, Richard Lock, Glenn Marshall, Chelsea Mayoh, Scott Mead, Murray Norris, Tracey O'Brien, Mark Pinese, Dong Anh Khuong Quang, Toby Trahair, Maria Tsoli, Katherine Tucker, Meera Warby, Marie Wong, Jinhan Xie, David Ziegler, Vanessa Tyrrell. Zero Childhood Cancer: A comprehensive precision medicine platform for children with high-risk cancer abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-138.
Abstract
Despite the increase in overall child cancer survival rates, pediatric malignancies such as high-risk neuroblastoma, high-risk leukemias (including MLL-translocated infant ALL), and ...aggressive brain tumors (including DIPG) remain refractory to current multimodal therapies. We have been developing new treatment approaches for these aggressive childhood cancers by (i) utilizing novel targeted therapies either alone or combined with other new agents or established chemotherapeutic drugs, and (ii) by developing new drugs that target key pathways in these child cancers.
In neuroblastoma, we have targeted polyamines, showing that combined inhibition of polyamine synthesis by the ODC1 inhibitor DFMO, and of polyamine uptake using the small-molecule drug AMXT 1501, is highly effective at inhibiting tumor growth in Th-MYCN transgenic mice. This combination also shows great efficacy in preclinical models of DIPG, and clinical trials for these diseases are now being planned. We are also targeting metabolism of arginine, the precursor of ornithine, using the pegylated-recombinant arginase BCT-100, which significantly delays tumor development and prolongs survival of neuroblastoma-prone Th-MYCN mice. We have further shown that combining BCT-100 with either DFMO or conventional chemotherapy results in increased survival benefit.
CBL0137 is a nontoxic novel anticancer drug currently in phase I trial for adult refractory and relapsed cancers. CBL0137 destabilizes nucleosomes and traps histone chaperone FACT into chromatin, thereby modulating several anticancer mechanisms. We have shown that CBL0137 is effective in mouse models of neuroblastoma, MLL-rearranged leukemia, and DIPG, and that its action is potentiated by the HDAC inhibitor, panobinostat. Moreover, we have developed OT-82, a novel nontoxic NAMPT inhibitor with impressive anticancer activity against mouse models of high-risk childhood ALL, potentiating standard-of-care drugs, and showing similar efficacy as the three-drug induction-type treatment used for pediatric ALL.
In addition, for all Australian children with high-risk malignancies, we have developed the Zero Childhood Cancer national precision medicine program. ZERO utilizes whole-genome and whole-transcriptome sequencing, methylation profiling, and where possible, in vitro and in vivo drug testing. To date (July 2019), 74% of 207 patients on the national clinical trial have received a Multidisciplinary Tumor Board recommendation (therapy, germline referral, or change of diagnosis), and of 25 patients with evaluable response data thus far who have received the ZERO recommended therapy, a significant proportion have had a complete response, partial response, or maintained stable disease. Moreover, early experience with drug efficacy studies suggests these data may corroborate genomic therapeutic recommendations and may also identify unanticipated active therapeutics.
Citation Format: Michelle Haber, Laura Gamble, Lin Xiao, Ruby Pandher, Klaartje Somers, Jayne Murray, Aaminah Khan, Denise Yu, Laura Franshaw, Mark R. Burns, Maria Tsoli, Anahid Ehteda, Anthony Cesare, Aisling O’Connor, Francis Mussai, Carmela de Santo, Paul Cheng, Lioubov Korotchkina, Katerina Gurova, Vanessa Tyrrell, Emily Mould, Loretta Lau, Dong Anh Khuong Quang, Chelsea Mayoh, Greg Arndt, Paulette Barahona, Tim Failes, Jamie Fletcher, Noemi Fuentes- Bolanos, Marie-Emilie Gauthier, Andrew Gifford, Dylan Grebert-Wade, Alvin Kamili, Amit Kumar, Sumanth Nagabushan, Tracey O’Brien, Patrick Strong, Alexandra Sherstyuk, David Thomas, Toby Trahair, Katherine Tucker, Meera Warby, Marie Wong, Jinhan Xie, Kathryn Evans, Richard Lock, Olga B. Chernova, Michelle Henderson, Andrei V Gudkov, Paul Ekert, Mark J. Cowley, Glenn M. Marshall, David S. Ziegler, Murray D. Norris. Molecular targeted therapies and precision medicine for children with neuroblastoma and other refractory malignancies abstract. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr IA13.
