ORCID Profile
0000-0002-3172-0970
Current Organisations
Sydney Children's Hospital Randwick
,
Children's Cancer Institute Australia
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 04-2004
DOI: 10.1097/00043426-200404000-00003
Abstract: Despite advances in multimodal therapy for neuroblastoma, survival from advanced disease remains poor. Children are now offered a wide variety of salvage regimens following relapse. A retrospective review was performed on 31 patients with recurrent neuroblastoma treated at one institution between 1995 and 2001. At initial diagnosis, 27 patients had metastatic disease and 11 had N-myc lification (NMA). The median time to recurrence from diagnosis was 16.1 months. Seventeen patients received salvage therapy, with a median of three salvage regimens per patient. The median survival time from relapse was 8.4 months. The median survival time was significantly shorter for recurrence less than 6 months after stem cell transplantation (2.9 vs. 13.3 months P = 0.003) and for patients with NMA (2.7 vs. 15.1 months P < 0.0001). Overall, salvage therapy led to a significantly longer median survival time (22.4 vs. 3.3 months P = 0.0003) however, salvage therapy extended the median survival time only from 2.2 to 3.2 months for patients with NMA and from 0.7 to 5.8 months for patients with early relapse after stem cell transplantation. Multiple salvage regimens prolong survival significantly, especially for patients with no NMA and for relapses more than 6 months after stem cell transplantation, but the long-term disease-free survival after recurrent disease remains dismal.
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Publisher: Oxford University Press (OUP)
Date: 24-08-2012
DOI: 10.1093/NAR/GKS781
Publisher: Wiley
Date: 27-06-2023
DOI: 10.1002/CNCR.34914
Abstract: Precision medicine is projected to become integral to childhood cancer care. As such, it is essential to support families to understand what precision medicine entails. A total of 182 parents and 23 adolescent patients participating in Precision Medicine for Children with Cancer (PRISM), an Australian precision medicine clinical trial for high‐risk childhood cancer, completed questionnaires after study enrollment (time 0 [T0]). Of the parents, 108 completed a questionnaire and 45 completed an interview following return of precision medicine results (time 1 [T1]). We analyzed the mixed‐methods data comprising measures exploring families’ perceptions and understanding of PRISM’s participant information sheet and consent form (PISCF), and factors associated with understanding. Most parents were satisfied with the PISCF, rating it as at least “somewhat” clearly presented ( n = 160/175 91%) and informative ( n = 158/175 90%). Many suggested improvements including the use of clearer language and a more visually engaging format. Parents’ actual understanding of precision medicine was low on average, but scores improved between T0 and T1 (55.8/100‐60.0/100 p = .012). Parents from culturally and/or linguistically erse backgrounds ( n = 42/177 25%) had lower actual understanding scores than those from a Western/European background whose first language was English ( p = .010). There was little correlation between parents’ perceived and actual understanding scores ( p = .794 Pearson correlation –0.020 95% CI, –0.169 to 0.116). Most adolescent patients read the PISCF either “briefly” or “not at all” (70%) and had a perceived understanding score of 63.6/100 on average. Our study revealed gaps in families’ understanding of childhood cancer precision medicine. We highlighted areas for potential intervention such as through targeted information resources. Precision medicine is projected to become part of the standard of care for children with cancer. Precision medicine aims to give the right treatment to the right patient and involves several complex techniques, many of which may be challenging to understand. Our study analyzed questionnaire and interview data from parents and adolescent patients enrolled in an Australian precision medicine trial. Findings revealed gaps in families’ understanding of childhood cancer precision medicine. Drawing on parents’ suggestions and the literature, we make brief recommendations about improving information provision to families, such as through targeted information resources.
Publisher: American Association for Cancer Research (AACR)
Date: 07-2018
DOI: 10.1158/1538-7445.AM2018-LB-137
Abstract: Brain tumors represent the most common solid tumors in childhood and account for significant morbidity and mortality. The lack of advances in treatment of the brain tumors is hindered by our lack of knowledge about the molecular pathogenesis of these malignancies as well as the availability of brain-permeable therapies. Personalised medicine approaches have the potential to enhance diagnostic, prognostic and / or therapeutic information. The TARGET study is a feasibility pilot study which focused on the development of genomic platforms, high throughput drug screening (HTS), and PDX models in order to identify personalised therapies for patients with aggressive pediatric tumors. In the pilot phase 59 patients were enrolled of which 28 were brain tumor patients (47%). In 28 curated cases molecular analysis identified a reportable somatic anomaly (SNVs, gene fusions, CNVs) in 82% (23/28), of which 78% (18/23) had actionable molecular aberrations. Four cases had a reportable germline predisposition variant and in 1 case, the genomic findings changed the primary diagnosis. Fresh tissue collection permitted in vitro HTS (112 single agents) in 58% of cases to date. Four PDX models have been established with additional 8 currently still being evaluated. This feasibility study demonstrates that an integrated approach based on genomic, in vitro and in vivo drug efficacy testing may be useful to guide the management of aggressive pediatric brain tumors. Citation Format: Maria Tsoli, Carol Wadham, Mark Pinese, Tim Failes, Swapna Joshi, Emily Mould, Julia Yin, Velimir Gayevski, Amit Kumar, Warren Kaplan, Paul Ekert, Laura Franshaw, Andrew Gifford, Martin Weber, Michael Rodriguez, Chelsea Mayoh, Richard Cohn, Greg Arndt, Richard Lock, Vanessa Tyrrell, Murray Norris, Michelle Haber, Loretta Lau, Dong Anh Khuong Quang, Marie Wong, Toby Trahair, Glenn M. Marshall, Mark J. Cowley, David S. Ziegler. Integrated genomics: drug screening and personalized xenograft development approach to identify precision treatments for aggressive pediatric brain tumors [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 (13 Suppl):Abstract nr LB-137.
Publisher: American Association for Cancer Research (AACR)
Date: 07-2018
DOI: 10.1158/1538-7445.AM2018-LB-138
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 & %). 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 in idual 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 (13 Suppl):Abstract nr LB-138.
Publisher: Springer Science and Business Media LLC
Date: 05-2002
Abstract: For children with AML in CR1, the major consolidation therapies are BMT, ABMT and intensive chemotherapy. The relative effectiveness of these strategies is still debated. We conducted a systematic review and meta-analysis of trials to determine the effectiveness of BMT and ABMT in CR1 in paediatric AML. Eligible studies enrolled patients <21 years from 1985 to 2000 with AML in CR1. Two groups of studies were identified: (1) Those comparing the outcome of patients with and without a histocompatible family donor and (2) Randomised controlled trials (RCT) comparing ABMT with non-myeloablative chemotherapy. The relative risk statistic was calculated for outcomes of interest in each trial. If there was no excessive heterogeneity between trials the results were pooled, and an overall relative risk and risk difference for treatment effect across trials were calculated. Results of the analysis showed that allocation to BMT reduced risk of relapse and improved disease-free and overall survival. For ABMT, heterogeneity of effect between RCTs prevented pooling of results. In conclusion, BMT from a histocompatible family donor improves patient outcome. Data are insufficient to determine whether this is true for all subgroups of AML, and whether ABMT is superior to non-myeloablative chemotherapy. An in idual patient data meta-analysis is required to further evaluate the available data.
Publisher: MDPI AG
Date: 26-10-2021
Abstract: C-Circles, self-primed telomeric C-strand templates for rolling circle lification, are the only known alternative-lengthening-of-telomeres (ALT)-specific molecule. However, little is known about the biology of C-Circles and if they may be clinically useful. Here we show that C-Circles are secreted by ALT+ cancer cells inside exosomes, and that a blood-based C-Circle Assay (CCA) can provide an accurate diagnostic for ALT activity. Extracellular vesicles were isolated by differential centrifugation from the growth media of lung adenocarcinoma, glioblastoma, neuroblastoma, osteosarcoma, and soft tissue sarcoma cell lines, and C-Circles were detected in the exosome fraction from all eleven ALT+ cancer cell lines and not in any extracellular fraction from the eight matching telomerase positive cancer cell lines or the normal fibroblast strain. The existence of C-Circles in ALT+ exosomes was confirmed with exosomes isolated by iodixanol gradient separation and CD81-immunoprecipitation, and C-Circles in the exosomes were protected from nucleases. On average, 0.4% of the total ALT+ intracellular C-Circles were secreted in the exosomes every 24 h. Comparing the serum-based and tumor-based CCAs in 35 high risk neuroblastoma patients ided randomly into ALT+ threshold derivation and validation groups, we found the serum-based CCA to have 100% sensitivity (6/6), 70% specificity (7/10), and 81% concordance (13/16). We conclude that the secretion of C-Circles by ALT+ cancer cells in the exosomes provides a stable blood-based biomarker and a potential clinical diagnostic for ALT activity.
