bluuebunny/crossref_metadata_2025 huggingface dataset:
The Forum: Global Challenges to Democracy? Perspectives on Democratic Backsliding
Authors: Bartels Larry M , Daxecker Ursula E , Hyde Susan D , Lindberg Staffan I , Nooruddin Irfan
Published: June 2023

There is a widespread perception that we are witnessing a period of democratic decline, manifesting itself in varieties of democratic backsliding such as the manipulation of elections, marginalization and repression of regime opponents and minorities, or more incremental executive aggrandizement. Yet others are more optimistic and have argued that democracy is in fact resilient, or that we are observing coinciding trends of democratic decline but also expansion. This forum highlights key issues in the debate on democracy's decline, which center on conceptual and measurement issues, agreement on the phenomenon but not its nature or severity, the importance of international factors, the emphasis we should put on political elites versus citizens, and the consequences of backsliding for global politics. Staffan I. Lindberg provides an empirical perspective on the scope and severity of democracy's decline, and argues that polarization and misinformation are important drivers for this current wave of autocratization. Susan D. Hyde highlights the detrimental consequences of reduced support for democracy by the international community, which has affected civil society organizations—important arbiters of democracy—especially severely. Challenging some of these conclusions, Irfan Nooruddin claims that any gains for democracy after the end of the Cold War were short-lived, failing to sustain democracy because of an overemphasis on elections and a disregard for structural factors. Finally, Larry M. Bartels argues that we need to look to political elites and not citizens if we want to protect democracy in the United States and elsewhere, which has important implications for how we study democracy and its challenges.
Doravirine responses to HIV-1 viruses bearing mutations to NRTIs and NNRTIs under in vitro selective drug pressure
Authors: Brenner Bluma G , Oliveira Maureen , Ibanescu Ruxandra-Ilinca , Routy Jean-Pierre , Thomas Réjean
Published: June 2023

Objectives

The NNRTI doravirine has been recently approved for the first-line treatment of HIV-infected patients, eliciting favourable responses against viruses bearing the K103N, Y181C and G190A mutations. This study used in vitro drug selections to elaborate the breadth of doravirine responses against viruses bearing NNRTI and NRTI resistance-associated mutations (RAMs).

Methods

WT clinical isolates (n = 6) and viruses harbouring common NRTI and NNRTI RAMs (n = 6) were serially passaged in escalating concentrations of doravirine, doravirine/islatravir, doravirine/lamivudine and rilpivirine over 24 weeks. Genotypic analysis ascertained the appearance and accumulation of NNRTI RAMs. Phenotypic drug susceptibility assays assessed resistance conferred by acquired NNRTI RAMs.

Results

For WT viruses, doravirine pressure led to the appearance of V108I or V106A/I/M RAMs after 8 weeks, conferring low-level (∼2-fold) resistance. After 24 weeks, the accumulation of three to six secondary RAMs, including F227L, M230L, L234I and/or Y318, resulted in high-level (>100-fold) resistance to doravirine. Notably, viruses with these doravirine RAMs remained susceptible to rilpivirine and efavirenz. This contrasted with rilpivirine where acquisition of E138K, L100I and/or K101E resulted in >50-fold cross-resistance to all NNRTIs. Doravirine selection of viruses bearing common NRTI and NNRTI RAMs showed delayed acquisition of RAMs compared with WT virus. Pairing doravirine with islatravir or lamivudine attenuated the development of NNRTI RAMs.

Conclusions

Doravirine showed favourable resistance profiles against viruses harbouring NRTI and NNRTI RAMs. The high barrier to resistance to doravirine coupled with the long intracellular half-life of islatravir may provide the opportunity for long-acting treatment options.
Boundary recognition of tunnel lining void from ground-penetrating radar data
Authors: Li Chuan , Li Minmin , Yang Xiumei , Zhang Weiping , Fan Mingkun , Yang Xi , Wang Lulu
Published: June 2023

