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The children's brain tumor network (CBTN) - Accelerating research in pediatric central nervous system tumors through collaboration and open science

Lilly, Jena V; Rokita, Jo Lynne; Mason, Jennifer L; Patton, Tatiana; Stefankiewiz, Stephanie; Higgins, David; Trooskin, Gerri; Larouci, Carina A; Arya, Kamnaa; Appert, Elizabeth; Heath, Allison P; Zhu, Yuankun; Brown, Miguel A; Zhang, Bo; Farrow, Bailey K; Robins, Shannon; Morgan, Allison M; Nguyen, Thinh Q; Frenkel, Elizabeth; Lehmann, Kaitlin; Drake, Emily; Sullivan, Catherine; Plisiewicz, Alexa; Coleman, Noel; Patterson, Luke; Koptyra, Mateusz; Helili, Zeinab; Van Kuren, Nicholas; Young, Nathan; Kim, Meen Chul; Friedman, Christopher; Lubneuski, Alex; Blackden, Christopher; Williams, Marti; Baubet, Valerie; Tauhid, Lamiya; Galanaugh, Jamie; Boucher, Katie; Ijaz, Heba; Cole, Kristina A; Choudhari, Namrata; Santi, Mariarita; Moulder, Robert W; Waller, Jonathan; Rife, Whitney; Diskin, Sharon J; Mateos, Marion; Parsons, Donald W; Pollack, Ian F; Goldman, Stewart; Leary, Sarah; Caporalini, Chiara; Buccoliero, Anna Maria; Scagnet, Mirko; Haussler, David; Hanson, Derek; Firestein, Ron; Cain, Jason; Phillips, Joanna J; Gupta, Nalin; Mueller, Sabine; Grant, Gerald; Monje-Deisseroth, Michelle; Partap, Sonia; Greenfield, Jeffrey P; Hashizume, Rintaro; Smith, Amy; Zhu, Shida; Johnston, James M; Fangusaro, Jason R; Miller, Matthew; Wood, Matthew D; Gardner, Sharon; Carter, Claire L; Prolo, Laura M; Pisapia, Jared; Pehlivan, Katherine; Franson, Andrea; Niazi, Toba; Rubin, Josh; Abdelbaki, Mohamed; Ziegler, David S; Lindsay, Holly B; Stucklin, Ana Guerreiro; Gerber, Nicolas; Vaske, Olena M; Quinsey, Carolyn; Rood, Brian R; Nazarian, Javad; Raabe, Eric; Jackson, Eric M; Stapleton, Stacie; Lober, Robert M; Kram, David E; Koschmann, Carl; Storm, Phillip B; Lulla, Rishi R; Prados, Michael; Resnick, Adam C; Waanders, Angela J
Pediatric brain tumors are the leading cause of cancer-related death in children in the United States and contribute a disproportionate number of potential years of life lost compared to adult cancers. Moreover, survivors frequently suffer long-term side effects, including secondary cancers. The Children's Brain Tumor Network (CBTN) is a multi-institutional international clinical research consortium created to advance therapeutic development through the collection and rapid distribution of biospecimens and data via open-science research platforms for real-time access and use by the global research community. The CBTN's 32 member institutions utilize a shared regulatory governance architecture at the Children's Hospital of Philadelphia to accelerate and maximize the use of biospecimens and data. As of August 2022, CBTN has enrolled over 4700 subjects, over 1500 parents, and collected over 65,000 biospecimen aliquots for research. Additionally, over 80 preclinical models have been developed from collected tumors. Multi-omic data for over 1000 tumors and germline material are currently available with data generation for > 5000 samples underway. To our knowledge, CBTN provides the largest open-access pediatric brain tumor multi-omic dataset annotated with longitudinal clinical and outcome data, imaging, associated biospecimens, child-parent genomic pedigrees, and in vivo and in vitro preclinical models. Empowered by NIH-supported platforms such as the Kids First Data Resource and the Childhood Cancer Data Initiative, the CBTN continues to expand the resources needed for scientists to accelerate translational impact for improved outcomes and quality of life for children with brain and spinal cord tumors.
PMID: 36335802
ISSN: 1476-5586
CID: 5356872

Clinical, Pathological, and Molecular Characteristics of Diffuse Spinal Cord Gliomas