Publisher: American Society of Hematology
Date: 03-12-2015
DOI: 10.1182/BLOOD.V126.23.5445.5445
Abstract: Introduction Telomeres are specialized DNA structures found at the end of linear chromosomes. In humans, they contain the repetitive sequence (TTAGGG)nalong with its complementary strand and associated proteins. With each cell ision, the telomere shortens due to incomplete replication of the lagging strand, a phenomenon known as the end replication problem. Oxidative damage, as well as the action of nucleases also leads to telomere attrition. Once the telomere reaches a critically short length, cells enter senescence or apoptosis. In the general population, telomere length (TL) varies greatly, and is seen to decline with age. Patients with Dyskeratosis Congenita (DC) have inherently short telomeres, which leads to multiple organ dysfunction. These patients suffer increased organ toxicity when given standard myeloablative conditioning regimens during hematopoietic stem cell transplantation (HSCT). This is most likely due to the reduced ability of their cells to replicate and recover following cytotoxic treatment. It is not known whether patients without DC, who have telomere lengths at the lower end of the normal spectrum also suffer increased rates of toxicity. Thus we undertook a retrospective analysis to determine if there was an association between short TL and increased transplant-related mortality (TRM) following HSCT in children. Method Medical records of patients who underwent allogeneic HSCT at the Children's Hospital at Westmead (Sydney, Australia) between 2002 to 2013 were examined and demographic, prior treatment, transplant, toxicity and transplant information was extracted. The primary outcome measured was TRM, while overall survival, relapse and graft versus host disease (GVHD) being secondary outcomes of interest. Stored DNA, extracted from bone marrow, taken within 3 months prior to HSCT was used for telomere length testing, as a surrogate marker for TL in other tissues in the body. Quantitative PCR was carried out to determine relative telomere length, which was converted to an age adjusted TL (AATL) by subtracting the expected relative TL (i.e. 50th percentile for age of the patient) from the measured relative TL, so that patients of all ages could be analyzed together. Results Between 2002 and 2013, there were 121 patients who underwent allogeneic HSCT at our institution. Of these, 78 had DNA stored, with appropriate consent and ethics approval to be used in our study. Most children were undergoing HSCT for hematological malignancies (acute lymphoblastic leukemia 52%, acute myeloid leukemia 39%), with 55% having relapse or refractory disease. Matched sibling donors made up 46% of cases. At a median follow up of 3.2 years, 64% of patients remained alive. The single leading cause of death was relapse (48%) with 52% of deaths attributable to transplant-related causes. The median AATL for the entire cohort was -0.21 (range -0.61-0.28). Telomere length was not associated with relapse or refractory disease. There was no correlation between AATL and specific organ toxicity, relapse or overall survival. When the cohort was ided into 2 groups based on AATL, there was a trend (p=0.055) towards increased TRM in patients who had AATL below the median for the cohort (Figure 1). Multivariate analysis adjusting for age at transplant, CMV status, disease status and HLA matching showed a reduced risk (HR 0.33 p value 0.072) of TRM in patients with AATL above the median for the cohort. Conclusion AATL was shorter in patients pre-HSCT compared with age matched controls. There was a trend towards increased TRM in patients with shorter telomere length, however most likely due to small s le size, this did not achieve significance. If extended to a larger cohort of patients, TL may prove to be a significant marker for children at increased risk of TRM prior to HSCT. This could influence the choice to use less myeloablative conditioning in these patients. Support: NHMRC GNT1056667 No relevant conflicts of interest to declare.
Publisher: Cold Spring Harbor Laboratory
Date: 03-11-2020
DOI: 10.1101/MCS.A005710
Abstract: The identification of rearrangements driving expression of neurotrophic receptor tyrosine kinase ( NTRK ) family kinases in tumors has become critically important because of the availability of effective, specific inhibitor drugs. Whole-genome sequencing (WGS) combined with RNA sequencing (RNA-seq) can identify novel and recurrent expressed fusions. Here we describe three SPECC1L–NTRK fusions identified in two pediatric central nervous system cancers and an extracranial solid tumor using WGS and RNA-seq. These fusions arose either through a simple balanced rearrangement or in the context of a complex chromoplexy event. We cloned the SPECC1L–NTRK2 fusion directly from a patient s le and showed that enforced expression of this fusion is sufficient to promote cytokine-independent survival and proliferation. Cells transformed by SPECC1L–NTRK2 expression are sensitive to a TRK inhibitor drug. We report here that SPECC1L–NTRK fusions can arise in a range of pediatric cancers. Although WGS and RNA-seq are not required to detect NTRK fusions, these techniques may be of benefit when NTRK fusions are not suspected on clinical grounds or not identified by other methods.
Publisher: American Association for Cancer Research (AACR)
Date: 15-08-2023
DOI: 10.1158/0008-5472.23952251
Abstract: Supplementary Figures
Publisher: Springer Science and Business Media LLC
Date: 12-02-2021
DOI: 10.1038/S41698-021-00145-8
Abstract: The prognosis of recurrent malignant peripheral nerve sheath tumors (MPNST) is dismal, with surgical resection being the only definitive salvage therapy. Treatment with chemoradiation approaches has not significantly improved patient outcomes. Similarly, trials of therapies targeting MPNST genomic drivers have thus far been unsuccessful. Improved understanding of the molecular pathogenesis of MPNST indicates frequent activation of the mitogen-activated protein kinase (MAPK) cell signaling pathway. MEK inhibitors have shown activity in preclinical studies however, their clinical efficacy has not been reported to date. We describe here a case of sustained complete response to MEK inhibition in an adolescent patient with a recurrent metastatic MPNST with multiple alterations in the MAPK pathway, guided by a precision oncology approach.
Publisher: Oxford University Press (OUP)
Date: 2022
Abstract: Changes in telomere length have been observed in cancer and can be indicative of mechanisms involved in carcinogenesis. Most methods used to estimate telomere length require laboratory analysis of DNA s les. Here, we present qmotif, a fast and easy tool that determines telomeric repeat sequences content as an estimate of telomere length directly from whole-genome sequencing. qmotif shows similar results to quantitative PCR, the standard method for high-throughput clinical telomere length quantification. qmotif output correlates strongly with the output of other tools for determining telomere sequence content, TelSeq and TelomereHunter, but can run in a fraction of the time—usually under a minute. qmotif is implemented in Java and source code is available at github.com/AdamaJava/adamajava, with instructions on how to build and use the application available from adamajava.readthedocs.io/en/latest/. Supplementary data are available at Bioinformatics Advances online.
Publisher: Research Square Platform LLC
Date: 03-10-2023
Publisher: Springer Science and Business Media LLC
Date: 27-09-2017
DOI: 10.1038/NATURE24026
Abstract: This corrects the article DOI: 10.1038/nature21063.
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Publisher: Elsevier BV
Date: 06-2017
DOI: 10.1016/J.CELREP.2017.05.087
Abstract: Acquisition of replicative immortality is currently regarded as essential for malignant transformation. This is achieved by activating a telomere lengthening mechanism (TLM), either telomerase or alternative lengthening of telomeres, to counter normal telomere attrition. However, a substantial proportion of some cancer types, including glioblastomas, liposarcomas, retinoblastomas, and osteosarcomas, are reportedly TLM-negative. As serial s les of human tumors cannot usually be obtained to monitor telomere length changes, it has previously been impossible to determine whether tumors are truly TLM-deficient, there is a previously unrecognized TLM, or the assay results are false-negative. Here, we show that a subset of high-risk neuroblastomas (with ∼50% 5-year mortality) lacked significant TLM activity. Cancer cells derived from these highly aggressive tumors initially had long telomeres and proliferated for >200 population doublings with ever-shorter telomeres. This indicates that prevention of telomere shortening is not always required for oncogenesis, which has implications for inhibiting TLMs for cancer therapy.
Publisher: Wiley
Date: 2006
DOI: 10.1002/PBC.20479
Abstract: To evaluate the clinical course and outcome of infants with Langerhans cell histiocytosis (LCH) involving skin and to estimate the incidence of progression to multi-system (M-S) disease in those with isolated skin involvement. A retrospective review was conducted on 22 LCH patients who were younger than 12 months at the onset of their skin eruption. Twelve patients had isolated skin involvement at diagnosis and 10 were evaluable for progression. Four of the 10 (40%) evaluable patients progressed to multi-system (M-S) disease. Of the 10 patients with M-S disease at diagnosis, 5 had a history of a preceding skin eruption 2 to 13 months prior to diagnosis. Eleven of the 14 (79%) patients with M-S disease had risk organ involvement. The mortality rate of M-S disease was 50%. It is important for primary caregivers to recognize that isolated cutaneous LCH in infants is not always a benign disorder. The diagnosis of self-healing cutaneous LCH should only be made in retrospect. Careful, albeit non-invasive, follow-up is recommended to monitor for disease progression and development of long-term complications.
Publisher: Springer Science and Business Media LLC
Date: 03-05-2014
DOI: 10.1007/S11060-014-1456-8
Abstract: Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere length maintenance mechanism that enables the unlimited proliferation of a subset of cancer cells. Some neuroblastoma (NB) tumors appear to maintain telomere length by activating ALT. Of 40 NB cell lines, we identified four potential ALT cell lines (CHLA-90, SK-N-FI, LA-N-6, and COG-N-291) that were telomerase-negative and had long telomeres (a feature of ALT cells). All four cell lines lacked MYCN lification and were p53 non-functional upon irradiation. Two of these cell lines (CHLA-90 and SK-N-FI) were positive for C-circles (telomeric DNA circles) and ALT-associated promyelocytic leukemia nuclear bodies, both of which are phenotypic characteristics of ALT. Mutation of ATRX (associated with ALT in tumors) was only found in CHLA-90. Thus, the ALT phenotype in NB may not be limited to tumors with ATRX mutations but is associated with a lack of MYCN lification and alterations in the p53 pathway.
Publisher: Informa UK Limited
Date: 2002
DOI: 10.1080/08880010252825669
Abstract: Between 1985 and 1999, 128 children with neuroblastoma were treated at the Royal Alexandra Hospital for Children. The objective of this retrospective study was to report on a single institution's experience with neuroblastoma and to evaluate clinical and biological prognostic factors using univariate and multivariate assessment. Fifty-two percent presented with localized disease, 41% had stage IV disease, and 7% had stage IVs disease. The 5-year overall survival rate was 65%. Significant prognostic factors in univariate analysis included stage, site, histology, N-myc lification, neuron-specific enolase (NSE), lactate dehydrogenase (LDH), and urinary dopamine. In multivariate assessment, the adjusted hazard ratio was 3.5 (95 %CI 1.4-8.5) for N-myc lification, 8.7 (95% CI 3.0-25) for NSE > 300 ng/mL, and 3.6 (95% CI 1.3-10) for-LDH > 3000 U/L. This study confirmed that survival was heavily influenced by closely interrelated clinical and biological factors. Prospective studies including more recently identified molecular prognostic factors are warranted to predict the biological heterogeneity of neuroblastoma.
