bluuebunny/crossref_metadata_2025_split huggingface dataset:
ATRT-11. PREVALENCE OF GERMLINE VARIANTS IN SMARCB1 INCLUDING SOMATIC MOSAICISM IN AT/RT AND OTHER RHABDOID TUMORS
Authors: Shirai Ryota , Osumi Tomoo , Terashima Keita , Kiyotani Chikako , Uchiyama Meri , Tsujimoto Shinichi , Yoshida Masanori , Yoshida Kaoru , Uchiyama Toru , Tomizawa Daisuke , Shioda Yoko , Sekiguchi Masahiro , Watanabe Kenichiro , Keino Dai , Ueno-Yokohata Hitomi , Ohki Kentaro , Takita Junko , Ito Shuichi , Deguchi Takao , Kiyokawa Nobutaka , Ogiwara Hideki , Hishiki Tomoro , Ogawa Seishi , Okita Hajime , Matsumoto Kimikazu , Yoshioka Takako , Kato Motohiro 
Published: December 2020

Abstract

BACKGROUND
Genetic hallmark of atypical teratoid/rhabdoid tumor (AT/RT) is loss-of-function variants or deletions in SMARCB1 gene on 22q11.2 chromosome, which is common to extracranial malignant rhabdoid tumors (MRT). Previous studies demonstrated that approximately one-thirds of AT/RT and extracranial MRT patients harbored germline SMARCB1 variants as the rhabdoid tumor predisposing syndrome. We studied herein intensive analysis of the SMARCB1 gene in AT/RT and extracranial MRT patients focusing on prevalence of germline genetic variants. PROCEDURE: In total, 16 patients were included. Both tumor-derived DNA and germline DNA were obtained from all patients. First, screening for SMARCB1 alterations in the tumor specimens was done by direct sequencing, ddPCR and SNP array analysis. Then, analysis of germline DNA samples focusing on the genomic abnormalities detected in the paired tumors in each case was performed.

RESULTS
In eight of 16 cases (50%), genomic alterations observed in the tumor-derived DNA were also detected in the germline DNA. It is worth noting that three patients had germline mosaicism. Two of three patients had mosaic deletion, including SMARCB1 region, and the average copy number of the deleted region in the SMARCB1 gene in the germline was 1.60 and 1.76. For another patient, the fraction of SMARCB1 variants in normal cells was as low as 1.7%.

CONCLUSIONS
Approximately half the MRT cases in this study had SMARCB1 germline alterations. Considering the presence of low-frequency mosaicisms which conventional methods might overlook, inherited germline variants in predisposition genes are more important than previously assumed for the pathogenesis of pediatric cancers.
ATRT-25. INTEGRATED QUANTITATIVE SWATH-MS PROTEOMICS ANALYSIS OF ATRTs UNCOVERS NEW THERAPEUTIC OPPORTUNITIES
Authors: Finetti Martina Anna , Hacking James , Lishman-Walker Emma , Synowsky Silvia A , Crosier Stephen , Martin Emmma , Burns Jess , Shirran Sally L , Bailey Simon , Clifford Steven C , Huang Paul , Williamson Daniel 
Published: December 2020