Garcia, Mekka R; Feng, Yang; Vasudevaraja, Varshini; Galbraith, Kristyn; Serrano, Jonathan; Thomas, Cheddhi; Radmanesh, Alireza; Hidalgo, Eveline T; Harter, David H; Allen, Jeffrey C; Gardner, Sharon L; Osorio, Diana S; William, Christopher M; Zagzag, David; Boué, Daniel R; Snuderl, Matija
Diffuse spinal cord gliomas (SCGs) are rare tumors associated with a high morbidity and mortality that affect both pediatric and adult populations. In this retrospective study, we sought to characterize the clinical, pathological, and molecular features of diffuse SCG in 22 patients with histological and molecular analyses. The median age of our cohort was 23.64 years (range 1-82) and the overall median survival was 397 days. K27M mutation was significantly more prevalent in males compared to females. Gross total resection and chemotherapy were associated with improved survival, compared to biopsy and no chemotherapy. While there was no association between tumor grade, K27M status (p = 0.366) or radiation (p = 0.772), and survival, males showed a trend toward shorter survival. K27M mutant tumors showed increased chromosomal instability and a distinct DNA methylation signature.
PMID: 35997552
ISSN: 1554-6578
CID: 5338172

Genomic Microsatellite Signatures Identify Germline Mismatch Repair Deficiency and Risk of Cancer Onset

Chung, Jiil; Negm, Logine; Bianchi, Vanessa; Stengs, Lucie; Das, Anirban; Liu, Zhihui Amy; Sudhaman, Sumedha; Aronson, Melyssa; Brunga, Ledia; Edwards, Melissa; Forster, Victoria; Komosa, Martin; Davidson, Scott; Lees, Jodi; Tomboc, Patrick; Samuel, David; Farah, Roula; Bendel, Anne; Knipstein, Jeffrey; Schneider, Kami Wolfe; Reschke, Agnes; Zelcer, Shayna; Zorzi, Alexandra; McWilliams, Robert; Foulkes, William D; Bedgood, Raymond; Peterson, Lindsay; Rhode, Sara; Van Damme, An; Scheers, Isabelle; Gardner, Sharon; Robbins, Gabriel; Vanan, Magimairajan Issai; Meyn, M Stephen; Auer, Rebecca; Leach, Brandie; Burke, Carol; Villani, Anita; Malkin, David; Bouffet, Eric; Huang, Annie; Taylor, Michael D; Durno, Carol; Shlien, Adam; Hawkins, Cynthia; Getz, Gad; Maruvka, Yosef E; Tabori, Uri
PURPOSE/OBJECTIVE:Diagnosis of Mismatch Repair Deficiency (MMRD) is crucial for tumor management and early detection in patients with the cancer predisposition syndrome constitutional mismatch repair deficiency (CMMRD). Current diagnostic tools are cumbersome and inconsistent both in childhood cancers and in determining germline MMRD. PATIENTS AND METHODS/METHODS:We developed and analyzed a functional Low-pass Genomic Instability Characterization (LOGIC) assay to detect MMRD. The diagnostic performance of LOGIC was compared with that of current established assays including tumor mutational burden, immunohistochemistry, and the microsatellite instability panel. LOGIC was then applied to various normal tissues of patients with CMMRD with comprehensive clinical data including age of cancer presentation. RESULTS:). CONCLUSION/CONCLUSIONS:LOGIC was a robust tool for the diagnosis of MMRD in multiple cancer types and in normal tissues. LOGIC may inform therapeutic cancer decisions, provide rapid diagnosis of germline MMRD, and support tailored surveillance for individuals with CMMRD.
PMID: 36240479
ISSN: 1527-7755
CID: 5361252

Serial H3K27M cell-free tumor DNA (cf-tDNA) tracking predicts ONC201 treatment response and progression in diffuse midline glioma