Publisher: Wiley
Date: 09-01-2008
DOI: 10.1002/PBC.21322
Abstract: The skeleton is the most frequently involved organ in Langerhans cell histiocytosis (LCH) in children, and bone LCH generally has an excellent long-term survival. Although permanent consequences (PC) are described in half of the survivors thus raising concerns for quality of life (QOL), the impact on quality of life has not been formally studied. A retrospective review was performed on 124 LCH patients with skeletal involvement, followed by prospective evaluation of PC and health-related QOL using age-appropriate validated study tools (PedsQL or SF-36). Of the 116 survivors, PC were found in 34 (29%) patients, of whom 8 had more than 1 PC. PC were significantly more frequent in multi-system (M-S) than in single system (S-S) LCH (73% vs. 17% P < 0.0001). While diabetes insipidus (65%) was the most common PC in M-S LCH, cosmetic and orthopedic problems made up the majority of PC in S-S LCH. The median follow-up time was 8.5 years. 27 patients completed the PedsQL survey and 22 the SF-36 survey. The QOL scores for LCH patients were not significantly different from healthy children in the PedsQL survey and from young adults in the SF-36 survey. In addition, the QOL scores were very similar between patients with and without PC and between patients with M-S and S-S LCH. Children with M-S LCH had a significantly higher risk of developing PC. Skeletal LCH did not adversely affect the quality of life of survivors, including those with PC who appeared to adapt to their disabilities and medical problems.
Publisher: Springer Science and Business Media LLC
Date: 28-08-2020
DOI: 10.1038/S41467-020-17359-2
Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.
Publisher: Springer Science and Business Media LLC
Date: 19-09-2023
Publisher: Elsevier BV
Date: 02-2017
DOI: 10.1016/J.YMETH.2016.08.016
Abstract: The C-Circle Assay has satisfied the need for a rapid, robust and quantitative ALT assay that responds quickly to changes in ALT activity. The C-Circle Assay involves (i) extraction or simple preparation (Quick C-Circle Preparation) of the cell's DNA, which includes C-Circles (ii) lification of the self-primed C-Circles with a rolling circle lification reaction and (iii) sequence specific detection of the lification products by native telomeric DNA dot blot or telomeric qPCR. Here we detail the protocols and considerations required to perform the C-Circle Assay and its controls, which include exonuclease removal of linear telomeric DNA, production of the synthetic C-Circle C96 and modulation of ALT activity by γ-irradiation.
Publisher: Wiley
Date: 27-05-2021
DOI: 10.1002/CNCY.22448
Abstract: The development of high‐throughput drug screening (HTS) using primary cultures provides a promising, clinically translatable approach to tailoring treatment strategies for patients with cancer. However, this has been challenging for solid tumors because of often limited amounts of tissue available. In most cases, in vitro expansion is required before HTS, which may lead to overgrowth and contamination by non‐neoplastic cells. In this study, hematoxylin and eosin staining and immunohistochemical staining were performed on 129 cytopathology cases from 95 patients. These cytopathology cases comprised cell block preparations derived from primary tumor specimens or patient‐derived xenografts as part of a pediatric precision oncology trial. Cytopathology cases were compared with the morphology and immunohistochemical staining profile of the original tumor. Cases were reported as tumor cells present , equivocal , or tumor cells absent . The HTS results from cytopathologically validated cultures were incorporated into a multidisciplinary tumor board report issued to the treating clinician to guide clinical decision making. On cytopathologic examination, tumor cells were present in 77 of 129 cases (60%) and were absent in 38 of 129 cases (29%), whereas 14 of 129 cases (11%) were equivocal. Cultures that contained tumor cells resembled the tumors from which they were derived. Cytopathologic examination of tumor cell block preparations is feasible and provides detailed morphologic characterization. Cytopathologic examination is essential for ensuring that s les submitted for HTS contain representative tumor cells and that in vitro drug sensitivity data are clinically translatable.
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.PATHOL.2018.07.002
Abstract: 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.
Publisher: Springer Science and Business Media LLC
Date: 09-2018
Publisher: Springer Science and Business Media LLC
Date: 05-2017
DOI: 10.1038/NATURE22071
Abstract: Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. Here we report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. However, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequences was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. Most melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals erse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.
Publisher: Cold Spring Harbor Laboratory
Date: 21-07-2023
DOI: 10.1101/2023.07.19.548825
Abstract: No targeted agents are approved for pediatric sarcomas. Tyrosine kinase (TK) inhibitors represent attractive therapeutic candidates, however, beyond rare TK-activating fusions or mutations, predictive biomarkers are lacking. RNA overexpression of TKs is more commonly observed in pediatric sarcomas, however, an unresolved question is when upregulated TK expression is associated with kinase activation and signaling dependence. We explored the TK molecular landscape of 107 sarcoma patients from the ZERO Childhood Cancer precision medicine program using whole genomic and transcriptomic sequencing. Phosphoproteomic analyses of tyrosine phosphorylation (pY) and functional in vitro and in vivo assays were also performed in cell lines and patient-derived xenografts (PDXs). Our integrated analysis shows that although novel genomic driver lesions are rare, they are present and therapeutically actionable in selected patients as exemplified by a novel LSM1-FGFR1 fusion identified in an osteosarcoma patient. We further show that in certain contexts, TK expression data can be used to indicate TK pathway activity and predict TK-inhibitor sensitivity. We exemplify the utility of FGFR-inhibitors in PAX3-FOXO1 fusion-positive rhabdomyosarcomas (FP-RMS) mediated by high FGFR4 and FGF8 RNA expression levels, and overt activation of FGFR4 (FGFR4_pY). We demonstrate marked tumor growth inhibition in all FP-RMS PDXs treated with single agent FGF401 (FGFR4-specific inhibitor) and single agent lenvatinib (multi-kinase FGFR-inhibitor). Clinical benefit of lenvatinib in a relapsed metastatic FP-RMS patient further exemplifies that FGFR-inhibitors deserve additional investigation in FP-RMS patients. Our multi-omic interrogation of sarcomas in the ZERO Childhood Cancer program illustrates how an RNA-expression biomarker signature ( FGFR4+/FGF8+ ) in association with FGFR4 activation identifies that PAX3-FOXO1 -positive rhabdomyosarcoma patients could benefit from FGFR-inhibitors.
Publisher: American Association for Cancer Research (AACR)
Date: 15-01-2005
DOI: 10.1158/1078-0432.672.11.2
Abstract: Purpose: To determine the dose-limiting toxicity (DLT) and the maximum tolerated dose of ecteinascidin-743 (ET-743, Yondelis) in children with refractory solid tumors, to establish the recommended dose for pediatric phase II trials, and to characterize the pharmacokinetics of ET-743 in children. Experimental Design: ET-743 was administered as a 3-hour i.v. infusion every 21 days. The starting dose was 1,100 μg/m2 with planned dose escalation of 200 μg/m2 increments. Pharmacokinetic s ling was done during the first treatment course. Results: Twelve evaluable patients received a total of 29 courses. One grade 4 DLT (prolonged grade 4 neutropenia) was noted at the first dose level. At the second dose level (1,300 μg/m2), there were two DLTs (reversible grade 4 elevations of hepatic transaminase) hence the maximum tolerated dose was defined as 1,100 μg/m2. Overall, reversible hepatic toxicity, manifested as grade 3 or 4 elevations in hepatic transaminase, occurred in more than 50% of the patients. No grade 3 or 4 thrombocytopenia was reported at either dose level and only one episode of isolated creatine phosphokinase grade 4 elevation was observed. One complete response was documented after six courses in a patient with metastatic Ewing sarcoma. The pharmacokinetics of ET-743 in 8 children was characterized by a terminal disposition phase with a mean half-life of 43.8 ± 18.4 hours, a total body clearance of 28.2 ± 10.5 L/h/m2, and a 959 ± 807 L/m2 steady-state apparent volume of distribution. Conclusion: ET-743 is safe. The phase II recommended dose of ET-743 administered as a 3-hour i.v. infusion following premedication with dexamethasone is 1,100 μg/m2.
Publisher: EMBO
Date: 20-12-2022
Publisher: Springer Science and Business Media LLC
Date: 08-12-2021
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.24000210
Abstract: Supplementary Figures
Publisher: American Association for Cancer Research (AACR)
Date: 15-07-2020
DOI: 10.1158/1538-7445.PEDCA19-A03
Abstract: Introduction: Zero Childhood Cancer’s National Precision Medicine for Children with Cancer Study (PRISM) utilizes novel technologies to guide in idualized 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 (14 Suppl):Abstract nr A03.
Publisher: Springer Science and Business Media LLC
Date: 21-09-2020
DOI: 10.1038/S41467-020-18151-Y
Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA s les, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological ergences between two reproducible somatic variant detection efforts.