Abstract
The consequences of SMARCB1 loss in Atypical Teratoid Rhabdoid Tumors (ATRTs) have been extensively characterized at the epigenetic/transcriptomic level. In this study we detail the functional effect of SMARCB1 mutation on the MRT proteome, its relationship with RNA deregulation or lack thereof. We performed unlabeled discovery proteomics using MS-SWATH on MRT cells in which SMARCB1 was forcibly re-expressed (5 cell lines, +/-SMARCB1); analyzing changes in protein abundance within 3 fractions (total, membrane, nuclear). We generated a custom spectral library, covering &gt;8,000 proteins, for analysis of the ATRT proteome using a pH fractionated pool of each cellular subfraction. This SMARCB1-dependent ATRT spectral library constitutes a powerful tool for profiling proteins of potentially therapeutic relevance in both model systems and primary ATRT samples. We show that whilst gene expression and protein abundance are significantly related there are many instances whereby expression changes do not reliably predict protein abundances. Several hundred proteins show significantly increased abundance (p&lt;0.01) with no concomitant change by RNA-seq. SMARCB1 mutation is able to invoke critical changes in post-transcriptional/translational regulation as well as sub-cellular localization. By integration with whole-genome CRISPR/cas9 screening we describe functionally essential SMARCB1 dependent pathway/membrane biomarkers, evident at the protein but not the RNA level. We describe several which are druggable and suggest certain therapeutic modalities e.g. specific combinations of RTKs, RNA-binding proteins/splicing factors (SpliceosomeA, U4:U5:U6 tri-snRNP complexes). Our analysis links, for the first time in ATRT, genome-wide transcriptomic and proteome aberrations and reveals broad mechanisms underlying the effect of SMARCB1 mutation.
DIPG-01. REIRRADIATION PRACTICES FOR DIFFUSE INTRINSIC PONTINE GLIOMA
Authors: Cacciotti Chantel , Liu Kevin , Haas-Kogan Daphne , Warren Katherine 
Published: December 2020

Abstract

INTRODUCTION
Diffuse intrinsic pontine gliomas (DIPG) are a leading cause of brain tumor deaths in children. Current standard of care includes focal radiation therapy (RT). Despite clinical improvement in the majority of patients, the effect is temporary and median survival is less than one year. The use of reirradiation and possible benefit has been reported in progressive DIPG, yet standardized approaches are lacking. We conducted an internet-based survey to assess physicians’ practices in pediatric DIPG.

METHODS
A 14-question REDCap survey regarding re-irradiation practices was emailed to 396 physicians identified through an International Pediatric Neuro-Oncology and Radiation-Oncology database.

RESULTS
Response rate was 35% overall (radiation-oncologists, 28%; pediatric oncologists, 57%). Two participants were excluded (did not treat DIPG). Participants included radiation-oncologists (62%), pediatric oncologists (7%), and pediatric neuro-oncologists (29%). Most physicians (62%) treated 1–5 DIPG patients per year, with 10% treating &gt;10/year. Reirradiation was considered a treatment option in 88%. Progressive disease or worsening clinical status were the most common reasons to consider reirradiation. The majority (84%) considered reirradiation a minimum of 6 months following initial RT. Doses varied, with median total dose 24Gy (range 12–60); 2Gy/fraction (range 1–9). Concurrent use of systemic agents with reirradiation was considered in 46%, mainly with targeted agents (37%), biologics (34%), or immunotherapy (25%). One-time reirradiation was the most common practice (71%). Interestingly, 9% of respondents would not consider reirradiation.

CONCLUSION
Although, the vast majority of physicians agree with re-irradiation as a treatment option for DIPG the total doses varied, and further clinical trials are needed.
DIPG-10. OPTIMAL HDAC INHIBITION IN DIFFUSE INTRINSIC PONTINE GLIOMA
Authors: Vitanza Nicholas , Biery Matt , Myers Carrie , Ferguson Eric , Park Giulia , Noll Alyssa , Pakiam Fiona , Girard Emily , Morris Shelli , Cole Bonnie , Brusniak Mi-Youn , Mhyre Andrew , Olson James 
Published: December 2020