Relatively low ground-penetrating radar antenna frequencies are usually selected for tunnel inspection due to the thickness of the lining, which causes the geometric features of voids in the image to be blurred and difficult to identify. Therefore, the boundary points of the voids are determined by combining reflection and attenuation coefficients, and the geometric features are constructed to identify the voids. Depending on the electromagnetic differences between the void and other mediums in the lining, when the electromagnetic wave propagates from the lining concrete to the void, the reflection coefficient is positive, and the phase of the reflected wave is the same as the incident wave. Conversely, the phase of the reflected wave is opposite to the incident wave. Therefore, the boundary point can be determined in the one dimension time-waveform diagram (A-Scan) based on the phase change. Moreover, the amplitude of the electromagnetic wave attenuates exponentially in the concrete, but it attenuates slowly in the void. Also, electromagnetic waves exhibit high-frequency characteristics in the lining but low-frequency characteristics in the voids. Boundary points that conform to the variation of amplitude and frequency characteristics in the void are screened. These boundary points are then constructed in two-dimensional scan data (B-Scan) to identify the voids by using the geometry of the voids. This method is applied to the Hu Sa Tunnel. The voids are successfully identified in the mileage section YK81+310–YK81+422 of the Hu Sa Tunnel, and the depth of cover and the area of voids are correctly estimated.
SIO-ASCO guideline on integrative medicine for cancer pain management: implications for racial and ethnic pain disparities
Authors: Liou Kevin T , Ashare Rebecca , Worster Brooke , Jones Katie F , Yeager Katherine A , Acevedo Amanda M , Ferrer Rebecca , Meghani Salimah H
Published: June 2023

Racial and ethnic disparities in pain management pose major challenges to equitable cancer care delivery. These disparities are driven by complex interactions between patient-, provider-, and system-related factors that resist reductionistic solutions and require innovative, holistic approaches. On September 19, 2022, the Society for Integrative Oncology and the American Society of Clinical Oncology published a joint guideline to provide evidence-based recommendations on integrative medicine for cancer pain management. Integrative medicine, which combines conventional treatments with complementary modalities from cultures and traditions around the world, are uniquely equipped to resonate with diverse cancer populations and fill existing gaps in pain management. Although some complementary modalities, such as music therapy and yoga, lack sufficient evidence to make a specific recommendation, other modalities, such as acupuncture, massage, and hypnosis, demonstrated an intermediate level of evidence, resulting in moderate strength recommendations for their use in cancer pain management. However, several factors may hinder real-world implementation of the Society for Integrative Oncology and the American Society of Clinical Oncology guideline and must be addressed to ensure equitable pain management for all communities. These barriers include, but are not limited to, the lack of insurance coverage for many complementary therapies, the limited diversity and availability of complementary therapy providers, the negative social norms surrounding complementary therapies, the underrepresentation of racial and ethnic subgroups in the clinical research of complementary therapies, and the paucity of culturally attuned interventions tailored to diverse individuals. This commentary examines both the challenges and the opportunities for addressing racial and ethnic disparities in cancer pain management through integrative medicine.
Novel human STING activation by hydrated-prenylated xanthones from Garcinia cowa
Authors: Tran Thi Thu Thuy , Le Phuong Mai , Nguyen Thi Kim An , Hoang Thi Minh Nguyet , Do Thi Quynh An , Martel Alexandrine L , Lewicky Jordan D , Klem Alexandra , Le Hoang-Thanh
Published: June 2023

Objectives

We investigate the anticancer activity and human stimulator of interferon genes pathway activation by a new hydrated-prenylated tetraoxygenated xanthone, garcicowanone I (1) and two known xanthones (2 and 3) that were isolated from the root bark of Garcinia cowa Roxb. ex Choisy.

Methods

The anticancer activity of each compound was evaluated by sulforhodamine B assay in immortalized cancer cell lines. Stimulator of interferon genes pathway activation was assessed by western blot analysis using human THP-1-derived macrophages. The production of pro-inflammatory cytokines from these macrophages was also evaluated via enzyme-linked immunosorbent assay.

Key findings

Both compounds 1 and 3 displayed moderate inhibitory effects on the cancer cells, including a cisplatin-resistant cell line, with IC50 values in the range of 10–20 µM. All three xanthones activated the stimulator of interferon genes, as evidenced by phosphorylation of tank-binding kinase 1, the stimulator of interferon genes protein and interferon regulatory factor 3. Furthermore, treatment of these macrophages with compounds 1–3 led to the production of pro-inflammatory cytokines, including interleukin 6, tumour necrosis factor α and interleukin 1β.