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.24000213
Abstract: Supplementary Figures 1-7 and Figure Legends
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.C.6767498
Abstract: Abstract For one-third of patients with pediatric cancer enrolled in precision medicine programs, molecular profiling does not result in a therapeutic recommendation. To identify potential strategies for treating these high-risk pediatric patients, we performed i in vitro /i screening of 125 patient-derived s les against a library of 126 anticancer drugs. Tumor cell expansion did not influence drug responses, and 82% of the screens on expanded tumor cells were completed while the patients were still under clinical care. High-throughput drug screening (HTS) confirmed known associations between activating genomic alterations in i NTRK /i , i BRAF /i , and i ALK /i and responses to matching targeted drugs. The i in vitro /i results were further validated in patient-derived xenograft models i in vivo /i and were consistent with clinical responses in treated patients. In addition, effective combinations could be predicted by correlating sensitivity profiles between drugs. Furthermore, molecular integration with HTS identified biomarkers of sensitivity to WEE1 and MEK inhibition. Incorporating HTS into precision medicine programs is a powerful tool to accelerate the improved identification of effective biomarker-driven therapeutic strategies for treating high-risk pediatric cancers. Significance: Integrating HTS with molecular profiling is a powerful tool for expanding precision medicine to support drug treatment recommendations and broaden the therapeutic options available to high-risk pediatric cancers. /
Publisher: Elsevier BV
Date: 07-2019
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Publisher: Springer Science and Business Media LLC
Date: 03-04-2023
DOI: 10.1186/S13073-023-01170-X
Abstract: Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. We combined immunohistochemistry (IHC) with RNA sequencing and whole-genome sequencing across a erse spectrum of high-risk paediatric cancers to develop an alternative, expression-based signature associated with CD8 + T-cell infiltration of the TIME. Furthermore, we explored transcriptional features of immune archetypes and T-cell receptor sequencing ersity, assessed the relationship between CD8 + and CD4 + abundance by IHC and deconvolution predictions and assessed the common adult biomarkers such as neoantigen load and TMB. A novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), was identified. Using this signature, we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. In addition, we showed that PD-L1 protein expression is poorly correlated with PD-L1 RNA expression and TMB and neoantigen load are not predictive of T-cell infiltration in paediatrics. Furthermore, deconvolution algorithms are only weakly correlated with IHC measurements of T-cells. Our data provides new insights into the variable immune-suppressive mechanisms d ening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require in idualised analysis of the TIME.
Publisher: Springer Science and Business Media LLC
Date: 07-09-2021
DOI: 10.1186/S40478-021-01248-W
Abstract: Diffuse leptomeningeal glioneuronal tumours (DLGNT) represent rare enigmatic CNS tumours of childhood. Most patients with this disease share common radiological and histopathological features but the clinical course of this disease is variable. A radiological hallmark of this disease is widespread leptomeningeal enhancement that may involve the entire neuroaxis with predilection for the posterior fossa and spine. The classic pathologic features include low- to moderate-density cellular lesions with OLIG2 expression and evidence of ‘oligodendroglioma-like’ appearance. The MAPK/ERK signaling pathway has recently been reported as a potential driver of tumourigenesis in up to 80% of DLGNT with KIAA1549:BRAF fusions being the most common event seen. Until now, limited analysis of the biological drivers of tumourigenesis has been undertaken via targeted profiling, chromosomal analysis and immunohistochemistry. Our study represents the first ex les of comprehensive genomic sequencing in DLGNT and shows that it is not only feasible but crucial to our understanding of this rare disease. Moreover, we demonstrate that DLGNT may be more genomically complex than single-event MAPK/ERK signaling pathway tumours.
Publisher: MDPI AG
Date: 23-06-2023
DOI: 10.3390/JPM13071033
Abstract: Precision medicine programs aim to utilize novel technologies to identify personalized treatments for children with cancer. Delivering these programs requires interdisciplinary efforts, yet the many groups involved are understudied. This study explored the experiences of a broad range of professionals delivering Australia’s first precision medicine trial for children with poor-prognosis cancer: the PRecISion Medicine for Children with Cancer (PRISM) national clinical trial of the Zero Childhood Cancer Program. We conducted semi-structured interviews with 85 PRISM professionals from eight professional groups, including oncologists, surgeons, clinical research associates, scientists, genetic professionals, pathologists, animal care technicians, and nurses. We analyzed interviews thematically. Professionals shared that precision medicine can add complexity to their role and result in less certain outcomes for families. Although many participants described experiencing a greater emotional impact from their work, most expressed very positive views about the impact of precision medicine on their profession and its future potential. Most reported navigating precision medicine without formal training. Each group described unique challenges involved in adapting to precision medicine in their profession. Addressing training gaps and meeting the specific needs of many professional groups involved in precision medicine will be essential to ensure the successful implementation of standard care.
Publisher: American Association for Cancer Research (AACR)
Date: 07-2019
DOI: 10.1158/1538-7445.AM2019-3111
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 & %). 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 (13 Suppl):Abstract nr 3111.
Publisher: American Association for Cancer Research (AACR)
Date: 04-04-2023
DOI: 10.1158/1538-7445.AM2023-4670
Abstract: There has been dramatic improvement in treatment outcomes for many pediatric cancers over the last three decades. However, for the 20% of young people with relapsed or refractory cancer, the prognosis remains grim. Canada’s PRecision Oncology For Young peopLE (PROFYLE) and Australia’s Zero Childhood Cancer (ZERO) programs, leverage nation-wide scientific and clinical oncology expertise to provide personalized precision medicine to children, adolescent and young adult (CAYA) cancer patients who lack treatment options. Beyond improving the lives of young cancer patients nationally, PROFYLE and ZERO have partnered to create an international pipeline for knowledge sharing and s le acquisition. A key component of both programs is the use of mice for patient-derived xenografts (PDXs). However, long lead times for mouse PDX generation make the timely return of preclinical drug response data challenging. PROFYLE has uniquely incorporated zebrafish larval xenografts, which have the potential to provide comparable information in a clinically actionable timeframe. In a pilot study, we compared retrospective matched ZERO patient and mouse PDX therapeutic response data with prospective zebrafish larval PDX data as a proof-of-principle that drug efficacy signals were maintained across model systems. Three ZERO avatars: high-risk neuroblastoma, Ewing’s sarcoma, and anaplastic large cell lymphoma were shipped from Australia to Canada and transplanted into 48h casper zebrafish. Following dose optimization, zebrafish PDXs were treated with targeted single and combination drug treatments by immersion therapy. Strikingly, in as little time as a week, cell proliferation rates and drug responses to single agents and combinatorial therapy in zebrafish PDXs recapitulated mouse and patient data. To expand on this pilot project, we tested additional patient s les, including multiple subtypes of sarcomas, T-cell acute lymphoblastic leukemia and an embryonal tumor with multilayered rosettes. Results further validated the practical utility of the zebrafish larval PDX model and in fact provided drug response data when mouse PDX data were unavailable. This study demonstrates the robustness and feasibility of the zebrafish larval PDX model as a preclinical tool for personalized precision therapeutic decision-making and highlights the value of international collaboration in improving outcomes of rare childhood cancers. Citation Format: Nadine Azzam, Nicole Melong, Lissandra Tuzi, Lisa Pinto, Jamie I. Fletcher, Alvin Kamili, Biljana Dumevska, Loretta Lau, Jennifer A. Chan, Donna L. Senger, Stephanie A. Grover, Michelle Haber, David Malkin, Jason N. Berman. True bench-to-bedside science: An international pilot study modeling hard-to-cure pediatric cancers to prioritize therapeutic intervention. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023 Part 1 (Regular and Invited Abstracts) 2023 Apr 14-19 Orlando, FL. Philadelphia (PA): AACR Cancer Res 2023 (7_Suppl):Abstract nr 4670.
Publisher: American Society of Clinical Oncology (ASCO)
Date: 20-05-0002
DOI: 10.1200/JCO.2017.35.15_SUPPL.10539
Abstract: 10539 Background: Genomic analyses can identify actionable mutations in a subset of childhood cancers. However it has been challenging to translate actionable mutations into substantial benefits for adult cancers despite high mutation frequency. Methods: To test whether we could enhance identification of personalised therapies for high risk (HR) childhood cancers we conducted a pilot study (TARGET) evaluating a novel, comprehensive precision medicine platform incorporating molecular profiling, in vitro and in vivo drug testing. Results: We evaluated the first 29 patients with HR cancer (expected survival 30%) enrolled prospectively over 15 months. S les were collected from 15 CNS tumors, 10 solid tumors and 4 leukemias. All s les underwent targeted DNA sequencing. Pathogenic or likely pathogenic mutations were found in 59% (17/29) of tumors. 41% (12/29) had potentially actionable mutations. RNA-sequencing was performed on 27 s les. Previously described fusions were identified in 19% (5/27 1 targetable, 1 clinical relevant and 3 diagnostic fusions). 37% (10/27) of s les also had actionable aberrations related to copy number changes or RNA expression. In vitro culture and establishment of patient-derived xenograft (PDX) were attempted in 19 and 21 fresh s les, respectively. The success rate of establishing a primary culture was 42% (8/19) and PDX engraftment rate was 67% (14/21). At least 1 drug hit was identified in 5 (56%) of the 9 s les screened using a high throughput drug screen of up to 165 compounds. Drug testing has been completed in 4 PDXs and was informative in all 4 cases allowing prioritisation of treatment recommendations. Genomic analysis in combination with RNA-seq, in vitro drug screening and PDX drug testing enriched the analysis and increased the ability to make personalised treatment recommendations from 41% (targeted panel alone) to 66%. Conclusions: This pilot study demonstrates that this novel, comprehensive platform is feasible and has the potential to improve outcome for HR childhood cancers. A multicentre study testing the implementation of the platform on a national level (PRISM trial) will open for Australian children with HR cancer under the Zero Childhood Cancer Program in 2017.