Abstract
As the majority of diffuse intrinsic pontine glioma (DIPG) have H3K27M mutations, epigenetic-targeting agents have been studied, though evaluations have been limited by their model systems, untranslatable drug concentrations, and/or evasive mechanisms of action. To develop a more translational model, we used biopsy samples from newly diagnosed DIPG patients to create treatment-naïve in vitro and in vivo models (molecular aberrations in parentheses), including PBT-09FH (H3FA3, PI3KCA), PBT-22FH (H3F3A, TP53), PBT-24FH (PMS2), and PBT-27FH (HIST1H3B, TP53, NTRK2). Models demonstrated radiation-resistance similar to the patient from whom the culture was generated, supporting the models’ relevance (e.g. cell viability after 8 Gy was 36%, 81%, 71%, and 61% in PBT-09FH, -22FH, -24FH, and -27FH, respectively, compared to 7% in the medulloblastoma model MED-411FH). We evaluated cell viability and apoptosis following treatment with a panel of HDAC inhibitors, identifying the low nanomolar IC50 of quisinostat (~50 nM) and romidepsin (~5 nM). While RNA expression changes induced by 100 nM panobinostat and quisinostat included shared overexpression of the top 20/25 genes (e.g. FSTL5, ITIH5) and shared downregulation of the top 22/25 (e.g. GPR37L1, HEPACAM), only 9/25 were downregulated by panobinostat, quisinostat, and romidepsin (e.g. C21orf62, IFIT2), identifying these as potential vulnerabilities or biomarkers of lethal HDAC inhibition. Mass-spectrometry (LC-MS) demonstrated panobinostat as the greatest acetylator of cortactin, potentially related to thrombocytopenia. While PBT-09 flank models demonstrated quisinostat’s on-target acetylation and efficacy, orthotopic xenograft models did not, supporting our model’s intact blood-brain barrier and emphasizing the need for CNS penetrant versions of potentially efficacious agents.
DIPG-16. COMBINATION OF ARGININE DEPLETION AND POLYAMINE INHIBITION AS AN ANTICANCER STRATEGY FOR DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG)
Authors: Khan Aaminah , Gamble Laura , Pandher Ruby , Burns Mark R , Mussai Francis , Norris Murray , Haber Michelle , Tsoli Maria , Ziegler David S 
Published: December 2020

Abstract
DIPG is an aggressive pediatric brainstem tumor, with a median survival below 12 months. Tumor cells are dependent upon arginine, a semi-essential amino acid, metabolised by arginase enzymes into ornithine, a pivotal precursor to the polyamine pathway. Polyamines, frequently upregulated in cancer, are intracellular polycations controlling key biological processes – the inhibition of which we have previously shown to be highly efficacious in preclinical DIPG models. Pegylated arginase (BCT-100) has recently been shown to significantly delay tumor development, prolonging survival of neuroblastoma-prone Th-MYCN mice. This study investigated the effects of arginine depletion therapy as a single agent and in combination with polyamine pathway inhibitors in DIPG. We found that ARG2, the gene encoding for arginase II, is expressed significantly more highly in DIPG tumors compared to normal brain. Arginine depletion via BCT-100 reduced DIPG cell proliferation and colony formation in patient-derived cell lines. Using orthotopic patient-derived xenograft models of DIPG, we found that frequent dosing of BCT-100 (4x/week) significantly delayed tumor development and increased the survival of the mice (p&lt;0.0001). DFMO is an FDA-approved inhibitor of the enzyme ornithine decarboxylase, a key driver of polyamine synthesis. The combination of BCT-100 with DFMO led to significant enhancement in DIPG survival (p&lt;0.005 compared to single agent treatments). Triple combination therapy with addition of the polyamine transport inhibitor AMXT-1501 led to a potent and profound improvement in survival. These data show that arginine depletion therapy using BCT-100 combined with dual polyamine inhibitory agents represents a potentially exciting new approach for the treatment of DIPG.
DIPG-19. TARGETING ATM MUTATION IN METASTATIC DIFFUSE MIDLINE GLIOMA – A CASE OF SUSTAINED RESPONSE USING PARP INHIBITOR
Authors: Tsui Karen , Law Andrew , Watson Michael K 
Published: December 2020

Abstract
Diffuse midline glioma (DMG) with H3.3K27M mutation is associated with an extremely poor prognosis, with a median survival of 10 to 12 months. Radiation remains the standard of care however there is no established curative therapy available. We describe a patient diagnosed with a diffuse intrinsic pontine glioma at 5 years of age by clinical and radiological criteria. He was treated with focal radiation 59Gy which resulted in reduction in size of the tumour, and partial improvement of T2 changes on MRI. At 18 months post diagnosis, the patient developed metastatic recurrence at the anterior fornix. This was biopsied and histopathology demonstrated a high grade glioma. Next generation sequencing revealed a H3F3A K27M mutation, and an ATM R3008H mutation. He received whole ventricular radiation 36Gy and boost to the lesion to 45Gy, followed by Olaparib 135mg/m2/day twice daily. He remains in radiological remission 20 months post metastatic relapse and has no organ toxicity to Olaparib. CONCLUSION: H3.3K27M and ATM co-segregating mutations are described in DMG. This is the first case report of targeting ATM mutation with a PARP inhibitor which resulted in prolonged remission of metastatic DMG. Olaparib was well tolerated.
DIPG-20. DETERMINATION AND MANAGEMENT OF HYDROCEPHALUS IN PATIENTS WITH DIPG, AN INSTITUTIONAL EXPERIENCE
Authors: Fonseca Adriana , Solano-Paez Palma , Zapotocky Michal , Bartels Ute , Bouffet Eric 
Published: December 2020

