Access to Chimeric Antigen Receptor T Cell Clinical Trials in Underrepresented Populations: A Multicenter Cohort Study of Pediatric and Young Adult Acute Lymphobastic Leukemia Patients

Chimeric antigen receptor T cell (CAR-T) therapy is a promising approach to improve survival for children and adults with relapsed/refractory (r/r) B cell acute lymphoblastic leukemia (B-ALL), but these clinical trials might not be equally accessible to patients of low socioeconomic status (SES) or to patients from racial or ethnic minority groups. We sought to describe the sociodemographic characteristics of pediatric and adolescent and young adult (AYA) patients enrolled in CAR-T clinical trials and to compare these characteristics to those of other patients with r/r B-ALL. We conducted a multicenter retrospective cohort study at 5 pediatric consortium sites to compare the sociodemographic characteristics of patients treated and enrolled in CAR-T trials at their home institution, other patients with r/r B-ALL treated at these sites, and patients referred from an external hospital for CAR-T trials. The patients were age 0 to 27 years with r/r B-ALL treated at 1 of the consortium sites between 2012 and 2018. Clinical and demographic data were collected from the electronic health record. We calculated distance from home to treating institution and assigned SES scores based on census tract. Among the 337 patients treated for r/r B-ALL, 112 were referred from an external hospital to a consortium site and enrolled in a CAR-T trial and 225 were treated primarily at a consortium site, with 34% enrolled in a CAR-T trial. Patients treated primarily at a consortium site had similar characteristics regardless of trial enrollment. Lower proportions of Hispanic patients (37% versus 56%; P = .03), patients whose preferred language was Spanish (8% versus 22%; P = .006), and publicly insured patients (38% versus 65%; P = .001) were referred from an external hospital than were treated primarily at a consortium site and enrolled in a CAR-T trial. Patients who are Hispanic, Spanish-speaking, or publicly insured are underrepresented in referrals from external hospitals to CAR-T centers. External provider implicit bias also may influence referral of these patients. Establishing partnerships between CAR-T centers and external hospital sites may improve provider familiarity, patient referral, and patient access to CAR-T clinical trials.

Establishing guidelines to harmonize tumor mutational burden (TMB): in silico assessment of variation in TMB quantification across diagnostic platforms: phase I of the Friends of Cancer Research TMB Harmonization Project

Background

Tumor mutational burden (TMB), defined as the number of somatic mutations per megabase of interrogated genomic sequence, demonstrates predictive biomarker potential for the identification of patients with cancer most likely to respond to immune checkpoint inhibitors. TMB is optimally calculated by whole exome sequencing (WES), but next-generation sequencing targeted panels provide TMB estimates in a time-effective and cost-effective manner. However, differences in panel size and gene coverage, in addition to the underlying bioinformatics pipelines, are known drivers of variability in TMB estimates across laboratories. By directly comparing panel-based TMB estimates from participating laboratories, this study aims to characterize the theoretical variability of panel-based TMB estimates, and provides guidelines on TMB reporting, analytic validation requirements and reference standard alignment in order to maintain consistency of TMB estimation across platforms.

Methods

Eleven laboratories used WES data from The Cancer Genome Atlas Multi-Center Mutation calling in Multiple Cancers (MC3) samples and calculated TMB from the subset of the exome restricted to the genes covered by their targeted panel using their own bioinformatics pipeline (panel TMB). A reference TMB value was calculated from the entire exome using a uniform bioinformatics pipeline all members agreed on (WES TMB). Linear regression analyses were performed to investigate the relationship between WES and panel TMB for all 32 cancer types combined and separately. Variability in panel TMB values at various WES TMB values was also quantified using 95% prediction limits.

Results

Study results demonstrated that variability within and between panel TMB values increases as the WES TMB values increase. For each panel, prediction limits based on linear regression analyses that modeled panel TMB as a function of WES TMB were calculated and found to approximately capture the intended 95% of observed panel TMB values. Certain cancer types, such as uterine, bladder and colon cancers exhibited greater variability in panel TMB values, compared with lung and head and neck cancers.

Conclusions

Increasing uptake of TMB as a predictive biomarker in the clinic creates an urgent need to bring stakeholders together to agree on the harmonization of key aspects of panel-based TMB estimation, such as the standardization of TMB reporting, standardization of analytical validation studies and the alignment of panel-based TMB values with a reference standard. These harmonization efforts should improve consistency and reliability of panel TMB estimates and aid in clinical decision-making.

A mixed methods study exploring the role of perceived side effects on treatment decision-making in older adults with acute myeloid leukemia (AML)

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Background: AML patients may be treated with intensive chemotherapy (IC), or non-intensive chemotherapy (NIC) or they may receive best supportive care (BSC) or hospice care. Balancing treatment efficacy and toxicities is key in treatment decision-making. IC is efficacious with extensive toxicities, while NIC has lower risk of toxicities but reduced efficacy. This study provides an international, multi-stakeholder perspective on the role of side effects in AML treatment decision-making. Methods: We conducted one-on-one, 60-minute interviews with 28 AML patients (>65 years, not receiving IC), 25 of their family members and 10 independent physicians from the US, UK and Canada. Interviews included open-ended questions to explore the treatment decision-making process. Participants also rated the importance of various factors in AML treatment decision-making from 0 (not important) to 3 (very important). Results: The sample included patients with varying treatment histories (13 no treatment, 11 on NIC, 3 discontinued NIC, 1 BSC). Side effects were rated as a ‘very important’ factor in treatment decision-making by a greater proportion of patients not on treatment (n = 9/13; 69.2%) and their relatives (n = 12/13; 92.3%) compared to those with experience of NIC (n = 5/11 who answered, 45.5%), their relatives (n = 3/11; 27.3%), and physicians (n = 4/10; 40.0%). When discussing side effects in detail, there was a disconnect between perceptions of patients not on treatment, and side effects that patients on NIC actually experienced. Many patients with no treatment experience were worried that side effects would be worse than their current symptoms (n = 6/13), referring to constant vomiting, hair loss, organ failure, or death. Fear of side effects was the primary reason for opting not to take treatment (n = 9/13), though it was not clear if these patients were distinguishing between IC and NIC. In contrast, although two patients’ experiences of side effects resulted in them discontinuing NIC (n = 2/14), a higher proportion (n = 9/14) reported that the side effects had little impact on their life. Side effects most frequently reported by patients with experience of NIC (n = 11/14) were considered mild and included fatigue, reduced appetite, generally feeling unwell, nausea and injection site irritation (all n = 3). It was most commonly reported that the worst aspect of NIC was the time commitment (n = 4/8 asked). When accounting for different treatments paths no international variation in findings was observed. Conclusions: The nature and severity of side effects of AML treatment were perceived to be worse than reality. This incorrect perception may lead to undertreatment of patients and result in worse outcomes. There is a need for more patient education and resources about the lived treatment experience, to enhance understanding and mitigate pre-conceived notions of side effects.