Publisher: American Association for Cancer Research (AACR)
Date: 31-07-2023
DOI: 10.1158/0008-5472.23808560.V1
Abstract: Supplementary Figures
Publisher: American Association for Cancer Research (AACR)
Date: 31-07-2023
DOI: 10.1158/0008-5472.23808560
Abstract: Supplementary Figures
Publisher: American Society of Clinical Oncology (ASCO)
Date: 12-2019
DOI: 10.1200/PO.19.00235
Abstract: Children with high-risk cancers have low survival rates because current treatment options are limited. Precision medicine trials are designed to offer patients in idualized treatment recommendations, potentially improving their clinical outcomes. However, parents’ understanding is often limited, and expectations of benefit to their own child can be high. Health care professionals (HCPs) are often not familiar with precision medicine and might find managing families’ expectations challenging. Scientists find themselves working with high expectations among different stakeholders to rapidly translate their identification of actionable targets in real time. Therefore, we wanted to gain an in-depth understanding of the experiences of all stakeholders involved in a new precision medicine pilot trial called TARGET, including parents, their child’s HCPs, and the scientists who conducted the laboratory research and generated the data used to make treatment recommendations. We conducted semistructured interviews with all participants and analyzed the interviews thematically. We interviewed 15 parents (9 mothers 66.7% bereaved), 17 HCPs, and 16 scientists. We identified the following themes in parents’ interviews: minimal understanding and need for more information, hope as a driver of participation, challenges around biopsies, timing, and drug access, and few regrets. HCP and scientist interviews revealed themes such as embracing new technologies and collaborations and challenges managing families’ expectations, timing of testing and test results, and drug access. Educating families, HCPs, and scientists to better understand the benefits and limitations of precision medicine trials may improve the transparency of the translation of discovery genomics to novel therapies, increase satisfaction with the child’s care, and ameliorate the additional long-term psychosocial burden for families already affected by high-risk childhood cancer.
Publisher: Springer Science and Business Media LLC
Date: 13-08-2008
Abstract: Nutlin-3, a small molecule inhibitor, activates p53 by disrupting p53-HDM2 association. In this study, we found that Nutlin-3 suppressed cell growth and induced apoptosis in the absence of wild-type p53, suggesting a p53-independent mechanism for Nutlin-3-induced cell death. Like p53, its homolog p73 transactivates proapoptotic genes and induces cell death. Since HDM2, a key negative regulator of p53, also binds to and inhibits p73, we asked whether p73 could mediate Nutlin-3-induced apoptosis. We demonstrate that Nutlin-3 inhibits endogenous binding between the proapoptotic p73 isoform TAp73alpha and HDM2 in p53-null cells. Dissociation of p73 and HDM2 leads to increased p73 transcriptional activity with upregulation of p73 target genes noxa, puma and p21, as well as enhanced apoptosis. p73 knockdown by siRNA results in rescue of Nutlin-3-treated cells, indicating that Nutlin-3-induced apoptosis is, at least in part, p73 dependent. In addition, Nutlin-3 treatment increases TAp73alpha protein levels with prolongation of p73 half-life. These results provide the first evidence that Nutlin-3 disrupts endogenous p73-HDM2 interaction and enhances the stability and proapoptotic activities of p73 and thus, provides a rationale for the use of Nutlin-3 in the large number of human tumors in which p53 is inactivated.
Publisher: American Association for Cancer Research (AACR)
Date: 07-2021
DOI: 10.1158/1538-7445.AM2021-3044
Abstract: In adult cancer, immune signatures such as the T cell-inflamed gene expression profile (GEP) have been developed to predict which patients are likely to respond to immune checkpoint inhibitors (ICIs) beyond high tumor mutation burden (TMB) and PD-L1 expression. The GEP infers T cell infiltration and activation in the tumor microenvironment (TME) from transcriptomic data. However, it is not known whether tools such as GEP are applicable in pediatric cancer, as the TME in childhood cancers is largely unexplored and response to ICIs are rare. We have undertaken an integrated analysis of the pediatric TME using RNA-sequencing (RNA-seq) and immunohistochemistry (IHC). Our goal is to identify patients with T cell-inflamed or “hot” tumors who may benefit from ICIs. Through Australia's ZERO childhood cancer precision medicine program we performed RNA-seq on 347 high-risk pediatric cancers (estimated & % chance of survival) and performed IHC for CD4, CD8, CD45 and PD-L1 on 112 matching s les. Using both informatic assessments and IHC as independent measures of immune infiltration, we mapped the immune landscape of the TME across a broad range of high-risk pediatric cancers. As RNA-seq is increasingly used in the analysis of patient tumors, we investigated numerous molecular correlates of immune infiltration, tailored specifically to pediatric patients. RNA-seq was used to generate the GEP and map expression profiles of immune checkpoint genes, and deconvolution algorithms were used to extract the immune cell composition for every tumor. The correlation analysis between IHC, deconvolution of cell mixture composition and GEP were assessed, including PD-L1 protein and mRNA expression. We observed significant correlation between PD-L1 protein and mRNA expression and a weak correlation of CD8+ T cells with GEP. Deconvoluted TME estimates were most tightly correlated with the presence of T cell infiltrates (CD4 and CD8) with IHC. TMB and tumor purity estimates were derived from whole genome sequencing for each case. No correlation was observed between TMB and immune infiltration, however, tumor purity was negatively correlated with immune infiltration. Using IHC as an independent marker of a T cell-inflamed TME, we have identified a novel pediatric immune signature that includes markers of CD4 and CD8 T cells, T cell cytotoxicity, T and NK cell recruitment and activation, MHC Class II molecules and immune checkpoints. This is the first study to comprehensively analyze the pediatric TME in a cohort of this size and ersity, with matching IHC for orthogonal validation. Through the combination of RNA-seq and IHC, we have devised a novel immune signature specific to pediatrics and these techniques have identified a subset of patients that are immune “hot” and may potentially respond to ICIs. Conversely, we also highlight the potential of identifying immune “cold” patients who may need immunomodulatory combination strategies to maximize immune response. Citation Format: Chelsea Mayoh, Rachael L. Terry, Marie Wong, Loretta M. Lau, Dong Anh Khuong-Quang, Marion K. Mateos, Vanessa Tyrrell, Michelle Haber, David S. Ziegler, Mark J. Cowley, Joseph A. Trapani, Paul J. Neeson, Paul G. Ekert. The unexplored immune landscape of high-risk pediatric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR Cancer Res 2021 (13_Suppl):Abstract nr 3044.
Publisher: American Association for Cancer Research (AACR)
Date: 31-07-2023
DOI: 10.1158/0008-5472.CAN-22-3702
Abstract: Integrating HTS with molecular profiling is a powerful tool for expanding precision medicine to support drug treatment recommendations and broaden the therapeutic options available to high-risk pediatric cancers.
Publisher: Oxford University Press (OUP)
Date: 06-2018
Publisher: American Association for Cancer Research (AACR)
Date: 31-07-2023
DOI: 10.1158/0008-5472.C.6767498.V1
Abstract: Abstract For one-third of patients with pediatric cancer enrolled in precision medicine programs, molecular profiling does not result in a therapeutic recommendation. To identify potential strategies for treating these high-risk pediatric patients, we performed i in vitro /i screening of 125 patient-derived s les against a library of 126 anticancer drugs. Tumor cell expansion did not influence drug responses, and 82% of the screens on expanded tumor cells were completed while the patients were still under clinical care. High-throughput drug screening (HTS) confirmed known associations between activating genomic alterations in i NTRK /i , i BRAF /i , and i ALK /i and responses to matching targeted drugs. The i in vitro /i results were further validated in patient-derived xenograft models i in vivo /i and were consistent with clinical responses in treated patients. In addition, effective combinations could be predicted by correlating sensitivity profiles between drugs. Furthermore, molecular integration with HTS identified biomarkers of sensitivity to WEE1 and MEK inhibition. Incorporating HTS into precision medicine programs is a powerful tool to accelerate the improved identification of effective biomarker-driven therapeutic strategies for treating high-risk pediatric cancers. Significance: Integrating HTS with molecular profiling is a powerful tool for expanding precision medicine to support drug treatment recommendations and broaden the therapeutic options available to high-risk pediatric cancers. /
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Publisher: Springer Science and Business Media LLC
Date: 05-10-2020
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Publisher: Oxford University Press (OUP)
Date: 04-2019
Publisher: Oxford University Press (OUP)
Date: 12-2020
DOI: 10.1093/NEUONC/NOAA222.117
Abstract: The Australian Zero Childhood Cancer (ZERO) program aims to assess the feasibility of a comprehensive precision medicine approach to improve outcomes for patients with an expected survival & %. ZERO combines molecular profiling (whole genome sequencing, whole transcriptome sequencing, DNA methylation profiling) with in vitro high-throughput drug screening (HTS) and patient-derived xenograft drug efficacy testing. We report on the cohort of patients with midline high-grade glioma (HGG), including H3-K27M DMG, enrolled on the pilot study (TARGET) and on the ongoing ZERO clinical trial (PRISM). We identified 48 patients with midline HGG. Fresh or cryopreserved s les were submitted in 37 cases and cell culture was attempted in 30/37 cases with 45% success rate. The most commonly mutated genes athways identified by molecular profiling include H3-K27M mutations, DNA repair pathway, and PI3K/mTOR pathway. Two targetable fusions (NTRK and FGFR1) were reported. Five patients with germline alterations were identified. Thirty-five (72%) patients received a therapeutic recommendation from the ZERO molecular tumour board and the main recommended therapies were mTOR inhibitors, PARP inhibitors or tyrosine kinase inhibitors. HTS added evidence for the recommended therapy (n=3) or identified novel potential therapy (n=1). Out of the 35 patients, 16 received a recommended drug. Response to treatment was complete response for five months (n=1), partial response for nine months (n=1), stable disease (n=4), and progressive disease (n=10). These results highlight the feasibility of the ZERO platform and the value of fresh biopsy, necessary for pre-clinical drug testing. Targetable alterations were identified leading to clinical benefit in six patients.