Abstract

BACKGROUND
The is no consensus in best practices for the management of hydrocephalus in patients with Diffuse Intrinsic Pontine Glioma (DIPG). To date, the impact on survival of hydrocephalus and Cerebro-Spinal Fluid (CSF) diversion in this population remains to be elucidated. Herein, we describe our institutional experience.

METHODS
Patients with a clinical and radiological diagnosis of DIPG were identified at the Hospital for Sick Children between 2000–2019. Images at diagnosis and at disease progression were assessed for hydrocephalus using the frontal-occipital ratio (FOR) method. Proportional hazard analyses were used to identify factors correlated with survival.

RESULTS
Eighty-nine consecutive patients diagnosed with DIPGs were treated at our institution. At diagnosis, 29% (n=26) of patients presented with hydrocephalus, seven patients underwent CSF diversion. Out of the remaining nineteen patients, n=6 had stable or improved hydrocephalus in follow-up scans, n=6 had persistent hydro and n=2 required CSF diversion at the time of disease progression. Seven did not undergo a follow-up scan. Out of sixty-five patients with imaging at the time of progression, fifty-five percent of patients (n=36) presented with hydrocephalus and ten of them required CSF diversion. On univariate analysis, the presence of hydrocephalus or CSF diversion at diagnosis and/or did not correlate with a survival advantage.

CONCLUSIONS
CSF diversion for the management of hydrocephalus in patients with DIPG does not impact survival and in some cases resolves spontaneously after the initiation of radiotherapy and steroids. This observation needs to be validated in a prospective cohort.
DIPG-21. INDUCTION OF MITOTIC ABNORMALITIES AND BMI-1 MODULATION TO TREAT DIFFUSE INTRINSIC PONTINE GLIOMA
Authors: Kumar Shiva Senthil , Sengupta Satarupa , Zhu Xiaoting , Mishra Deepak Kumar , Fuller Christine , Fouladi Maryam , Drissi Rachid 
Published: December 2020

Abstract
Diffuse intrinsic pontine glioma (DIPG) is a poor-prognosis pediatric brain tumor with a median survival of less than one year. No effective therapy is currently available, and no therapeutic advances have been made in several decades. BMI-1 is a member of the multimeric protein complex Polycomb repressor complex 1 (PRC1). It has been implicated in self-renewal of normal and cancer cells, and in DNA damage signaling. We have previously identified BMI-1 as a potential therapeutic target in DIPG and have shown that BMI-1 is highly expressed in DIPG tumors regardless of histone 3 subtype. In the present study, we show that the modulation of BMI-1 leads to DNA damage, M phase cell cycle arrest, chromosome abnormalities and cell death. Furthermore, modulation of BMI-1 sensitizes DIPG patient-derived stem-like cells to ionizing radiation (IR). Treatment of DIPG stem-like cells with PTC596, a BMI-1 modulator, and IR, impairs the kinetics of DNA damage response (DDR). Both DDR foci formation and resolution were delayed, resulting in further reduction in cell viability compared with either treatment alone. In vivo, treatment of mice bearing DIPG xenografts with PTC596 leads to decreased tumor volume and growth kinetics, increased in-tumor apoptosis and sustained animal survival benefit. Gene expression analysis indicates that BMI-1 expression correlates positively with DIPG stemness and BMI-1 signature. Together our findings indicate that BMI-1 modulation is associated with mitotic abnormalities, impaired DDR and cell death, supporting the combination of BMI-1 modulation and radiation as a promising novel therapy to treat children with DIPG.
DIPG-23. SINGLE CASE REPORT OF LOW DOSE RADIOTHERAPY AND CHEMOTHERAPY IN THE TREATMENT OF DIPG
Authors: Tseng Chen Kan , Chou I-Jun 
Published: December 2020