Cantor, Evan; Wierzbicki, Kyle; Tarapore, Rohinton S; Ravi, Karthik; Thomas, Chase; Cartaxo, Rodrigo; Yadav, Viveka Nand; Ravindran, Ramya; Bruzek, Amy K; Wadden, Jack; John, Vishal; Babila, Clarissa May; Cummings, Jessica R; Kawakibi, Abed Rahman; Ji, Sunjong; Ramos, Johanna; Paul, Alyssa; Walling, Dustin; Leonard, Marcia; Robertson, Patricia; Franson, Andrea; Mody, Rajen; Garton, Hugh J L; Venetti, Sriram; Odia, Yazmin; Kline, Cassie; Vitanza, Nicholas A; Khatua, Soumen; Mueller, Sabine; Allen, Joshua E; Gardner, Sharon; Koschmann, Carl
BACKGROUND:Diffuse Midline Glioma (DMG) with the H3K27M mutation is a lethal childhood brain cancer, with patients rarely surviving 2 years from diagnosis. METHODS:We conducted a multi-site Phase 1 trial of the imipridone ONC201 for children with H3K27M-mutant glioma (NCT03416530). Patients enrolled on Arm D of the trial (n=24) underwent serial lumbar puncture for cell-free tumor DNA (cf-tDNA) analysis and patients on all arms at the University of Michigan underwent serial plasma collection. We performed digital droplet polymerase chain reaction (ddPCR) analysis of cf-tDNA samples and compared variant allele fraction (VAF) to radiographic change (maximal 2D tumor area on MRI). RESULTS:Change in H3.3K27M VAF over time ("VAF delta") correlated with prolonged PFS in both CSF and plasma samples. Non-recurrent patients that had a decrease in CSF VAF displayed a longer progression free survival (p=0.049). Decrease in plasma VAF displayed a similar trend (p=0.085). VAF "spikes" (increase of at least 25%) preceded tumor progression in 8/16 cases (50%) in plasma and 5/11 cases (45.4%) in CSF. In individual cases, early reduction in H3K27M VAF predicted long-term clinical response (>1 year) to ONC201, and did not increase in cases of later-defined pseudo-progression. CONCLUSION/CONCLUSIONS:Our work demonstrates the feasibility and potential utility of serial cf-tDNA in both plasma and CSF of DMG patients to supplement radiographic monitoring. Patterns of change in H3K27M VAF over time demonstrate clinical utility in terms of predicting progression and sustained response and possible differentiation of pseudo-progression and pseudo-response.
PMID: 35137228
ISSN: 1523-5866
CID: 5156782


Robison, N; Pauly, J; Malvar, J; Gardner, S; Allen, J; Margol, A; MacDonald, T; Bendel, A; Kilburn, L; Cluster, A; Bowers, D; Dorris, K; Ullrich, N; De, Mola R L; Alva, E; Leary, S; Baxter, P; Khatib, Z; Cohen, K; Davidson, T B; Plant, A; Bandopadhayay, P; Stopka, S; Agar, N; Wright, K; Nelson, M; Chi, Y -Y; Kieran, M
BACKGROUND: RAS/RAF/MEK/ERK pathway activation is the primary driver for most pediatric low-grade gliomas (pLGG). MEK162 (binimetinib) is an orally bioavailable MEK1/2 inhibitor with superior brain penetration in a preclinical model. The primary objective of this multi-institutional phase II and target validation study was to assess stratum-specific efficacy of binimetinib in progressive pLGG.
METHOD(S): Eligible children aged 1-18 years with previously treated radiographically progressive pLGG were enrolled and treated with binimetinib, starting dose 32mg/m2/dose twice daily. Stratum 1 included patients with pLGG with documented BRAF fusion; stratum 2, neurofibromatosis 1 (NF1)-associated pLGG; stratum 3, sporadic pLGG without documented BRAF fusion; and stratum 4, patients undergoing planned tumor biopsy who began binimetinib preoperatively. Partial and minor responses (PR and MR) were defined as >=50% and >=25% decrease in maximal two-dimensional measurements.
RESULT(S): Of 86 patients enrolled, 85 were evaluable for response. Of these, 48 (56%) showed a radiographic response (30 PR and 18 MR) in the first year of treatment. Response rate for stratum 1 (n=28) was 50% (12 PR and 2 MR); 12 (43%) had stable disease (SD) and 2 (7%) progressive disease (PD). Stratum 2 (n=21) response rate was 43% (5 PR, 4 MR), with 12 (57%) SD and no PD. Stratum 3 (n=29) response rate was 69% (10 PR, 10 MR), 4 (14%) SD and 5 (17%) PD. Stratum 4 (n=7) include 3 PR, 2 MR, 2 SD. Nineteen (22%) discontinued treatment for toxicity (most commonly dermatologic), and an additional 42 (49%) required dose reduction. Median dose at the time of PR/MR was 28mg/m2; responses were seen at doses as low 16mg/m2.
CONCLUSION(S): Binimetinib is highly effective in the treatment of both NF1-associated and sporadic pLGG, with or without documented BRAF fusion. Modified dosing strategies to improve tolerability may be considered in future trials
ISSN: 1523-5866
CID: 5292062