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.24000207
Abstract: Supplementary Materials and Methods
Publisher: Springer Science and Business Media LLC
Date: 30-11-2020
DOI: 10.1038/S41467-020-20128-W
Abstract: Correction to this paper has been published: 0.1038/s41467-020-20128-w
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.24000204
Abstract: Supplementary Tables S1-S7
Publisher: Oxford University Press (OUP)
Date: 12-11-2014
DOI: 10.1093/NAR/GKT1117
Publisher: Wiley
Date: 2006
DOI: 10.1002/PBC.20676
Abstract: Pulmonary Langerhans cell histiocytosis (PLCH) is rare in childhood but occurs most commonly in children with multisystem (MS) LCH. In adults, by contrast, the lung is the most common and usually the sole organ affected. This retrospective study describes the clinical manifestation, course, and outcome of PLCH in children consecutively diagnosed at two Canadian institutions. The medical records of children (<18 years of age) consecutively diagnosed with LCH at the two institutions, were examined to ascertain the demographic details, pathological diagnosis, and organs involved. Further clinical details including, the clinical manifestation, details of therapy, course of lung disease, and clinical outcome were extracted for patients with PLCH. Initial and follow-up lung radiographs and CT scans were re-reviewed. Of the 178 patients with LCH, 40 (22.5%) presented with MS disease. Thirteen (7.3%) had PLCH, seven at initial diagnosis, and six at the time of disease progression. The median age was 10.1 months and mean was 11.9 months at diagnosis of PLCH. Lung involvement was always in the context of MS LCH, and half of the patients had no respiratory symptoms. Disease-free survival was around 70%, with a mean follow-up duration of 7 years. Of the four patients who died, three had other risk-organ involvement. Five of the nine surviving patients have had complete radiological resolution of PLCH. PLCH is seen in less than 10% of childhood LCH, but more than 30% of MS LCH. About half of children with PLCH may be asymptomatic, and the prognosis appears to depend on the presence or absence of other risk-organ involvement. The MS PLCH found in children appears to be a different disease from the single system (SS) PLCH seen in adults.
Publisher: American Society of Hematology
Date: 03-12-2015
DOI: 10.1182/BLOOD.V126.23.4984.4984
Abstract: Introduction Telomeres are specialized DNA structures found at the end of linear chromosomes, which in humans contains the repetitive DNA sequence, (TTAGGG)n and associated proteins. Telomere length (TL) is important for replicative capacity of cells, and, in somatic cells, telomere length shortens with each cell ision. Once a critically short length is reached, cells enter senescence or undergo apoptosis. In the general population, TL varies greatly and declines with age. Chemotherapy can increase the rate of telomere shortening, although these findings have not been consistently demonstrated. There is evidence, mostly in adults, suggesting that patients with shorter TL experience increased toxicity from cancer treatment. Patients with the short telomere syndrome, Dyskeratosis Congenita undergoing hematopoietic stem cell transplantation have increased rates and degree of organ toxicity when given myeloablative conditioning. In the pediatric population there have been no studies assessing the relationship between TL and rates of toxicity after chemotherapy, and few investigating telomere dynamics following chemotherapy. We undertook a retrospective analysis to investigate the relationship between TL and chemotherapy toxicity, and also telomere dynamics in children treated for acute lymphoblastic leukemia (ALL). Methods Patients enrolled on the Australian and New Zealand Children's Hematology and Oncology Group's (ANZCHOG) Study 8 for ALL at the Children's Hospital at Westmead and the Sydney Children's Hospital from October 2002 to November 2011 who had provided consent and who had stored s les suitable for TL analysis were included in the study. Organ toxicity information was collected from the Study 8 database, as well as examination of patient medical records and pathology information systems. Liver and renal toxicities were documented based on abnormalities in transaminases, bilirubin and creatinine respectively. Pulmonary and neurotoxicities were determined through medical record and imaging findings. Standard common terminology criteria for adverse events (CTCAE) criteria were used to systematically grade toxicity. Infectious disease information and intensive care admissions as well as time to complete each cycle of therapy were used as surrogate markers for toxicity and bone marrow recovery. Survival and relapse rates were also analyzed. Relative TL was measured using a quantitative PCR technique on DNA extracted from mononuclear cells taken at Day 79 following commencement of induction and consolidation therapy, and also at the end of treatment, typically 24 months from diagnosis. The relative TL was converted to an age adjusted TL (AATL) by subtracting the expected relative TL (i.e. 50th percentile for age of the patient) from the measured relative TL, so that patients of all ages could be analyzed together. For analysis the cohort was separated into four groups based on AATL quartiles. Results In all, 460 patients with research consent were enrolled on ANZCHOG ALL Study 8 at the 2 hospitals included in this study. Of these 157 patients with AATL measurement and toxicity information were included in our analysis with 149 being standard or medium risk. The median age of diagnosis was 4.79 years (range 1.1 - 17.89) with a median follow up of 53 months (range 9-124 months). The median AATL on Day 79 was 0.035 (range -0.41 to 0.73). The average change in TL from day 79 to end of treatment was -0.126 (range -0.81 to 0.40), which is equivalent to approximately 8-10 years of natural ageing. There was no significant association between survival (Figure 1) or rates of grade 3 or 4 organ toxicity, relapse (Table 2) or bone marrow recovery and AATL. Renal toxicity was significantly increased in the second shortest quartile, however numbers are small (4 patients in second quartile vs 1 in fourth quartile). Conclusion There is an increased rate of telomere attrition during treatment for childhood ALL, however telomere length does not appear to be associated with increased rates of organ toxicity. Support: NHMRC APP1057746 and NHMRC GNT1056667 No relevant conflicts of interest to declare.
Publisher: American Association for Cancer Research (AACR)
Date: 15-08-2023
DOI: 10.1158/0008-5472.23952251.V1
Abstract: Supplementary Figures
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.C.6767498.V3
Abstract: Abstract For one-third of patients with pediatric cancer enrolled in precision medicine programs, molecular profiling does not result in a therapeutic recommendation. To identify potential strategies for treating these high-risk pediatric patients, we performed i in vitro /i screening of 125 patient-derived s les against a library of 126 anticancer drugs. Tumor cell expansion did not influence drug responses, and 82% of the screens on expanded tumor cells were completed while the patients were still under clinical care. High-throughput drug screening (HTS) confirmed known associations between activating genomic alterations in i NTRK /i , i BRAF /i , and i ALK /i and responses to matching targeted drugs. The i in vitro /i results were further validated in patient-derived xenograft models i in vivo /i and were consistent with clinical responses in treated patients. In addition, effective combinations could be predicted by correlating sensitivity profiles between drugs. Furthermore, molecular integration with HTS identified biomarkers of sensitivity to WEE1 and MEK inhibition. Incorporating HTS into precision medicine programs is a powerful tool to accelerate the improved identification of effective biomarker-driven therapeutic strategies for treating high-risk pediatric cancers. Significance: Integrating HTS with molecular profiling is a powerful tool for expanding precision medicine to support drug treatment recommendations and broaden the therapeutic options available to high-risk pediatric cancers. /
Publisher: American Association for Cancer Research (AACR)
Date: 15-08-2023
DOI: 10.1158/0008-5472.C.6767498.V2
Abstract: Abstract For one-third of patients with pediatric cancer enrolled in precision medicine programs, molecular profiling does not result in a therapeutic recommendation. To identify potential strategies for treating these high-risk pediatric patients, we performed i in vitro /i screening of 125 patient-derived s les against a library of 126 anticancer drugs. Tumor cell expansion did not influence drug responses, and 82% of the screens on expanded tumor cells were completed while the patients were still under clinical care. High-throughput drug screening (HTS) confirmed known associations between activating genomic alterations in i NTRK /i , i BRAF /i , and i ALK /i and responses to matching targeted drugs. The i in vitro /i results were further validated in patient-derived xenograft models i in vivo /i and were consistent with clinical responses in treated patients. In addition, effective combinations could be predicted by correlating sensitivity profiles between drugs. Furthermore, molecular integration with HTS identified biomarkers of sensitivity to WEE1 and MEK inhibition. Incorporating HTS into precision medicine programs is a powerful tool to accelerate the improved identification of effective biomarker-driven therapeutic strategies for treating high-risk pediatric cancers. Significance: Integrating HTS with molecular profiling is a powerful tool for expanding precision medicine to support drug treatment recommendations and broaden the therapeutic options available to high-risk pediatric cancers. /
Publisher: Springer Science and Business Media LLC
Date: 24-05-2004
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.24000213.V1
Abstract: Supplementary Figures 1-7 and Figure Legends
Publisher: Springer Science and Business Media LLC
Date: 07-03-2023
DOI: 10.1038/S41598-023-30395-4
Abstract: Diffuse midline gliomas (DMG) harbouring H3K27M mutation are paediatric tumours with a dismal outcome. Recently, a new subtype of midline gliomas has been described with similar features to DMG, including loss of H3K27 trimethylation, but lacking the canonical H3K27M mutation (H3-WT). Here, we report a cohort of five H3-WT tumours profiled by whole-genome sequencing, RNA sequencing and DNA methylation profiling and combine their analysis with previously published cases. We show that these tumours have recurrent and mutually exclusive mutations in either ACVR1 or EGFR and are characterised by high expression of EZHIP associated to its promoter hypomethylation. Affected patients share a similar poor prognosis as patients with H3K27M DMG. Global molecular analysis of H3-WT and H3K27M DMG reveal distinct transcriptome and methylome profiles including differential methylation of homeobox genes involved in development and cellular differentiation. Patients have distinct clinical features, with a trend demonstrating ACVR1 mutations occurring in H3-WT tumours at an older age. This in-depth exploration of H3-WT tumours further characterises this novel DMG, H3K27-altered sub-group, characterised by a specific immunohistochemistry profile with H3K27me3 loss, wild-type H3K27M and positive EZHIP. It also gives new insights into the possible mechanism and pathway regulation in these tumours, potentially opening new therapeutic avenues for these tumours which have no known effective treatment. This study has been retrospectively registered on clinicaltrial.gov on 8 November 2017 under the registration number NCT03336931 ( t2/show/NCT03336931 ).