Subsequent Neoplasm Risk Associated With Rare Variants in DNA Damage Response and Clinical Radiation Sensitivity Syndrome Genes in the Childhood Cancer Survivor Study

PURPOSE

Radiotherapy for childhood cancer is associated with elevated subsequent neoplasm (SN) risk, but the contribution of rare variants in DNA damage response and radiation sensitivity genes to SN risk is unknown.

PATIENTS AND METHODS

We conducted whole-exome sequencing in a cohort of childhood cancer survivors originally diagnosed during 1970 to 1986 (mean follow-up, 32.7 years), with reconstruction of doses to body regions from radiotherapy records. We identified patients who developed SN types previously reported to be related to radiotherapy (RT-SNs; eg, basal cell carcinoma [BCC], breast cancer, meningioma, thyroid cancer, sarcoma) and matched controls (sex, childhood cancer type/diagnosis, age, SN location, radiation dose, survival). Conditional logistic regression assessed SN risk associated with potentially protein-damaging rare variants (SnpEff, ClinVar) in 476 DNA damage response or radiation sensitivity genes with exact permutation-based P values using a Bonferroni-corrected significance threshold of P < 8.06 × 10^-5.

RESULTS

Among 5,105 childhood cancer survivors of European descent, 1,108 (21.7%) developed at least 1 RT-SN. Out-of-field RT-SN risk, excluding BCC, was associated with homologous recombination repair (HRR) gene variants (patient cases, 23.2%; controls, 10.8%; odds ratio [OR], 2.6; 95% CI, 1.7 to 3.9; P = 4.79 × 10^-5), most notably but nonsignificantly for FANCM (patient cases, 4.0%; matched controls, 0.6%; P = 9.64 × 10^-5). HRR variants were not associated with likely in/near-field RT-SNs, excluding BCC (patient cases, 12.7%; matched controls, 12.9%; P = .92). Irrespective of radiation dose, risk for RT-SNs was also associated with EXO1 variants (patient cases, 1.8%; controls, 0.4%; P = 3.31 × 10^-5), another gene implicated in DNA double-strand break repair.

CONCLUSION

In this large-scale discovery study, we identified novel associations between RT-SN risk after childhood cancer and potentially protein-damaging rare variants in genes involved in DNA double-strand break repair, particularly HRR. With replication, these results could affect screening recommendations for childhood cancer survivors and risk-benefit assessments of treatment approaches.

A fork in the road: A mixed methods study exploring why older adults with acute myeloid leukemia choose different treatment paths

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Background: Current treatment options for acute myeloid leukemia (AML) are diverse, including intensive chemotherapy (IC), low intensity therapy, best supportive care (BSC), and hospice care. Despite continued development of new therapies, recent data suggest that approximately 60% of older US patients remain untreated, but reasons for this are not well understood. By gathering insights from physicians, patients, and their family members, this study aims to better understand the factors that influence treatment decisions for adults with AML. Methods: Physicians in the US (n=4), UK (n=3) and Canada (n=3), and 15 US AML patient-family member dyads took part in one-on-one, 60-minute semi-structured interviews. Each participant rated a series of factors on a scale from 0 (not at all important) to 3 (very important) to determine their importance in treatment decision-making. Among the 15 adults with AML (>65 years, not taking IC) interviewed thus far, 13 had not received any treatment. Additional interviews are scheduled in the UK and Canada with patients having varied treatment experiences (data will be available for presentation). Results: To date, findings highlight the key role perceptions of side effects and patient health play in treatment decision making. A fear of treatment side effects was the primary reason patients (n=9/13) opted not to receive treatment. For the 2/15 study patients who had received treatment, side effects were considered the worst part of their treatment experience. Physicians also stated patients on BSC would be more willing to take low intensity treatments if risks (e.g., side effects) were minimized. Patients (n=11/15), their family members (n=11/15), and physicians (n=10/10) agreed that patients’ health (including age and comorbidities) influenced if treatment was pursued. Additionally, US physicians suggested that some patients have little desire to pursue treatment, with patients’ perception of low intensity therapy having poor efficacy and proximity of care influencing their choice for BSC or hospice care. Further analysis will explore other factors influencing patients’ treatment decisions and differences among patients who receive treatment versus those who do not. Conclusions: The treatment decision-making process for older adults with AML is complex and multifactorial. Understanding factors that influence treatment decisions is important if drug developers and prescribers are to ensure the availability of therapies that better align with individual patients’ needs.

Correction to: DNA methylation signature is prognostic of choroid plexus tumor aggressiveness

After publication of the original article [1], authors have requested to add a 'J' as middle name for Richard Gilbertson. Hence, full name should be Richard J Gilbertson.