Conclusions

In conclusion, the isolated xanthones, including the novel garcicowanone I, displayed promising anticancer and immunomodulatory activity that warrants further research.
Transmissibility of mpox to the general population from travellers returning to South Korea
Authors: Lee Dayeong , Choi Sangbum , Do Hyunkyung , Chiara Achangwa , Kim Min-Kyung , Chin BumSik , Ryu Sukhyun
Published: June 2023

Based on data from three imported mpox cases in South Korea, the overall attack rate was determined to be 1%, while a secondary attack rate of 14% was estimated in the high-exposure group.
A novel pyrosequencing strategy for RHD zygosity for predicting risk of hemolytic disease of the fetus and newborn
Authors: Lv Piao , Li Jixin , Yao Yuan , Fan Xinxin , Liu Chixiang , Li Hui , Zhou Huayou
Published: June 2023

Objective

The aim of this study was the development of an accurate and quantitative pyrosequence (PSQ) method for paternal RHD zygosity detection to help risk management of hemolytic disease of the fetus and newborn (HDFN).

Methods

Blood samples from 96 individuals were genotyped for RHD zygosity using pyrosequencing assay. To validate the accuracy of pyrosequencing results, all the samples were then detected by the mismatch polymerase chain reaction with sequence-specific primers (PCR-SSP) method and Sanger DNA sequencing. Serological tests were performed to assess RhD phenotypes.

Results

Serological results revealed that 36 cases were RhD-positive and 60 cases were RhD-negative. The concordance rate between pyrosequencing assay and mismatch PCR-SSP assay was 94.8% (91/96). There were 5 discordant results between pyrosequencing and the mismatch PCR-SSP assay. Sanger sequencing confirmed that the pyrosequencing assay correctly assigned zygosity for the 5 samples.

Conclusion

This DNA pyrosequencing method accurately detect RHD zygosity and will help risk management of pregnancies that are at risk of HDFN.
Virtuality: A Theory of Digital Judaism(S)
Authors: Margolis Peter
Published: June 2023

Digital media enable new possibilities in Jewish life and lived religion. This “digital Judaism” combines elements of Jewish tradition with the capabilities to create, modify, and transform digital objects in novel ways. It builds on American media history and has been greatly accelerated in response to the exigencies of the COVID-19 pandemic of 2020–2021. The Internet as a form of media functions as an amplifier of human capabilities and Jewish possibilities that can be integrated into Jewish life. This creates the contemporary online–offline media ecology to which I apply the theoretical concept of “virtuality.” Virtuality extends and builds upon Heidi Campbell’s religious-social shaping of technology (RSST), Michael Satlow’s “maps” for defining a Judaism, Uzi Rebhun’s study of symbolic Judaism, Ananda Mitra and Rae Lynn Schwatrz’s concept of online/offline cybernetic space, and Jack Wertheimer’s remix concept.
Chemical evolution with radial mixing redux: a detailed model for formation and evolution of the Milky Way
Authors: Chen Boquan , Hayden Michael R , Sharma Sanjib , Bland-Hawthorn Joss , Kobayashi Chiaki , Karakas Amanda I
Published: June 2023

We present a multizone galactic chemical evolution (GCE) model for the Milky Way that takes the most recently updated yields of major nucleosynthesis channels into account. It incorporates physical processes commonly found in previous GCE models like gas feedback from supernovae and star formation, the radial flow of gas in the disc, and the infall of fresh gas, along with stellar scattering processes like radial migration. We individually analyse the effect of different physical processes present in our model on the observed properties of the Galaxy. The radial flow of gas in the disc plays an important role in establishing the radial gradient for [Fe/H] in the low-[α/Fe] sequence. Our model with one episode of smooth gas infall and constant star formation efficiency is capable of reproducing the observed ([Fe/H], [α/Fe]) distribution of stars at different (R, |z|) positions in the Milky Way. Our results point to the rapid evolution of [α/Fe] after the onset of Type Ia supernovae and a high star formation rate during the formation of the high-[α/Fe] sequence as the origin of dual peaks in [α/Fe]. A secondary infall is unnecessary to reproduce the [α/Fe] gap and chemical spread in the disc in our model. We additionally compare the median age for various mono-abundance populations and the age–metallicity relation at different (R, |z|) positions from our fiducial model to observations. We discuss our results in relation to other related work in detail.
Versatile Detection of Diverse Selective Sweeps with Flex-Sweep
Authors: Lauterbur M Elise , Munch Kasper , Enard David
Published: June 2023