Publisher: Springer Science and Business Media LLC
Date: 08-12-2022
Publisher: Springer Science and Business Media LLC
Date: 23-08-2021
Publisher: Springer Science and Business Media LLC
Date: 05-02-2020
DOI: 10.1038/S41586-020-1969-6
Abstract: Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale 1–3 . Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution in acral melanoma, for ex le, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter 4 identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation 5,6 analyses timings and patterns of tumour evolution 7 describes the erse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity 8,9 and evaluates a range of more-specialized features of cancer genomes 8,10–18 .
Publisher: Springer Science and Business Media LLC
Date: 15-02-2017
DOI: 10.1038/NATURE21063
Abstract: The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2. Together with mutations in MEN1 and VHL, these mutations occur in 17% of patients. Somatic mutations, including point mutations and gene fusions, were commonly found in genes involved in four main pathways: chromatin remodelling, DNA damage repair, activation of mTOR signalling (including previously undescribed EWSR1 gene fusions), and telomere maintenance. In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling.
Publisher: Cold Spring Harbor Laboratory
Date: 19-09-2022
DOI: 10.1101/2022.09.16.508179
Abstract: Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. We combined immunohistochemistry (IHC) and molecular profiling to develop an alternative, expression-based signature associated with CD8 + T-cell infiltration of the TIME in high-risk paediatric tumours. Using this novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. Our data provides new insights into the variable immune-suppressive mechanisms d ening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require in idualised analysis of the TIME.
Publisher: Public Library of Science (PLoS)
Date: 20-11-2012
Publisher: Oxford University Press (OUP)
Date: 06-2023
DOI: 10.1093/NEUONC/NOAD073.169
Abstract: Noonan Syndrome (NS) is a genetic condition, known to be associated with low grade central nervous system tumours in children but only very rarely associated with high-grade gliomas. Here we describe the first reported case of a spinal high-grade astrocytoma with piloid features (HGAP) in a child with NS. This case presented as a diagnostic and treatment dilemma, prior to comprehensive molecular profiling with whole-genome germline and tumour sequencing, tumour transcriptome sequencing and DNA methylation analysis. The methylation profile was a strong match for HGAP and was critical to establish this child’s diagnosis, as this is an essential diagnostic criteria for confirmation of this relatively new tumour group. Sequencing results identified activation of the MAPK signalling pathway with somatic variants in FGFR1 and NF1 and the previously known germline pathogenic variant in PTPN11. The somatic molecular profile was consistent with those previously reported in other HGAP case series and reports, whereas the germline finding has not been previously described in in iduals with this tumour type. This patient’s molecular profile adds to the small group of paediatric cases reported in the literature, continuing to expand our understanding of this new WHO diagnostic category. Confirmation of this rare diagnosis was critical to this child’s management and targetable aberrations were identified, providing alternative therapeutic options. The therapeutic targets included known drivers within the MAPK pathway, but also changes not previously associated with HGAP such as differential expression of VEGFA and PD-L1. Together this case underscores the power of precision medicine from a diagnostic, therapeutic and clinical management perspective, and describes an association between HGAP and NS which has not previously been reported.
Publisher: American Association for Cancer Research (AACR)
Date: 09-10-2014
DOI: 10.1158/1538-7445.PEDCAN-B51
Abstract: Introduction: Neuroblastoma (NB) is the most common extracranial solid tumor of infants. We constructed a tissue microarray (TMA) including 47 diagnostic NB cases and performed immunohistochemical (IHC) staining for a number of biomarkers. Differential IHC staining was identified between duplicate tissue cores for a proportion of NB cases. Differential IHC staining occurs frequently in cancer specimens, and can be due to technical factors, tissue artefacts, or underlying biological differences between tumor sub-regions. As laser capture microdissection (LCM) allows isolation of cells from formalin-fixed paraffin-embedded (FFPE) tissue slides, we applied LCM to FFPE NB s les, to investigate the basis of differential IHC staining. Material and Methods: NSE, NB84, ALK, TPD52 and MGMT proteins were detected within diagnostic NB TMA cores and whole NB sections using IHC. Cells were isolated from FFPE sections using LCM, and genomic DNA was extracted using the QIA DNA FFPE Tissue Kit. Extracted genomic DNA was quantified using a Nanodrop spectrophotometer, and DNA quality was assessed by a Bioanalyzer 2100. All DNA s les were tested using PCR with TPD52 and ALK primers. Results including clinical and s le variables were analysed using SPSS version 19. Results: Of 47 NB cases within the TMA, 35 cases were represented by duplicate tissue cores, whereas the remaining 12 cases were represented by single cores. IHC analysis of 5 biomarkers showed visually different IHC staining in tumour tissue between duplicate tissue cores in 15/35 (43%) cases. Whole tissue sections from 6 of these 15 cases were then examined, which reproduced differential IHC staining. Isolation of NB cells by LCM was successfully performed after substantial optimisation. A total of 14 regions from 8 NB cases were microdissected, producing DNA yields ranging from 0.12 - 4.05 pg/ µm2 tissue. There were no significant associations between total yields of extracted DNA, and microdissected tissue areas, or tissue s le ages. All DNA s les were successfully lified by TPD52 but not by ALK PCR primers. Conclusions: Genomic DNA can be reliably extracted from microdissected FFPE NB tissues, although only one of 2 genes could be successfully PCR lified. Downstream assays of DNA extracted from FFPE s les may therefore have particular design requirements. Further application of this approach may help improve our understanding of the level of tumour heterogeneity present in NB s les at diagnosis. Citation Format: Le M. Thwe, Laurence C. Cantrill, Daniel R. Catchpoole, Loretta Lau, Jennifer A. Byrne. Extraction and analysis of genomic DNA from formalin-fixed paraffin-embedded neuroblastoma s les following laser capture microdissection. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes Nov 3-6, 2013 San Diego, CA. Philadelphia (PA): AACR Cancer Res 2013 (20 Suppl):Abstract nr B51.
Publisher: Elsevier BV
Date: 07-2012
Publisher: The Company of Biologists
Date: 2017
DOI: 10.1242/JCS.192930
Abstract: The Cas family of focal adhesion proteins contain a highly conserved C-terminal focal adhesion targeting (FAT) domain. To determine the role of the FAT domain we compared wildtype exogenous NEDD9 with a hybrid construct in which the NEDD9 FAT domain is exchanged for the p130Cas FAT domain. Fluorescence recovery after photobleaching (FRAP) revealed significantly slowed exchange of the fusion protein at focal adhesions and significantly slower 2D migration. No differences were detected in cell stiffness measured with Atomic Force Microscopy (AFM) and cell adhesion forces measured with a magnetic tweezer device. Thus the slowed migration was not due to changes in cell stiffness or adhesion strength. Analysis of cell migration on surfaces of increasing rigidity revealed a striking reduction of cell motility in cells expressing the p130Cas FAT domain. The p130Cas FAT domain induced rigidity-dependent tyrosine phosphorylation of the NEDD9 substrate domain. This in turn reduced post-translational cleavage of NEDD9 which we show inhibits NEDD9-induced migration. Collectively, our data therefore suggest that the p130Cas FAT domain uniquely confers mechanosensing function.
Publisher: American Association for Cancer Research (AACR)
Date: 15-07-2020
DOI: 10.1158/1538-7445.PEDCA19-A52
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 athways 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 (14 Suppl):Abstract nr A52.
Publisher: Hindawi Limited
Date: 31-10-2023
DOI: 10.1155/2023/2581698
Publisher: Elsevier BV
Date: 02-2018
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.24000207.V1
Abstract: Supplementary Materials and Methods
Publisher: Ovid Technologies (Wolters Kluwer Health)
Date: 04-2015
Publisher: BMJ
Date: 05-2023
DOI: 10.1136/BMJOPEN-2022-070082
Abstract: Identifying an underlying germline cancer predisposition (CP) in a child with cancer has potentially significant implications for both the child and biological relatives. Cohort studies indicate that 10%–15% of paediatric cancer patients carry germline pathogenic or likely pathogenic variants in cancer predisposition genes, but many of these patients do not meet current clinical criteria for genetic testing. This suggests broad tumour agnostic germline testing may benefit paediatric cancer patients. However, the utility and psychosocial impact of this approach remain unknown. We hypothesise that an approach involving trio whole-genome germline sequencing (trio WGS) will identify children and families with an underlying CP in a timely fashion, that the trio design will streamline cancer risk counselling to at-risk relatives if CP was inherited, and that trio testing will not have a negative psychosocial impact on families. To test this, we present the Cancer PREDisposition In Childhood by Trio sequencing study (PREDICT). This study will assess the clinical utility of trio WGS to identify CP in unselected patients with cancer 21 years or younger in New South Wales, Australia. PREDICT will perform analysis of biological parents to determine heritability and will examine the psychosocial impact of this trio sequencing approach. PREDICT also includes a broad genomics research programme to identify new candidate genes associated with childhood cancer risk. By evaluating the feasibility, utility and psychosocial impact of trio WGS to identify CP in paediatric cancer, PREDICT will inform how such comprehensive testing can be incorporated into a standard of care at diagnosis for all childhood cancer patients. NCT04903782 .