DNA methylation signature is prognostic of choroid plexus tumor aggressiveness

BACKGROUND

Histological grading of choroid plexus tumors (CPTs) remains the best prognostic tool to distinguish between aggressive choroid plexus carcinoma (CPC) and the more benign choroid plexus papilloma (CPP) or atypical choroid plexus papilloma (aCPP); however, these distinctions can be challenging. Standard treatment of CPC is very aggressive and often leads to severe damage to the young child's brain. Therefore, it is crucial to distinguish between CPC and less aggressive entities (CPP or aCPP) to avoid unnecessary exposure of the young patient to neurotoxic therapy. To better stratify CPTs, we utilized DNA methylation (DNAm) to identify prognostic epigenetic biomarkers for CPCs.

METHODS

We obtained DNA methylation profiles of 34 CPTs using the HumanMethylation450 BeadChip from Illumina, and the data was analyzed using the Illumina Genome Studio analysis software. Validation of differentially methylated CpG sites chosen as biomarkers was performed using pyrosequencing analysis on additional 22 CPTs. Sensitivity testing of the CPC DNAm signature was performed on a replication cohort of 61 CPT tumors obtained from Neuropathology, University Hospital Münster, Germany.

RESULTS

Generated genome-wide DNAm profiles of CPTs showed significant differences in DNAm between CPCs and the CPPs or aCPPs. The prediction of clinical outcome could be improved by combining the DNAm profile with the mutational status of TP53. CPCs with homozygous TP53 mutations clustered as a group separate from those carrying a heterozygous TP53 mutation or CPCs with wild type TP53 (TP53-wt) and showed the worst survival outcome. Specific DNAm signatures for CPCs revealed AK1, PER2, and PLSCR4 as potential biomarkers for CPC that can be used to improve molecular stratification for diagnosis and treatment.

CONCLUSIONS

We demonstrate that combining specific DNAm signature for CPCs with histological approaches better differentiate aggressive tumors from those that are not life threatening. These findings have important implications for future prognostic risk prediction in clinical disease management.

Spatial and Temporal Heterogeneity of Panel-Based Tumor Mutational Burden in Pulmonary Adenocarcinoma: Separating Biology From Technical Artifacts

BACKGROUND

Tumor mutational burden (TMB) is an emerging biomarker used to identify patients who are more likely to benefit from immuno-oncology therapy. Aside from various unsettled technical aspects, biological variables such as tumor cell content and intratumor heterogeneity may play an important role in determining TMB.

METHODS

TMB estimates were determined applying the TruSight Oncology 500 targeted sequencing panel. Spatial and temporal heterogeneity was analyzed by multiregion sequencing (two to six samples) of 24 pulmonary adenocarcinomas and by sequencing a set of matched primary tumors, locoregional lymph node metastases, and distant metastases in five patients.

RESULTS

On average, a coding region of 1.28 Mbp was covered with a mean read depth of 609x. Manual validation of the mutation-calls confirmed a good performance, but revealed noticeable misclassification during germline filtering. Different regions within a tumor showed considerable spatial TMB variance in 30% (7 of 24) of the cases (maximum difference, 14.13 mut/Mbp). Lymph node-derived TMB was significantly lower (p = 0.016). In 13 cases, distinct mutational profiles were exclusive to different regions of a tumor, leading to higher values for simulated aggregated TMB. Combined, intratumor heterogeneity and the aggregated TMB could result in divergent TMB designation in 17% of the analyzed patients. TMB variation between primary tumor and distant metastases existed but was not profound.

CONCLUSIONS

Our data show that, in addition to technical aspects such as germline filtering, the tumor content and spatially divergent mutational profiles within a tumor are relevant factors influencing TMB estimation, revealing limitations of single-sample-based TMB estimations in a clinical context.

Risk of Second Primary Bone and Soft-Tissue Sarcomas Among Young Adulthood Cancer Survivors

Excess sarcoma risks after childhood cancer are well established, but risks among young adulthood cancer survivors are poorly understood. Using US population-based cancer registry data, we compared bone and soft-tissue sarcoma risk vs the general population among 186 351 individuals who were diagnosed with nonsarcoma first primary malignancies at ages 20-39 years from 1975 to 2014 (follow-up through 2015) and survived at least 1 year. Bone sarcomas were rare (n = 50), but risk was statistically significantly elevated overall (2.9-fold) and greater than fivefold after Hodgkin lymphoma, non-Hodgkin lymphoma, and central nervous system tumors. Soft-tissue sarcomas were more common (n = 284) and risks were statistically significantly elevated approximately twofold overall and after melanoma and carcinomas of the breast, thyroid, and testis, and greater than fourfold after Hodgkin lymphoma and central nervous system tumors. Risks varied markedly by subtype, with the highest risks (greater than fourfold) for osteosarcoma and the soft-tissue subtypes of rhabdomyosarcoma and blood vessel and nerve sheath sarcomas. These data demonstrate elevated risk for sarcoma after a range of young adulthood cancers.

TMB standardization by alignment to reference standards: Phase II of the Friends of Cancer Research TMB Harmonization Project