Abstract
A 3 year-old girl, was noted to have progressive gait problem since Nov. 2017 and brought to hospital for checkup. Brain MRI on Jan. 2018 showed T2 hyperintensity infiltrative pontine lesion, favoring diffuse infiltrative pontine glioma and mild obstructive hydrocephalus, received VP-shunting on Jan. 15, 2018. Due to the refusal of surgical biopsy for tissue proof, we started the radiotherapy from Jan. 24, 2018, using Rapidarc technique with 6MV photon energy to treat the brain stem lesion, ended on Feb. 24, 2018 with total dose of 25.5Gy in 17 fractions as our usual practice. Following the completion of radiotherapy, we started the adjuvant chemotherapy using 1-week on, 1-week off regimen of temozolomide using dosage of 75 mg/sq-m/day, and this patient’s general condition returned back to nearly normal. Serial follow-up images of brain MRI on 04/30/2018, 08/01/2018, 11/30/2018, 02/26/2019, 05/30/2019, 08/28/2019 showed slow progression of the pontine lesion, without the development of contrast enhanced new lesion. She maintained the functional independent until Sep. 2019, she was noted to have symptoms of ataxic gait, esotropia and choking on drinking liquid. We started the retreatment of radiotherapy from Oct.7, 2019, using same technique, ended on Nov. 5, 2019 with total dose of 30Gy in 20 fractions. The symptoms improved partially after the treatment, with residual weakness over left extremity. We are still treating the patient with adjuvant temozolomide, and she has survived most of time functionally independent in these 2 years.
DIPG-29. PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE (PI3K) INHIBITION DRIVES PROTEIN KINASE C ACTIVATION (PKC) IN DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG)
Authors: Duchatel Ryan J , Mannan Abdul , Jackson Evangeline R , Staudt Dilana , Skerrett-Byrne David A , Jamaluddin M Fairuz B , Woldu Ameha S , Douglas Alicia , Hulleman Esther , Carcaboso Angel M , Monje Michelle , Alvaro Frank , Tsoli Maria , Ziegler David S , Dun Matthew D 
Published: December 2020

Abstract
Recurring somatic mutations and gene amplifications to members of the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K) signaling axis are overarching contributors to the aggressive growth and survival of diffuse intrinsic pontine gliomas (DIPG). However, targeting PI3K has thus far failed to improve outcomes for patients in the clinic. To identify the mechanisms underpinning PI3K/AKT/mTOR treatment failure in DIPG, we have employed high-resolution quantitative phosphoproteomic profiling in patient-derived DIPG cell lines harboring H3K27M and PI3K mutations, +/- the blood-brain barrier permeable PI3K inhibitor, paxalisib (previously “GDC-0084”, currently in Phase I trials - NCT03696355) and rapamycin. Paxalisib was significantly more potent than rapamycin at inducing PI3K/AKT/mTOR inhibition, however, both simultaneously activated protein kinase C signaling (pT500PKCβ +8.2 and +4.5 fold, respectively). PKC lies directly upstream of myristoylated alanine-rich C-kinase substrate (MARCKs), which was phosphorylated at Ser170 by +9.4 and +4.7 fold, respectively; promoting actin cytoskeletal remodeling and cellular migration. Indeed, activation of PKC signaling using phorbol 12-myristate 13-acetate (PMA), increased DIPG cell growth and migration by &gt;3 fold. Targeting PKC using midostaurin (FDA-approved for acute myeloid leukemia), and enzastaurin (blood-brain barrier penetrant inhibitor of PKCβ), in combination with paxalisib was highly synergistic (CI=&lt;0.9), reducing proliferation and driving apoptosis. Mechanistically, compensatory activation of PKC signaling following PI3K inhibition was regulated by the accumulation of Ca+2 ions, as chelation using BAPTA-AM significantly reduced PKC activity following PI3K inhibition. These data highlight the power of phosphoproteomic profiling for the rational design of drug combination strategies, which need to be tested in vivo prior to clinical trials for DIPG.
DIPG-34. SUPER ELONGATION COMPLEX AS A TARGETABLE DEPENDENCY IN H3K27M+ DIFFUSE MIDLINE GLIOMA
Authors: Dahl Nathan , Danis Etienne , Balakrishnan Ilango , Wang Dong , Pierce Angela , Walker Faye , Gilani Ahmed , Serkova Natalie , Madhaven Krishna , Fosmire Susan , Green Adam , Foreman Nicholas , Venkataraman Sujatha , Vibhakar Rajeev 
Published: December 2020