Understanding the impacts of selection pressures influencing modern-day genomic diversity is a major goal of evolutionary genomics. In particular, the contribution of selective sweeps to adaptation remains an open question, with persistent statistical limitations on the power and specificity of sweep detection methods. Sweeps with subtle genomic signals have been particularly challenging to detect. Although many existing methods powerfully detect specific types of sweeps and/or those with strong signals, their power comes at the expense of versatility. We present Flex-sweep, a machine learning–based tool designed to detect sweeps with a variety of subtle signals, including those thousands of generations old. It is especially valuable for nonmodel organisms, for which we have neither expectations about the overall characteristics of sweeps nor outgroups with population-level sequencing to otherwise facilitate detecting very old sweeps. We show that Flex-sweep has the power to detect sweeps with subtle signals, even in the face of demographic model misspecification, recombination rate heterogeneity, and background selection. Flex-sweep detects sweeps up to 0.125*4Ne generations old, including those that are weak, soft, and/or incomplete; it can also detect strong, complete sweeps up to 0.25*4Ne generations old. We apply Flex-sweep to the 1000 Genomes Yoruba data set and, in addition to recovering previously identified sweeps, show that sweeps disproportionately occur within genic regions and are close to regulatory regions. In addition, we show that virus-interacting proteins (VIPs) are strongly enriched for selective sweeps, recapitulating previous results that demonstrate the importance of viruses as a driver of adaptive evolution in humans.
ATRT-02. AN INFANTILE PINEAL EMBRYONAL TUMOR SHOWING PATHOLOGICAL FEATURES OF A CNS GANGLIONEUROBLASTOMA IN ADDITION TO SMARCA4 MUTATIONS AND THE METHYLATION PROFILING OF AN ATYPICAL TERATOID/RHABDOID TUMOR
Authors: Fukuoka Kohei , Nakazawa Atsuko , Hirato Junko , Nobusawa Sumihito , Itabashi Toshikazu , Arakawa Yuki , Tanami Yutaka , Ichimura Koichi , Kurihara Jun , Koh Katsuyoshi
Published: June 2023

Embryonal central nervous system tumors require genetic and epigenetic molecular analyses for further classification owing to the pathological, clinical, and molecular heterogeneity among these tumors. Here, we report a case of an infantile pineal tumor showing the pathological features of a CNS ganglioneuroblastoma; however, the specimen also contained SMARCA4 mutations and a methylation signature that is close to an atypical teratoid/rhabdoid tumor. A 2-year-old girl was referred to our hospital because of headache and dizziness presented with a pineal tumor and obstructive hydrocephalus. Radiologically, a large calcification was observed in the mass on head CT. The patient underwent tumor resection, and the pathological diagnosis was CNS ganglioneuroblastoma at that time. The specimen contained a variety of tumor cells, including undifferentiated embryonal cells, neurocytic cells, and ganglion cells embedded in a fibrillary matrix. The patient has been well for 5 years since they received multiagent chemotherapy and local proton irradiation. Subsequent genome-wide DNA methylation analysis revealed that the tumor was molecularly close to a sonic-hedgehog pathway-activated atypical teratoid/rhabdoid tumor. Genetic analysis also revealed SMARCA4 alterations in the splicing region of exons 10 and 34. This report indicates that genetic and epigenetic molecular approaches may facilitate elucidation of the clinical heterogeneity of CNS embryonal tumors, particularly the pathological appearance of CNS ganglioneuroblastomas.
ATRT-17. CAR T CELL THERAPY TARGETING CLAUDIN-6 IS EFFECTIVE IN CELLULAR AND XENOGRAFT MODELS OF ATYPICAL TERATOID/RHABDOID TUMOR
Authors: Madsen Peter , Stern Allison , Dickson Conor , Wilson Cullen , Patterson Luke , Harvey Kyra , Griffin Crystal , Oehm Petra , Rengstl Benjamin , Flemmig Carina , Storm Phillip , Resnick Adam , Foster Jessica
Published: June 2023