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Background: Tumor mutational burden (TMB) is a predictive biomarker of response to immune checkpoint inhibitors across multiple cancers. In Phase 1 of the Friends of Cancer Research Harmonization Project, we demonstrated a robust correlation between TMB estimated using targeted next-generation sequencing (NGS) gene panels and whole exome sequencing (WES) applied to MC3-TCGA data. These findings demonstrated variability in TMB estimates across different panels. Phase 2 evaluates sustainable TMB reference standard materials for TMB alignment to assess this variability. The goal of this effort is to establish best practices for estimating TMB in order to improve consistency across panels, for the sake of optimizing clinical application and facilitating integration of datasets generated from multiple assays. Methods: Fifteen laboratories with targeted panels at different stages of development participated. We identified a set of reference standards consisting of 10 well-characterized human-derived lung and breast tumor-normal matched cell lines. WES was performed using a uniform bioinformatics pipeline agreed upon by all team members (WES-TMB). Each laboratory used their own sequencing and bioinformatics pipelines (tumor-only and tumor-normal) to estimate TMB according to genes represented in their respective panels (panel-TMB). The association between WES-TMB and each panel-TMB was investigated using regression analyses. Bias (relative to WES-TMB) and variability in TMB estimates across panels were rigorously assessed. All analyses were blinded. Results: The set of reference standards spanned a clinically meaningful TMB range (4.3 to 31.4 mut/Mb). Preliminary data from 12 laboratories shows a good correlation between panel-TMB and WES-TMB in this empirical analysis. Across panels, regression R2 values range 0.77-0.96 with slopes ranging 0.60-1.26. Calibration analyses that seek to minimize variability of TMB estimates across panels using the established set of reference standards are ongoing, as well as investigating cancer type dependence on the relationship between panel-TMB vs. WES-TMB, which will be available at the time of presentation. Conclusions: Preliminary findings demonstrate feasibility of using sustainable reference control cell lines to standardize and align estimation of TMB across different targeted NGS assays. Future studies aim to validate reference standard material as a reliable alignment tool by using formalin-fixed paraffin-embedded human tumor samples.

Myc and Loss of p53 Cooperate to Drive Formation of Choroid Plexus Carcinoma

Choroid plexus carcinoma (CPC) is a rare brain tumor that occurs most commonly in very young children and has a dismal prognosis despite intensive therapy. Improved outcomes for patients with CPC depend on a deeper understanding of the mechanisms underlying the disease. Here we developed transgenic models of CPCs by activating the Myc oncogene and deleting the Trp53 tumor suppressor gene in murine neural stem cells or progenitors. Murine CPC resembled their human counterparts at a histologic level, and like the hypodiploid subset of human CPC, exhibited multiple whole-chromosome losses, particularly of chromosomes 8, 12, and 19. Analysis of murine and human CPC gene expression profiles and copy number changes revealed altered expression of genes involved in cell cycle, DNA damage response, and cilium function. High-throughput drug screening identified small molecule inhibitors that decreased the viability of CPC. These models will be valuable tools for understanding the biology of choroid plexus tumors and for testing novel approaches to therapy. SIGNIFICANCE: This study describes new mouse models of choroid plexus carcinoma and uses them to investigate the biology and therapeutic responsiveness of this highly malignant pediatric brain tumor.

Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions

Characterization of tumors utilizing next‐generation sequencing methods, including assessment of the number of somatic mutations (tumor mutational burden [TMB]), is currently at the forefront of the field of personalized medicine. Recent clinical studies have associated high TMB with improved patient response rates and survival benefit from immune checkpoint inhibitors; hence, TMB is emerging as a biomarker of response for these immunotherapy agents. However, variability in current methods for TMB estimation and reporting is evident, demonstrating a need for standardization and harmonization of TMB assessment methodology across assays and centers. Two uniquely placed organizations, Friends of Cancer Research (Friends) and the Quality Assurance Initiative Pathology (QuIP), have collaborated to coordinate efforts for international multistakeholder initiatives to address this need. Friends and QuIP, who have partnered with several academic centers, pharmaceutical organizations, and diagnostic companies, have adopted complementary, multidisciplinary approaches toward the goal of proposing evidence‐based recommendations for achieving consistent TMB estimation and reporting in clinical samples across assays and centers. Many factors influence TMB assessment, including preanalytical factors, choice of assay, and methods of reporting. Preliminary analyses highlight the importance of targeted gene panel size and composition, and bioinformatic parameters for reliable TMB estimation. Herein, Friends and QuIP propose recommendations toward consistent TMB estimation and reporting methods in clinical samples across assays and centers. These recommendations should be followed to minimize variability in TMB estimation and reporting, which will ensure reliable and reproducible identification of patients who are likely to benefit from immune checkpoint inhibitors.

Genome-Wide Association Study to Identify Susceptibility Loci That Modify Radiation-Related Risk for Breast Cancer After Childhood Cancer

Background

Childhood cancer survivors treated with chest-directed radiotherapy have substantially elevated risk for developing breast cancer. Although genetic susceptibility to breast cancer in the general population is well studied, large-scale evaluation of breast cancer susceptibility after chest-directed radiotherapy for childhood cancer is lacking.

Methods

We conducted a genome-wide association study of breast cancer in female survivors of childhood cancer, pooling two cohorts with detailed treatment data and systematic, long-term follow-up: the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. The study population comprised 207 survivors who developed breast cancer and 2774 who had not developed any subsequent neoplasm as of last follow-up. Genotyping and subsequent imputation yielded 16 958 466 high-quality variants for analysis. We tested associations in the overall population and in subgroups stratified by receipt of lower than 10 and 10 or higher gray breast radiation exposure. We report P values and pooled per-allele risk estimates from Cox proportional hazards regression models. All statistical tests were two-sided.

Results

Among survivors who received 10 or higher gray breast radiation exposure, a locus on 1q41 was associated with subsequent breast cancer risk (rs4342822, nearest gene PROX1 , risk allele frequency in control subjects [RAF controls ] = 0.46, hazard ratio = 1.92, 95% confidence interval = 1.49 to 2.44, P = 7.09 × 10 -9 ). Two rare variants also showed potentially promising associations (breast radiation ≥10 gray: rs74949440, 11q23, TAGLN , RAF controls = 0.02, P = 5.84 × 10 -8 ; <10 gray: rs17020562, 1q32.3, RPS6KC1 , RAF controls = 0.0005, P = 6.68 × 10 -8 ). Associations were restricted to these dose subgroups, with consistent findings in the two survivor cohorts.

Conclusions

Our study provides strong evidence that germline genetics outside high-risk syndromes could modify the effect of radiation exposure on breast cancer risk after childhood cancer.