Publisher: Oxford University Press (OUP)
Date: 30-04-2018
DOI: 10.1093/NAR/GKY297
Publisher: Springer Science and Business Media LLC
Date: 18-09-2007
Abstract: Cyclooxygenase-2 (COX-2) is upregulated in many tumors including neuroblastoma, and its overexpression has been implicated in resistance to p53-dependent apoptosis. Although p53 is rarely mutated in neuroblastoma, the p53 protein is rendered inactive via several mechanisms including sequestration in the cytoplasm. Here, we show that COX inhibitors inhibit the growth of neuroblastoma and when combined with low doses of chemotherapy, exert synergistic effects on neuroblastoma cells. Following COX inhibitor treatment, HDM2, which targets p53 for ubiquitin-mediated degradation, is downregulated, resulting in an attenuation of p53 ubiquitination and an increase in p53 half-life. The level of HDM2 phosphorylation at ser166, which influences both HDM2 and p53 subcellular distribution, is markedly diminished in response to COX inhibitors and is associated with increased p53 nuclear localization. Combining COX inhibitors with low-dose chemotherapy potentiates apoptosis and p53 stability, nuclear localization, and activity. p53 knockdown by siRNA resulted in the rescue of COX-inhibitor-treated cells, indicating that COX inhibitor-induced apoptosis is, at least in part, p53-dependent. Taken together, these results provide the first evidence that COX inhibitors enhance chemosensitivity in neuroblastoma via downregulating HDM2 and augmenting p53 stability and nuclear accumulation.
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.24000210.V1
Abstract: Supplementary Figures
Publisher: Wiley
Date: 06-03-2017
Publisher: MDPI AG
Date: 14-02-2020
DOI: 10.3390/JPM10010009
Abstract: Precision medicine is changing cancer care and placing new demands on oncology professionals. Precision medicine trials for high-risk childhood cancer exemplify these complexities. We assessed clinicians’ (n = 39) and scientists’ (n = 15) experiences in the first year of the PRecISion Medicine for Children with Cancer (PRISM) trial for children and adolescents with high-risk cancers, through an in-depth semi-structured interview. We thematically analysed participants’ responses regarding their professional challenges, and measured oncologists’ knowledge of genetics and confidence with somatic and germline molecular test results. Both groups described positive early experiences with PRISM but were cognisant of managing parents’ expectations. Key challenges for clinicians included understanding and communicating genomic results, balancing biopsy risks, and drug access. Most oncologists rated ‘good’ knowledge of genetics, but a minority were ‘very confident’ in interpreting (25%), explaining (34.4%) and making treatment recommendations (18.8%) based on somatic genetic test results. Challenges for scientists included greater emotional impact of their work and balancing translational outputs with academic productivity. Continued tracking of these challenges across the course of the trial, while assessing the perspectives of a wider range of stakeholders, is critical to drive the ongoing development of a workforce equipped to manage the demands of paediatric precision medicine.
Publisher: Wiley
Date: 15-03-2011
Publisher: Georg Thieme Verlag KG
Date: 11-2003
DOI: 10.1055/S-2003-45491
Abstract: The fast growing internet offers easy access to medical information. So far there are limited data concerning the quality of this information. This study examined quality and readability of paediatric neuro-oncological information on the internet in german language. Using the search terms "medulloblastoma", "ependymoma", "craniopharyngeoma", "brainstem glioma" and "low grade astrocytoma" in six different search engines, the first 30 universal/uniform resource locators (URLs) of each search engine were assessed. Appropriate Web sites were evaluated in regards to quality using DISCERN-Instrument and checklist rating system. Readability was rated by Flesch Reading Ease score. Out of 889,56 web sites remained evaluable. Most of the sites rated as poor to very poor (49 %), 30 % rated as fair and 21 % as good to very good. Readability was scored as very difficult with complex vocabulary content limiting the usefulness of good web sites. Search-ing for childhood brain tumours via internet is time consuming and most often ineffective. There is a lack of high-quality and comprehensible information on childhood brain tumours on german web sites. Cooperation of scientific medical societies and the Federal Ministry of Health is essential to provide comprehensible and high-quality information on internet as an effective and supportive resource for patients and their relatives.
Publisher: American Association for Cancer Research (AACR)
Date: 15-08-2020
DOI: 10.1158/1538-7445.AM2020-SY09-02
Abstract: Pediatric cancers have distinct molecular landscapes compared to adult cancers, with low point mutation rates, distinct mutated genes, and a prevalence of structural rearrangements. These complex features suggest genomic analyses alone will have limitations for translation into clinical benefit, and a multifaceted approach is therefore needed to maximize the number of patients for whom a therapeutic recommendation can be made. The Zero Childhood Cancer Program (ZERO) aims to assess the feasibility of precision medicine to identify targeted therapeutic agents for patients with high-risk (HR) pediatric malignancies (newly diagnosed, relapsed or refractory, overall expected survival & %). Comprehensive molecular profiling, involving whole genome sequencing (tumor, germline DNA), whole transcriptome RNA sequencing and methylation profiling (brain tumors and sarcomas), is combined with preclinical drug testing using in vitro high-throughput drug screening (HTS, 125 compound library, single agent) and patient-derived xenograft (PDX) drug efficacy testing. Results are curated and recommendations (targeted therapy, change of diagnosis or genetics referral for a germline cancer predisposition gene mutation) are made by a national Multidisciplinary Tumor Board. Following the successful completion of a 2-year pilot feasibility study (TARGET, 2015-17), results demonstrated high-throughput in vitro drug screening and patient-derived xenografting expanded the therapeutic options and improved clinical outcomes in a cohort of 56 high-risk pediatric patients, with the HTS and PDX providing orthogonal confirmation of targetable molecular aberrations in 21% of patients and unique therapeutic options for 16% of patients. The national multicenter prospective trial (PRISM, 2017-20) is open at all 8 pediatric oncology centers around Australia. PRISM has enrolled 290 patients at January 2020 across the broad spectrum of HR cancers. This unique comprehensive platform has resulted in at least one recommendation (tiered by the level of supportive evidence) being issued for 75% of patients, and a reportable germline finding in 17% of patients. Early clinical response data indicates that 54% of patients who were treated with a recommended therapy demonstrated clinical benefit (complete response, partial response or stable disease & =6 months), with 38% demonstrating an objective response. ZERO demonstrates the feasibility of a comprehensive precision medicine platform to identify treatment recommendations in HR pediatric cancer patients. Plans are underway for subsequent enrolment expansion, introduction of emerging methods and technologies and extension of research projects in immunoprofiling, liquid biopsy, psychosocial impact of pediatric precision medicine, health economics and health implementation. Citation Format: Michelle Haber, Mark J. Cowley, Paul Ekert, Loretta Lau, Emily Mould, ZCC PRISM Omics Core, ZCC Prelinical Drug Testing Core, Andrew Gifford, Richard B. Lock, Glenn M. Marshall, Murray D. Norris, Tracey O'Brien, Dong Anh Khuong Quang, David Thomas, Toby Trahair, Katherine Tucker, David S. Ziegler, Vanessa Tyrrell. Zero Childhood Cancer: A comprehensive precision medicine platform for children with high-risk cancer in Australia [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR Cancer Res 2020 (16 Suppl):Abstract nr SY09-02.
Publisher: American Association for Cancer Research (AACR)
Date: 21-08-2023
DOI: 10.1158/0008-5472.24000204.V1
Abstract: Supplementary Tables S1-S7
Publisher: Springer Science and Business Media LLC
Date: 25-01-2023
Publisher: Springer Science and Business Media LLC
Date: 10-11-2005
DOI: 10.1007/S00381-005-1238-X
Abstract: Internet information, now available in many different languages, can become a major source of information for patients and families in their own mother tongue. Chinese represent one of most frequently spoken language in the world. The aims of this study were to critically appraise the quantity and quality of Internet health information in childhood brain tumour in the Chinese language and to identify sufficient quality websites that can potentially be recommended to Chinese-speaking parents. Internet information on six common paediatric brain tumours was searched using six commonly used Chinese search engines. Websites were assessed systematically using two rating tools: DISCERN instrument and Checklist Rating System Instrument. Out of 946 sites accessed, only 13 assessable Chinese websites, displaying Traditional Chinese characters and providing information on brain tumour, were identified. Only four sites included specific discussion on brain tumours in children. Ten websites failed to provide satisfactory information on brain tumour as rated by DISCERN instrument. Overall only 41% of the 13 specific items relevant to brain tumours were mentioned (Checklist Rating System Instrument). Only a few satisfactory websites can be recommended to Chinese-speaking families for general information on brain tumour with caution from health care providers that such information may not apply to the child's in idual condition.
Publisher: Wiley
Date: 25-12-2020
DOI: 10.1002/PBC.28133
Abstract: The aim of this study was to improve the predictive power of patient-derived xenografts (PDXs, also known as mouse avatars) to more accurately reflect outcomes of clofarabine-based treatment in pediatric acute lymphoblastic leukemia (ALL) patients. Pharmacokinetic (PK) studies were conducted using clofarabine at 3.5 to 15 mg/kg in mice. PDXs were established from relapsed/refractory ALL patients who exhibited good or poor responses to clofarabine. PDX engraftment and response to clofarabine (either as a single agent or in combinations) were assessed based on stringent objective response measures modeled after the clinical setting. In naïve immune-deficient NSG mice, we determined that a clofarabine dose of 3.5 mg/kg resulted in systemic exposures equivalent to those achieved in pediatric ALL patients treated with clofarabine-based regimens. This dose was markedly lower than the doses of clofarabine used in previously reported preclinical studies (typically 30-60 mg/kg) and, when scheduled consistent with the clinical regimen (daily × 5), resulted in 34-fold lower clofarabine exposures. Using a well-tolerated clofarabine/etoposide/cyclophosphamide combination regimen, we then found that the responses of PDXs better reflected the clinical responses of the patients from whom the PDXs were derived. This study has identified an in vivo clofarabine treatment regimen that reflects the clinical responses of relapsed/refractory pediatric ALL patients. This regimen could be used prospectively to identify patients who might benefit from clofarabine-based treatment. Our findings are an important step toward in idualizing prospective patient selection for the use of clofarabine in relapsed/refractory pediatric ALL patients and highlight the need for detailed PK evaluation in murine PDX models.
No related grants have been discovered for Loretta Lau.