Novel therapies are needed to for the treatment of atypical teratoid/rhabdoid tumor (ATRT), an aggressive brain tumor that predominantly affects young children and has an average 5-year survival under 50%. Claudin-6 (CLDN6) is a tight junction protein present during development and is expressed in up to 70% of ATRT specimens but not in normal tissue, making it a promising immunotherapeutic target. CLDN6-targeted chimeric antigen receptor (CAR) T cells in combination with a CAR T cell-amplifying mRNA vaccine have demonstrated antitumor activity against other CLDN6-expressing cancers in pre-clinical and a phase I adult trial (NCT04503278; Haanen J et al AACR, 2022). To assess the effectiveness of CLDN6-targeted CAR T cells against ATRT, we utilized a second-generation mRNA CAR with a 4-1BB costimulatory domain and single-chain variable fragment against CLDN6 (Reinhard et al, 2020). CLDN6 expression in patient-derived ATRT specimens was profiled by RNAseq (mean FPKM 11.4) and immunohistochemistry (positive staining in 53% of specimens). Tumor-derived cell lines were assessed for CLDN6 expression by flow cytometry. Co-culture of CLDN6-directed mRNA CAR T cells resulted in tumor-specific cytotoxicity compared to CD19-directed control CAR T cells in CLDN6-positive ATRT cell lines 7316-2187 (92% versus 15% at 10:1, p < 0.0001; 86% versus 0% at 5:1, p<0.0001) and 7316-2141 (75% versus 7% at 10:1, p<0.0001; 53% versus 0% at 5:1, p< 0.0001). Patient-derived, orthotopic xenograft ATRT models were created through intracranial injection of tumor cells into the cerebellum of NSG mice. Following engraftment with 7316-2141, repeated intratumoral administration of mRNA CLDN6 CAR T cells resulted in significant tumor regression (-1.9x108 vs. +2.4x109 p/sec/cm2/sr, p<0.001) and improved survival compared to mRNA CD19 CAR T cells (median OS not reached vs. 13 days, p=0.002). This work highlights the potential for targeting CLDN6 via CAR T cell therapy in patients with ATRT as a novel therapeutic strategy.
BIOL-04. FROM MSWI/SNF’S ROLES IN PROTEIN SYNTHESIS TO NEW THERAPEUTIC OPPORTUNITIES
Authors: Van Rechem Capucine
Published: June 2023

The chromatin remodeler complexes mammalian SWI/SNF (SWItch/Sucrose Non-Fermentable) are altered in more than 40% of cancers and are involved in therapeutic resistance. In children, SMARCB1 is mutated in 95% of rhabdoid tumors, and the remaining 5% present mutations in SMARCA4. These tumors are typically identified in children younger than three years old and have a very poor prognosis with a survival under one year following diagnosis. SMARCB1 expression is also lost in more than 90% of epithelial sarcomas, a rare and aggressive tumor affecting young adults, and in 50% of pediatric chordomas. Additional mSWI/SNF subunits are also highly mutated in childhood cancers such as ARID1A and ARID1B in neuroblastomas, the most common solid tumor in children, and the ARID subunits and SMARCA4 in medulloblastomas, the most common brain cancer in children. To date, mSWI/SNF roles in normal and cancer cells are still largely undetermined and focus on nuclear functions. However, our assessment of genetic dependencies and drug sensitivity screens revealed that cancer cells mutated for mSWI/SNF are genetically dependent and exclusively sensitive to translation factors and translation pathway inhibitors. We demonstrate that mSWI/SNF complexes are extensively localized in the cytoplasm and that they interact with the translation initiation machinery. Furthermore, short-term inhibition, depletion and cancer mutations of specific subunits alter protein synthesis and increase sensitivity to translation inhibitors. Most mutations in these complexes being considered loss of function, these results suggest a potential therapeutic opportunity for diseases presenting mutations in these complexes. In conclusion, our work demonstrates the chromatin remodelers mSWI/SNF have direct roles in translation that will not only be relevant for the molecular understanding of cancer but also lead to new therapeutic opportunities.
BIOL-13. DEPLOYING NEW MODELS OF NF-1 MUTANT LOW GRADE GLIOMA TO ACCELERATE THERAPEUTIC DEVELOPMENT
Authors: Alaali Lujain , Xu Jinchong , Mumm Jeff , Yuan Ming , Eberhart Charles , Raabe Eric
Published: June 2023