Abstract 2691: Genome-wide association study identifies two susceptibility loci that modify radiation-related risk for breast cancer after childhood cancer: A report from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort

Background: Childhood cancer survivors treated with chest radiotherapy have substantially elevated risk for developing breast cancer. Although numerous breast cancer susceptibility variants have been established, genetic predisposition for breast cancer after childhood cancer remains poorly understood.

Methods: We conducted the first genome-wide association study of subsequent breast cancer in female childhood cancer survivors within two large-scale cohorts with detailed treatment data and systematic, long-term follow-up: the Childhood Cancer Survivor Study [CCSS; 178 breast cancer cases, 2200 controls (survivors without subsequent neoplasm) of European descent] and the St. Jude Lifetime Cohort (SJLIFE; 29 cases, 574 controls). Genotyping on the Illumina HumanOmni5MExome (CCSS) or Affymetrix 6.0 (SJLIFE) array and imputation based on the 1000 Genomes Project yielded &gt;16 million high quality genotyped or imputed variants available in both studies. Assuming an additive genetic model, we used multivariate Cox regression to quantify the effect of each variant in the overall population and stratified by receipt of ≥10 Gray (Gy) or &lt;10 Gy radiation exposure to the chest.

Results: We identified two loci associated with breast cancer risk among children who received ≥10 Gy radiation to the chest (131 cases, 493 controls): one at 1q41 [rs4342822, risk allele frequency (RAF) = 0.46 in controls, pooled per allele hazard ratio (HR) = 1.94, 95% confidence interval (CI) = 1.50-2.51, Pexact = 1.20×10−8] and another at 11q23 (rs74949440, RAF = 0.02 in controls, HR = 3.71, 95%CI = 2.18-6.32, Pexact = 2.00×10−9). Neither locus was associated with breast cancer risk among children who received &lt;10 Gy radiation to the chest (69 cases, 2144 controls; rs4342822: HR = 1.03, 95%CI = 0.75-1.44; rs74949440: HR = 1.21, 0.41-3.54). Results were consistent in the two studies, and the associations did not appear to be related to type of first primary childhood cancer. Both loci fall in or near biologically plausible candidate genes: the variant rs4342822 lies near PROX1, which is amplified in &gt;10% of breast cancers in The Cancer Genome Atlas data. The variant rs74949440 is intronic to TAGLN, whose expression levels have been associated with breast cancer prognosis and altered cell death resistance following irradiation in human carcinoma cell lines.

Conclusion: These findings represent the first evidence outside of identified high-risk cancer susceptibility genes that certain individuals are genetically predisposed to developing breast cancer after radiotherapy and suggest that radiation exposure may interact with germline genetics to modify breast cancer risk.

Citation Format: Lindsay M. Morton, Joshua N. Sampson, Gregory T. Armstrong, Ting-Huei Chen, Melissa Hudson, Eric Karlins, Casey L. Dagnall, Shenchao Li, Carmen L. Wilson, Kumar Srivastava, Wei Liu, Guolian Kang, Kevin Oeffinger, Tara O. Henderson, Chaya S. Moskowitz, Todd M. Gibson, Diana M. Merino, Jeannette R. Wong, Sue Hammond, Joseph P. Neglia, Lucie M. Turcotte, Jeremy Miller, Laura Bowen, William A. Wheeler, Wendy M. Leisenring, John A. Whitton, Laurie Burdette, Belynda D. Hicks, Mitchell J. Machiela, Aurelie Vogt, Zhaoming Wang, Meredith Yeager, Geoffrey Neale, Matthew Lear, Louise C. Strong, Yutaka Yasui, Marilyn Stovall, Rita E. Weathers, Susan A. Smith, Rebecca Howell, Stella M. Davies, Gretchen A. Radloff, Amy Berrington de González, Peter D. Inskip, Preetha Rajaraman, Joseph F. Fraumeni, Smita Bhatia, Stephen J. Chanock, Margaret A. Tucker, Leslie L. Robison. Genome-wide association study identifies two susceptibility loci that modify radiation-related risk for breast cancer after childhood cancer: A report from the Childhood Cancer Survivor Study and St. Jude Lifetime Cohort. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2691.

Cortical control of anticipatory postural adjustments prior to stepping

Human bipedal balance control is achieved either reactively or predictively by a distributed network of neural areas within the central nervous system with a potential role for cerebral cortex. While the role of the cortex in reactive balance has been widely explored, only few studies have addressed the cortical activations related to predictive balance control. The present study investigated the cortical activations related to the preparation and execution of anticipatory postural adjustment (APA) that precede a step. This study also examined whether the preparatory cortical activations related to a specific movement is dependent on the context of control (postural component vs. focal component). Ground reaction forces and electroencephalographic (EEG) data were recorded from 14 healthy adults while they performed lateral weight shift and lateral stepping with and without initially preloading their weight to the stance leg. EEG analysis revealed that there were distinct movement-related potentials (MRPs) with concurrent event-related desynchronization (ERD) of mu and beta rhythms prior to the onset of APA and also to the onset of foot-off during lateral stepping in the fronto-central cortical areas. Also, the MRPs and ERD prior to the onset of APA and onset of lateral weight shift were not significantly different suggesting the comparable cortical activations for the generation of postural and focal movements. The present study reveals the occurrence of cortical activation prior to the execution of an APA that precedes a step. Importantly, this cortical activity appears independent of the context of the movement.

Abstract 3280: Sequencing approaches define the mutation and fusion landscape of choroid plexus carcinomas

Background & Purpose: Choroid plexus carcinomas (CPCs) are aggressive intraventricular tumors accounting for ∼20% of brain tumors in children under 2 years of age. The clinical outcome of CPC patients is variable having an average 5-year overall survival of 50%. A recent study from our group has characterized copy number, DNA methylation and gene expression aberrations in these tumors and identified that a greater number of mutated copies of TP53 is significantly associated with reduced survival. The mutational landscape of these tumors is largely unknown, although this information is crucial to refine the understanding of CPC tumorigenesis and identify novel therapeutic targets. The purpose of this study is to complement the in-depth analysis of the molecular abnormalities driving CPC development by investigating single nucleotide alterations (SNAs), and structural variations (SVs) in CPC DNA and RNA.