Estimates of the number of childhood cancers with a genetic basis range from 5–8.5% found in germline samples to 29% based on clinical criteria. Family history-taking practice is a fundamental first ...step in detecting at risk individuals and families. This study focused on Li-Fraumeni Syndrome (LFS), a highly penetrant cancer syndrome. Reported family history in a cohort of 648 of cancer survivor cohort (CCS) was examined. Eligible CCS were: (i) aged up to 14 years at diagnosis; (ii) more than 5 years postdiagnosis; (iii) treated for a childhood cancer at the study hospitals in NSW, Australia; (iv) in remission for more than 3 years. CCS completed self-administered questionnaires. Medical records confirmed diagnosis and treatment-related information. Our findings reveal an increased cancer risk among sibling and relatives of CCS. 91% of siblings diagnosed with cancer were diagnosed under the age of 40 and about 30% diagnosed under the aged of 15 revealing a 5- (RR = 5.1; 95% CI, 3.3–7.9) and 44-fold (RR = 44.6; 95% CI, 18.4–108.3) increased risked of cancer compared with the Australian population, respectively. About 2% of CCS reported that they had been diagnosed with a genetic cancer syndrome. However, 11% of survivors described a family history pattern which met Chompret criteria for screening for TP53 mutations associated with LFS. Our data suggests that familial cancer predispositions may be initially overlooked. Aperiodic and accurate ascertainment of family cancer history of childhood cancer patients and survivors is therefore recommended.
Malignant gastrointestinal neuroectodermal tumour (GNET) is a recently characterised rare and aggressive tumour that typically arises in association with the small intestine of adults. We present a ...novel case of this entity and expand the spectrum of its reported morphological features. The patient was a 5-year-old female, the youngest reported patient affected by the condition, and presented with extra-abdominal disease. The histopathological features included the presence of a junctional component of the palatal tumour, which mimicked mucosal melanoma, a feature that has not been previously reported in GNET. Whole genome and RNA sequencing was performed that demonstrated the EWSR1-ATF1 translocation characteristic of GNET. Knowledge of this entity and its features, together with careful morphological assessment supplemented by judicious immunohistochemical and molecular studies should enable the correct diagnosis to be established.
Abstract
Brain tumours represent the most common solid tumour of childhood and result in significant morbidity and mortality. The Zero Childhood Cancer national child precision medicine program aims ...to identify targeted therapeutic agents for high-risk paediatric malignancies (expected survival <30%) including brain tumours. Here we will report on the Pilot Feasibility Study (TARGET) and the initial experience of the National Clinical Trial (PRISM), which opened in September of 2017. A total of 200 patients have been enrolled, 59 in the pilot phase (TARGET) and 141 in the National study (PRISM) out of which 77 patients (38.5%) had CNS malignancies, of which 64 cases have completed curation. Molecular analysis of these cases identified actionable molecular aberrations in 47 patients (73.4%). Ten cases (15.6%) had a reportable germline cancer predisposition variant. Overall, the most common aberrant genetic changes observed include TP53 mutations, CDKN2A/B biallelic loss, PDGFRA over-expression mainly in the presence of amplification, and fusions containing either NTRK or BRAF. In 2 cases, the somatic genomic findings changed the primary diagnosis. Fresh tissue collection permitted in vitro high throughput screening (HTS) (120 single agents) in 32/69 (46.3%) of cases with additional cultures currently under development. Hits were identified in 2 cultures and recommendations were made. Four PDX models from successful primary cultures were established where single and combination drug efficacy studies have been performed based on recommendations made from molecular profiling or HTS analysis. Currently multiple PDX models are under evaluation either from successful primary cultures or direct intracranial injection of biopsies. In this study we will present an overview of the molecular and preclinical platforms and their impact on the management of paediatric patients with aggressive brain tumours.
Genetic testing is becoming increasingly available for adolescents who are undergoing cancer treatment or at risk of cancer predisposition syndromes. With this narrative review, we aimed to ...synthesize the evidence on psychosocial outcomes and adolescents' understanding of genetic testing-thus far, an underresearched topic. Both psychological benefits and harms of predictive testing were reported in adolescents from high-risk families. Harms were mainly related to cancer-specific distress and increased worries. Findings on genetic understanding were sparse. Future studies should focus on psychosocial outcomes and adolescents' understanding undergoing genetic testing and enabling access to genetic counseling pre-testing and post-testing.
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