Kanakamedala, Siri; Gardner, Sharon; Allen, Jeffrey; Nicolaides, Theodore; Pudel, Miriam; Roman, Elizabeth
ISSN: 1545-5009
CID: 5243872

Clinical value of DNA methylation in practice: A prospective molecular neuropathology study [Meeting Abstract]

Galbraith, Kristyn; Shen, Guomiao; Serrano, Jonathan; Vasudevaraja, Varshini; Tran, Ivy; Movahed-Ezazi, Misha; Harter, David; Hidalgo, Eveline; Wisoff, Jeffrey; Orringer, Daniel; Placantonakis, Dimitris; Gardner, Sharon; William, Christopher; Zagzag, David; Allen, Jeffrey; Sulman, Erik; Golfinos, John; Snuderl, Matija
ISSN: 0022-3069
CID: 5244322

Phase I dose escalation and expansion trial of single agent ONC201 in pediatric diffuse midline gliomas following radiotherapy

Gardner, Sharon L; Tarapore, Rohinton S; Allen, Jeffrey; McGovern, Susan L; Zaky, Wafik; Odia, Yazmin; Daghistani, Doured; Diaz, Zuanel; Hall, Matthew D; Khatib, Ziad; Koschmann, Carl; Cantor, Evan; Kurokawa, Ryo; MacDonald, Tobey J; Aguilera, Dolly; Vitanza, Nicholas A; Mueller, Sabine; Kline, Cassie; Lu, Guangrong; Allen, Joshua E; Khatua, Soumen
BACKGROUND/UNASSIGNED:ONC201, a dopamine receptor D2 (DRD2) antagonist and caseinolytic protease P (ClpP) agonist, has induced durable tumor regressions in adults with recurrent H3 K27M-mutant glioma. We report results from the first phase I pediatric clinical trial of ONC201. METHODS/UNASSIGNED:This open-label, multi-center clinical trial (NCT03416530) of ONC201 for pediatric H3 K27M-mutant diffuse midline glioma (DMG) or diffuse intrinsic pontine glioma (DIPG) employed a dose-escalation and dose-expansion design. The primary endpoint was the recommended phase II dose (RP2D). A standard 3 + 3 dose escalation design was implemented. The target dose was the previously established adult RP2D (625 mg), scaled by body weight. Twenty-two pediatric patients with DMG/DIPG were treated following radiation; prior lines of systemic therapy in addition to radiation were permitted providing sufficient time had elapsed prior to study treatment. RESULTS/UNASSIGNED:The RP2D of orally administered ONC201 in this pediatric population was determined to be the adult RP2D (625 mg), scaled by body weight; no dose-limiting toxicities (DLT) occurred. The most frequent treatment-emergent Grade 1-2 AEs were headache, nausea, vomiting, dizziness and increase in alanine aminotransferase. Pharmacokinetics were determined following the first dose: <i>T</i> <sub>1/2</sub>, 8.4 h; <i>T</i> <sub>max</sub>, 2.1 h; <i>C</i> <sub>max</sub>, 2.3 µg/mL; AUC<sub>0-tlast</sub>, 16.4 hµg/mL. Median duration of treatment was 20.6 weeks (range 5.1-129). Five (22.7%) patients, all of whom initiated ONC201 following radiation and prior to recurrence, were alive at 2 years from diagnosis. CONCLUSIONS/UNASSIGNED:The adult 625 mg weekly RP2D of ONC201 scaled by body weight was well tolerated. Further investigation of ONC201 for DMG/DIPG is warranted.
PMID: 36382108
ISSN: 2632-2498
CID: 5384822

Long-term neuropsychological outcomes of survivors of young childhood brain tumors treated on the Head Start II protocol