Methods: A cohort of 29 high quality samples from 25 pediatric CPC patients was used for this study. DNA from 4 blood-tumor pairs and RNA from 27 CPCs were used for whole genome sequencing (WGS) and RNA sequencing (RNA seq), respectively, as part of the Pediatric Cancer Genome Project (PCGP) at St. Jude Children's Research Hospital, using the Illumina Genome Analyzer IIx or HiSeq platform with 100bp read length. Eighty-two percent of samples were primary tumors, while 17.2% were recurrences. Only one sample had sufficient high quality nucleic acid material to conduct both DNA and RNA sequencing.

Results: CPCs exhibited very low levels of SNAs ranging from 1 to 11 SNAs per genome. Copy number analysis using WGS confirmed the high levels of copy number alterations in CPCs. RNAseq analysis revealed that primary and recurrent CPC samples exhibited 100% similarity in fusion breakpoints, suggesting very little clonal divergence in these pediatric brain tumors. A recurrent fusion in chromosome 3 was observed in two independent CPCs (7%). Other fusion events generated in-frame alterations in genes involved in the MAP kinase pathway, such as PPP2R1A, and in apoptosis and cell proliferation pathways. The sample for which WGS and RNAseq was generated exhibited chromothripsis with numerous SVs affecting chromosomes 1 and 19. No other SV events were found in our CPC cohort.

Conclusions: CPCs exhibit very few SNAs and SVs, but are characterized by recurrent chromosome-wide copy number aberrations. Various RNA fusion events altering the MAP kinase pathway have been identified, suggesting a key role for kinase pathways in the development and growth of these devastating brain tumors.

Citation Format: Diana M. Merino, Yongjin Li, Xiaotu Ma, Jinghui Zhang, David Malkin, Richard J. Gilbertson. Sequencing approaches define the mutation and fusion landscape of choroid plexus carcinomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3280. doi:10.1158/1538-7445.AM2015-3280

Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers

DNA replication-associated mutations are repaired by two components: polymerase proofreading and mismatch repair. The mutation consequences of disruption to both repair components in humans are not well studied. We sequenced cancer genomes from children with inherited biallelic mismatch repair deficiency (bMMRD). High-grade bMMRD brain tumors exhibited massive numbers of substitution mutations (>250/Mb), which was greater than all childhood and most cancers (>7,000 analyzed). All ultra-hypermutated bMMRD cancers acquired early somatic driver mutations in DNA polymerase ɛ or δ. The ensuing mutation signatures and numbers are unique and diagnostic of childhood germ-line bMMRD (P < 10(-13)). Sequential tumor biopsy analysis revealed that bMMRD/polymerase-mutant cancers rapidly amass an excess of simultaneous mutations (∼600 mutations/cell division), reaching but not exceeding ∼20,000 exonic mutations in <6 months. This implies a threshold compatible with cancer-cell survival. We suggest a new mechanism of cancer progression in which mutations develop in a rapid burst after ablation of replication repair.

Molecular characterization of choroid plexus tumors reveals novel clinically relevant subgroups

PURPOSE

To investigate molecular alterations in choroid plexus tumors (CPT) using a genome-wide high-throughput approach to identify diagnostic and prognostic signatures that will refine tumor stratification and guide therapeutic options.

EXPERIMENTAL DESIGN

One hundred CPTs were obtained from a multi-institutional tissue and clinical database. Copy-number (CN), DNA methylation, and gene expression signatures were assessed for 74, 36, and 40 samples, respectively. Molecular subgroups were correlated with clinical parameters and outcomes.

RESULTS

Unique molecular signatures distinguished choroid plexus carcinomas (CPC) from choroid plexus papillomas (CPP) and atypical choroid plexus papillomas (aCPP); however, no significantly distinct molecular alterations between CPPs and aCPPs were observed. Allele-specific CN analysis of CPCs revealed two novel subgroups according to DNA content: hypodiploid and hyperdiploid CPCs. Hyperdiploid CPCs exhibited recurrent acquired uniparental disomy events. Somatic mutations in TP53 were observed in 60% of CPCs. Investigating the number of mutated copies of p53 per sample revealed a high-risk group of patients with CPC carrying two copies of mutant p53, who exhibited poor 5-year event-free (EFS) and overall survival (OS) compared with patients with CPC carrying one copy of mutant p53 (OS: 14.3%, 95% confidence interval, 0.71%-46.5% vs. 66.7%, 28.2%-87.8%, respectively, P = 0.04; EFS: 0% vs. 44.4%, 13.6%-71.9%, respectively, P = 0.03). CPPs and aCPPs exhibited favorable survival.

DISCUSSION

Our data demonstrate that differences in CN, gene expression, and DNA methylation signatures distinguish CPCs from CPPs and aCPPs; however, molecular similarities among the papillomas suggest that these two histologic subgroups are indeed a single molecular entity. A greater number of copies of mutated TP53 were significantly associated to increased tumor aggressiveness and a worse survival outcome in CPCs. Collectively, these findings will facilitate stratified approaches to the clinical management of CPTs.

Abstract 661: Identification of epigenomic markers on chromosome 11 that distinguish between choroid plexus carcinoma (CPC) and papilloma (CPP)

Choroid plexus tumors are rare epithelial brain tumors occurring predominantly in early childhood.

Understanding molecular events leading to development and progression of these tumors is critical in determining patient treatment and increased survival.