Pediatric low grade glioma (pLGG) research is hampered by a paucity of genetically accurate cell line models and xenografts. To address this need, we have developed and characterized multiple in vivo and organoid models. We used cell reprogramming conditions (CRC) to establish and propagate JHH-NF1-PA1, a NF1-mutant line derived from a low grade optic pathway glioma of a patient with type 1 neurofibromatosis. JHH-NF1-PA1 cells persist and take up midline positions when xenografted into the brains of zebrafish, allowing testing of therapeutics in vivo. We developed a human iPSC-brain organoid system comprising of midline neurons, glia, and microglia, largely recapitulating the microenvironment of midline low grade glioma. Our JHH-NF1-PA1 cells incorporate into these brain organoids, allowing us to test potential therapeutics in an in vitro setting in which the tumor cells grow in the appropriate microenvironment. We have also further defined the mouse BL6 NF1 null glioma cell line 1810, which forms orthotopic xenografts in mice. This last model will be useful for therapeutic testing in a syngeneic BL6 background, allowing assessment of immune infiltration and signaling downstream of NF1 loss and potential immunotherapeutics. Together, these in vitro and in vivo models of NF1-driven low grade glioma make an important contribution to our understanding of the biology of low grade glioma.
BIOL-22. CHILDREN’S BRAIN TUMOR NETWORK PRECLINICAL TUMOR MODELS DEVELOPMENT AND SHARING PLATFORM: COLLABORATIVE MODEL EMPOWERING PEDIATRIC BRAIN TUMOR DISCOVERY AND GLOBAL RESEARCH
Authors: Hollawell Madison , Baubet Valerie , Beale David , Patterson Luke , Biluck Ian , Anthony Ciana , Goel Peeyush , Beck Christopher , Sonawane Poonam , Griffin Crystal , Stern Allison , Madsen Peter , Foster Jessica , Lilly Jena , Mason Jennifer , Trooskin Gerri , Sullivan Catherine , Gehrand Ashley , Morgan Allison , Frenkel Beth , Lehmann Kaitlin , Lopez Lina , Nguyen Thinh , Agbodza Ena , Lopez-gil Valeria , Helili Zeinab , Plisiewicz Alexa , Coleman Noel , Zhu Yuankun , Huang Xiaoyan , Patton Tatiana , Mcgrory Stephanie , Arya Kamnaa , Velasco Ryan , Santi Mariarita , Viaene Angela , Storm Phillip , Koptyra Mateusz , Resnick Adam
Published: June 2023

Pediatric brain tumor preclinical development has suffered from the lack of robust in vitro and in vivo models that span the large number of brain tumor histologies. Opportunities for precision medicine approaches for solid and brain tumors are expanding, including immunotherapies, so it is essential to maximize access to preclinical models for studies of specificity, efficacy, and safety of treatments in ways that align patient models to patient samples and their clinical course. The Children’s Brain Tumor Network (CBTN) seeks to accelerate pediatric brain tumor research and discovery through support of the tumor model development program paired with molecularly characterized patient samples and longitudinal clinical data. This program focuses on the generation, characterization, and distribution of diverse models to investigators worldwide. Here we present currently available preclinical model resources comprising over 150 cell lines, organoids, and patient derived xenografts (PDX) developed and/or propagated at D3b at CHOP on behalf of CBTN. This platform maximizes the use of tumor tissue to generate a combination of cell lines, organoids and/or xenograft models grown in animals. To date, consortium-supported lines have been provided internationally to over 50 projects, encompassing basic biology and translational studies. Molecular data (whole genome sequencing and RNAseq) is currently available for over 80 models and a substantial portion of that cohort undergoes additional large-scale data generation and drug testing through collaborative work with Childhood Cancer Model Atlas, ProCan, and National Center for Advancing Translational Sciences. All models’ data are accompanied with patient molecular and clinical longitudinal information accessible through Kids First Data Resource, CAVATICA and PedcBio portals. This open-source repository model is an example of a unique research partnership supported by patients and their families and built with one mission – to accelerate therapeutic discovery for children suffering from brain tumors.
DIPG-04. TUMOR CELL-INTRINSIC TIM-3 PROMOTES DIFFUSE INTRINSIC PONTINE GLIOMA TUMORIGENESIS
Authors: Ausejo-Mauleon Iker , Laspidea Virginia , de la Nava Daniel , Nuin Sara , Palacios-Alonso Daniel , Marco-Sanz Javier , Becher Oren , Jiang Li , Filbon Mariella G , Pastor Fernando , Alonso Marta M
Published: June 2023