Levitch, Cara F; Malkin, Benjamin; Latella, Lauren; Guerry, Whitney; Gardner, Sharon L; Finlay, Jonathan L; Sands, Stephen A
Background/UNASSIGNED:The Head Start treatment protocols have focused on curing young children with brain tumors while avoiding or delaying radiotherapy through using a combination of high-dose, marrow-ablative chemotherapy and autologous hematopoietic cell transplantation (AuHCT). Late effects data from treatment on the Head Start II (HS II) protocol have previously been published for short-term follow-up (STF) at a mean of 39.7 months post-diagnosis. The current study examines long-term follow-up (LTF) outcomes from the same cohort. Methods/UNASSIGNED:Eighteen HS II patients diagnosed with malignant brain tumors <10 years of age at diagnosis completed a neurocognitive battery and parents completed psychological questionnaires at a mean of 104.7 months' post-diagnosis. Results/UNASSIGNED:There was no significant change in Full Scale IQ at LTF compared to baseline or STF. Similarly, most domains had no significant change from STF, including verbal IQ, performance IQ, academics, receptive language, learning/memory, visual-motor integration, and externalizing behaviors. Internalizing behaviors increased slightly at LTF. Clinically, most domains were within the average range, except for low average mathematics and receptive language. Additionally, performance did not significantly differ by age at diagnosis or time since diagnosis. Of note, children treated with high-dose methotrexate for disseminated disease or atypical teratoid/rhabdoid tumor displayed worse neurocognitive outcomes. Conclusions/UNASSIGNED:These results extend prior findings of relative stability in intellectual functioning for a LTF period. Ultimately, this study supports that treatment strategies for avoiding or delaying radiotherapy using high-dose, marrow-ablative chemotherapy and AuHCT may decrease the risk of neurocognitive and social-emotional declines in young pediatric brain tumor survivors.
PMID: 34594573
ISSN: 2054-2577
CID: 5067582

Serial plasma and CSF cell-free tumor DNA (CF-TDNA) Tracking in diffuse midline glioma patients undergoing treatment with ONC201 [Meeting Abstract]

Cantor, E; Wierzbicki, K; Tarapore, R S; Thomas, C; Cartaxo, R; Yadav, V N; Ravindran, R; Bruzek, A K; Wadden, J; Babilla, C M; Kawakibi, A R; Ji, S; Ramos, J; Paul, A; Wolfe, I; Leonard, M; Robertson, P; Franson, A; Mody, R; Garton, H; Odia, Y; Kline, C; Vitanza, N A; Khatua, S; Mueller, S; Allen, J E; Gardner, S; Koschmann, C
Diffuse midline glioma (DMG) with the H3K27M mutation is a lethal childhood brain cancer, with patients rarely surviving 2 years from diagnosis. We conducted a multi-site Phase 1 trial of the imipridone ONC201 for children with H3K27M-mutant glioma (NCT03416530). Patients enrolled on Arm D of the trial (n=24) underwent serial lumbar puncture (baseline, 2, 6 months) for cell-free tumor DNA (cf-tDNA) analysis at time of MRI. Additionally, patients on all arms of the trial at the University of Michigan underwent serial plasma collection. CSF collection was feasible in this cohort, with no procedural complications. We collected 96 plasma samples and 53 CSF samples from 29 patients, including those with H3F3A (H3.3) (n=13), HIST13HB (H3.1) (n= 4), and unknown H3 status/not biopsied (n=12) [range of 0-8 CSF samples and 0-10 plasma samples]. We performed digital droplet polymerase chain reaction (ddPCR) analysis and/or ampliconbased electronic sequencing (Oxford Nanopore) of cf-tDNA samples and compared variant allele fraction (VAF) to radiographic change (maximal 2D tumor area on MRI). Preliminary analysis of samples demonstrates a correlation between changes in tumor size and H3K27M cf-tDNA VAF, when removing samples with concurrent bevacizumab. In multiple cases, early reduction in CSF cf-tDNA predicts long-term clinical response (>1 year) to ONC201, and does not increase in cases of later-defined pseudo-progression (radiation necrosis). For example, a now 9-year old patient with thalamic H3K27M-mutant DMG underwent treatment with ONC201 after initial radiation and developed increase in tumor size at 4 months post-radiation (124% baseline) of unclear etiology at the time. Meanwhile, her ddPCR declined from baseline 6.76% VAF to <1%, which has persisted, with now near complete response (15% tumor reduction) at 30 months on treatment from diagnosis. In summary, we present the feasibility and utility of serial CSF/plasma monitoring of a promising experimental therapy for DMG
ISSN: 1523-5866
CID: 4982472