Loss of heterozygosity (LOH) is a common alteration observed during carcinogenesis. To investigate somatic genetic abnormalities in different subtypes of choroid plexus cancers and identify LOH hotspots, we utilized SNP 6.0 arrays (Affymetrix). Allele specific copy number analysis of 25 CPCs and 31 CPPs using Chromosome Analysis Suite (Affymetrix) revealed much higher frequency of LOH events throughout the genome in CPCs (8.4/case) compared with CPPs (1.2/case). One LOH hotspot, neutral copy loss of heterozygosity on chromosome 11, was identified in most CPCs but in no CPPs. Chromosome 11 is known to harbor an imprinted cluster that has been associated with growth dysregulation and pediatric cancer. Both maternal (KvDMR1) and paternal (H19DMR) differentially methylated regions overlap this imprinting cluster. Therefore, we investigated whether the observed LOH is related to uniparental disomy (UPD). Bisulfite pyrosequencing on a subset of CPP and CPC were studied for DNA methylation at both H19DMR and KvDMR1. Our data showed a reverse correlation in the degree of DNA methylation between the 2 DMRs in CPCs and CPPs. These data correlate well with the concept of UPD identified through our SNP arrays. Next, we investigated whether the observed higher expression of insulin like growth factor (IGF2) in CPP compared to CPC is associated with DNA methylation aberrations at the imprinted control region (H19 DMR) on 11p15.5. We identified higher DNA methylation at the H19DMR in CPC compared to CPP. Increased activity of the IGF2 gene has been associated with many types of cancer. To investigate the mechanism of CPC distinct IGF2 expression we examined the expression levels of microRNAs (miRNAs). MicroRNAs are often found to be misregulated in human cancer, and they can act posttranscriptionally as either potent oncogenes or tumor suppressor genes. We studied expression of miR-675-3p, miR-483-3p as well as miR-125-a-3p associated with IGF2/H19 imprinted locus. By quantitative RT-PCR, both miR-675 and miR-125 were found to be more significantly upregulated in CPCs than in CPPs whereas miR-483 was expressed at very low levels in CPCs and in higher levels in CPPs compared with normal control tissues . Misregulation of miR-483 was positively correlated with IGF2 levels in both groups. Our data suggest that dysregulation of epigenetic mechanisms contribute to the molecular events leading to tumor development and progression in CPC and may eventually facilitate identification of new diagnostic markers for CPC, as well as new therapeutic targets for this aggressive, lethal tumor.

Citation Format: Malgorzata Pienkowska, Sanaa Choufani, Boleslaw Lach, Diana M. Merino, Ana Novokmet, Uri Tabori, Richard Gilbertson, David Malkin. Identification of epigenomic markers on chromosome 11 that distinguish between choroid plexus carcinoma (CPC) and papilloma (CPP). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 661. doi:10.1158/1538-7445.AM2013-661

Abstract 2479: TP53 status as a marker of recurrence and survival in choroid plexus carcinomas

Choroid plexus carcinoma (CPC) is a rare intraventricular tumor more frequently observed in children, accounting for ∼20% of brain tumors in children under 2 yrs of age. This malignant neoplasm is categorized as a grade III tumor by the WHO, while benign choroid plexus papilloma (CPP) and atypical choroid plexus papilloma (aCPP) are categorized as grade I and II, respectively. More than 50% of CPC's carry a mutation in TP53. The role of p53 in the malignant progression of this tumor is not well understood, yet this knowledge is crucial to optimize patient treatment, increase survival and reduce long-term sequelae. The current treatment approach for CPC includes surgical resection and combination chemo- and radiation therapy. However, treatment response is highly variable; tumor progression and relapse is observed in ∼60% of patients, and most survivors experience significant long-term deficits. In this study, we sought to determine whether TP53 status could be used as a reliable marker to predict tumor aggressiveness and response to treatment in CPC patients. Thirty CPC, 26 CPP and 8 aCPP tumor samples for which TP53 status was available were selected from the SickKids Cancer Genetics tissue bank. Sequencing analysis revealed somatic TP53 in 60% of CPCs. These mutations were significantly less frequent in CPPs (12%, p=1.84x10−4). All aCPPs were wildtype (wt) for TP53. Relapse-free survival was only 12% in TP53 mut CPC patients compared to 40% for TP53 wt patients. Only 1 CPP patient relapsed 9 months after initial diagnosis. Five-year overall survival for TP53 mut CPC patients was significantly lower than that of TP53 wt patients (39% vs. 80%, respectively, p=0.04). Overall survival for 18 CPP patients for which we had 5-year survival data was 94%, and 100% for aCPP patients. Allele-specific copy number (ASCN) and FISH analysis, revealed extensive chromosomal imbalances in CPC tumors with TP53 mutations. TP53 wt CPCs had fewer chromosomal imbalances or none at all, very similar to CPPs. Gene expression data was used to examine the unsupervised clustering of our tumors. As expected, CPCs and CPPs cluster independently according to raw gene expression intensity, with TP53 wt CPCs segregating from the CPC mutant samples and clustering more closely to CPPs. Using an integrative analysis, we were able to identify unique behaviors and molecular characteristics that distinguish TP53 wt from TP53 mut CPCs. The clinical outcomes observed, supported by the genomic and transcriptomic data analyzed, suggest that TP53 mut and wt CPCs indeed form two distinct subgroups. This molecular genotyping approach may be valuable in stratifying patients to modulated therapy protocols in order to diminish treatment-related toxicity, and improve disease response and survival.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2479. doi:1538-7445.AM2012-2479

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations

Genomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in a one-step catastrophic event termed chromothripsis. We report the whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome), uncovering massive, complex chromosome rearrangements. Integrating TP53 status with microarray and deep sequencing-based DNA rearrangement data in additional patients reveals a striking association between TP53 mutation and chromothripsis in SHH-MBs. Analysis of additional tumor entities substantiates a link between TP53 mutation and chromothripsis, and indicates a context-specific role for p53 in catastrophic DNA rearrangements. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings connect p53 status and chromothripsis in specific tumor types, providing a genetic basis for understanding particularly aggressive subtypes of cancer.