Abstract
Mutations in the histone 3 gene (H3K27M) are the eponymous driver in diffuse intrinsic pontine gliomas (DIPGs) and other diffuse midline gliomas (DMGs), aggressive pediatric brain tumors for which no curative therapy currently exists. To identify specific epigenetic dependencies within the context of the H3K27M mutation, we performed an shRNA screen targeting 408 genes classified as epigenetic/chromatin-associated molecules in patient-derived DMG cultures. This identified AFF4, a component of the super elongation complex (SEC), as necessary for DMG cells to maintain growth and self-renewal. We hypothesized that aberrant SEC expression occurs as a consequence of the H3K27M mutation and that this dysregulated SEC signaling overcomes repressive transcriptional regulation in order to suppresses differentiation and promote self-renewal of DMG tumor stem cells. We interrogated the role of AFF4 in DMG using an shRNA lentiviral approach. We demonstrate a significant decrease in in vitro clonogenicity and stem cell maintenance following AFF4 depletion. We employed RNA-seq-based gene set enrichment analysis to delineate differentiation programs under SEC regulatory control. Finally, we sought to determine whether CDK9, the catalytic subunit of the SEC, represents a therapeutic vulnerability in DMG. Using RNA polymerase II ChIP-seq, we demonstrate that CDK9 pharmacologic inhibition restores regulatory Pol II pausing, promotes cellular differentiation, and leads to potent anti-tumor effect both in vitro and in patient-derived xenograft models. These studies present a biologic rationale for the translational exploration of CDK9 inhibition as a promising therapeutic approach.
DIPG-40. TARGETING MASTER REGULATOR DEPENDENCIES IN DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG)
Authors: Pavisic Jovana , Sethi Chankrit , Jones Chris , Zacharoulis Stergios , Califano Andrea 
Published: December 2020

Abstract
Diffuse intrinsic pontine glioma (DIPG) remains a fatal disease with no effective drugs to date. Mutation-based precision oncology approaches are limited by lack of targetable mutations and genetic heterogeneity. We leveraged systems biology methodologies to discover common targetable disease drivers—master regulator proteins (MRs)—in DIPG to expand treatment options. Using the metaVIPER algorithm, we interrogated an integrated low grade glioma and GBM gene regulatory network with 31 DIPG-gene expression signatures to identify tumor-specific MRs by differential expression of their transcriptional targets. Unsupervised clustering identified MR signatures of upregulated activity in RRM2/TOP2A in 13 patients, CD3D in 5 patients, and MMP7, TACSTD2, RAC2 and SLC15A1/SLC34A2 in individual patients, all of which can be targeted. Notably, intratumoral administration of etoposide by convection enhanced delivery was effective in murine proneural gliomas in which TOP2 was identified as a MR while RRM2—targetable by drugs such as cladribine—has been shown to be a positive regulator of glioma progression whose knock-down inhibits tumor growth. We also prioritized drugs by their ability to reverse MR-activity signatures using a large drug-perturbation database. Patients clustered by predicted drug sensitivities with distinct groups of tumors predicted to respond to proteasome inhibitors, Thiotepa or Volasertib all of which have early evidence in treating gliomas. We will refine this analysis in a multi-institutional study of &gt;100 patient gene expression profiles to define MR signatures driving known biological/molecular disease subtypes, use DIPG cell lines recapitulating common MR architectures to optimize therapy prioritization, and validate our findings in vivo.