Polymorphisms in FADS1 and FADS2 alter desaturase activity in young Caucasian and Asian adults

Recent evidence indicates that genetic variation in fatty acid desaturases 1 and 2 (FADS1 and FADS2) is associated with changes in plasma fatty acid profiles; however, the association with altered desaturase activity has not been examined in different ethnic populations. The present study examined whether genetic variation in the FADS gene cluster regulates desaturase activity in two populations of young Canadian adults (Caucasian and Asian) and whether altered desaturase activity was reflected in both n-3 and n-6 fatty acid profiles. FADS1 and FADS2 were genotyped in a random subset of participants (Caucasian, n=78; Asian, n=69) from the Toronto Nutrigenomics and Health study using MALDI-TOF mass spectrometry, and plasma fatty acids were measured by gas chromatography. Desaturase activities were estimated using the following fatty acid ratios: γ-linoleic acid to linoleic acid (GLA:LA), arachidonic acid to linoleic acid (AA:LA), arachidonic acid to dihomo-γ-linoleic acid (AA:DGLA), and eicosapentaneoic acid to α-linolenic acid (EPA:ALA). Nineteen single nucleotide polymorphisms (SNPs) were examined, and several SNPs (9 in Caucasians and 8 in Asians) were associated with various desaturase activities. The most significant association detected was between the FADS1 rs174547 SNP and AA:LA in both Caucasians (p=4.0 × 10(-8)) and Asians (p=5.0 × 10(-5)). Although the minor allele for this SNP differed between Caucasians (T) and Asians (C), carriers of the C allele had a lower desaturase activity than carriers of the T allele in both groups. To determine whether rs174547 was a dominant SNP in the FADS gene cluster, we constructed an additional model which included this SNP as a covariate. Only one SNP (rs498793 in FADS2) remained associated with the EPA:ALA ratio (p=1.1 × 10(-5)) in Asians. This study shows that genetic variation in the FADS gene cluster (in particular rs174547) can alter desaturase activity in subjects of Caucasians and Asian descent.

Abstract 3460: Genome-wide copy number analysis reveals novel somatic mutations associated with choroid plexus tumorigenesis

Choroid plexus carcinomas (CPCs) are aggressive pediatric neoplasms accounting for less than 1% of brain tumors, but representing more than 10% of brain tumors in children under 1 year of age. CPCs are frequently observed in the context of the Li-Fraumeni Syndrome (LFS), yet this association has not been fully elucidated. The genetic mechanisms leading to this disease are poorly understood; however, we have recently demonstrated that TP53 status and total structural variation are correlated with tumor subtype and clinical outcome in choroid plexus tumor (CPT) patients, distinguishing between individuals with CPC and choroid plexus papilloma (CPP), a benign tumor with a more favorable prognosis. We set out to characterize genomic regions in which copy number variation and gene expression changes are uniquely associated with CPC tumors in order to identify genes that may serve as markers in tumor diagnosis and prognosis.

DNA and RNA from 59 choroid plexus tumors (CPC, n=29 and CPP, n=30) and two samples of normal choroid plexus tissue were obtained from a multi-institutional tissue and clinical database. We conducted high-resolution copy number alteration (CNA) and gene expression analysis for each tumor sample using highly dense microarrays (Affymetrix SNP 6.0 and Exon 1.0 ST array, respectively). DNA microarray data was segmented using a Hidden Markov Model (HMM) approach. Statistical analysis was carried out using Partek Genomics Suite in which CNAs and gene expression changes between CPC, CPP, and normal choroid plexus samples were contrasted. We identified 14 CPC-unique loci harboring CNAs with corresponding gene expression changes (p&gt;0.05). We observed that CNAs were found at loci where cancer genes with well-characterized oncogenic functions have been previously identified (1p13.2, 1p13.3, 1p21.3, 1p22.1 and 5q13.3). Furthermore, more than 90% of tumors with copy number alterations and expression changes at these five loci also harbored mutant TP53.

These observations suggest involvement of several genes in the malignant progression of CPCs, which may help elucidate the aggressiveness and poor clinical outcome of this tumor subtype compared to the more favorable CPP. Further analysis of CNAs and expression at these loci in the context of TP53 mutations, will provide a more refined genetic profile that will facilitate diagnosis of CPTs and aid in predicting patient outcome.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3460. doi:10.1158/1538-7445.AM2011-3460

Genetic variation in lipid desaturases and its impact on the development of human disease

Perturbations in lipid metabolism characterize many of the chronic diseases currently plaguing our society, such as obesity, diabetes, and cardiovascular disease. Thus interventions that target plasma lipid levels remain a primary goal to manage these diseases. The determinants of plasma lipid levels are multi-factorial, consisting of both genetic and lifestyle components. Recent evidence indicates that fatty acid desaturases have an important role in defining plasma and tissue lipid profiles. This review will highlight the current state-of-knowledge regarding three desaturases (Scd-1, Fads1 and Fads2) and their potential roles in disease onset and development. Although research in rodent models has provided invaluable insight into the regulation and functions of these desaturases, the extent to which murine research can be translated to humans remains unclear. Evidence emerging from human-based research demonstrates that genetic variation in human desaturase genes affects enzyme activity and, consequently, disease risk factors. Moreover, this genetic variation may have a trans-generational effect via breastfeeding. Therefore inter-individual variation in desaturase function is attributed to both genetic and lifestyle components. As such, population-based research regarding the role of desaturases on disease risk is challenged by this complex gene-lifestyle paradigm. Unravelling the contribution of each component is paramount for understanding the inter-individual variation that exists in plasma lipid profiles, and will provide crucial information to develop personalized strategies to improve health management.