Diffuse intrinsic pontine glioma (DIPG) is an aggressive brain tumor and the leading cause of pediatric death caused by cancer. Despite great strides in the understanding of this disease, the median overall survival is still dismal. TIM-3 is emerging as an alternative to the classic immune checkpoints CTLA-4 and PD-1, and its expression regulates by various mechanisms the function of innate and adaptative immunity. In our work, we demonstrated that TIM-3 is expressed in murine and human DIPG tumor cell lines in vitro and in vivo. TIM-3 knockout using CRISPR/Cas9 was lethal in all human DIPG cell lines evaluated. However, a doxycycline-inducible shRNA-TIM-3 significantly reduced the proliferation of DIPG human cell lines (100% control vs. 25% shRNA TIM-3). Additionally, TIM-3KO murine cell lines displayed a significant decrease in clonogenicity, proliferation, and migration in vitro compared with parental DIPG murine cell lines. Interestingly, loss of TIM-3 expression did not result in cell death, as shown by the evaluation of apoptosis. In vivo evaluation of TIM-3KO cell lines tumorigenicity demonstrated that mice bearing TIM3-KO cells had an overall median survival (35 days) significantly higher than the ones bearing the control guide cells (16 days). RNAseq data indicated that TIM-3 plays a critical role in DIPG murine cells tumorigenesis and survival through the MAPK signaling pathway. Finally, single-cell sequencing and immunochemistry of human tumor samples uncovered TIM-3 expression in patients. TIM-3 expression in DIPG tumor cells correlated with genes positively involved in regulating ion transport, IL-6 production, and response to IFN-γ pathways. We also observed enrichment in genes regulating MAPK and ERK1/ERK2 cascades in these patients. Collectively, these data suggest that TIM-3 expression might have a role in the survival and tumorigenesis of DIPG cells.
DIPG-37. TRANSCRIPTIONAL, EPIGENETIC, AND IMMUNOLOGICAL FEATURES OF PAEDIATRIC-TYPE H3 K27-ALTERED DIFFUSE MIDLINE GLIOMAS ORIGINATING FROM DIFFERENT BRAIN LOCATIONS
Authors: Grabovska Yura , Mackay Alan , Pereira Rita , Sejdiu Drenusha , Burford Anna , Temelso Sara , Clarke Matt , Jones Chris
Published: June 2023

Diffuse midline gliomas (DMG) are highly aggressive brain tumours predominantly affecting young children. The main oncogenic driver is the substitution of lysine 27 to methionine (K27M) in histone 3 (H3) or overexpression of EZHIP resulting in global loss of H3K27me3. Recent single-cell (epi-)genomic studies have identified developmentally-restricted origins and cell states associated with tumour location and patient age, and we aimed to further explore the underlying biology of distinct subgroups of DMG using orthogonal data modalities. A retrospective reanalysis identified 242 patient genome-wide DNA methylation array profiles with a methylation classification of DMG_K27. H3 status was known for 168 cases (H3.3 K27M n=130, H3.1 K27M n=20, H3 WT n=18), with EZHIP overexpression or loss of H3K27me3 was confirmed in 13/18 H3 WT cases. Unsupervised clustering identified two distinct methylation subtypes, specific to brainstem (62/64) or thalamic (25/29) location, and highly enriched for gain of chromosome 1q or loss of 5q, respectively. Differential expression analysis from bulk RNA-Seq data recapitulated the recently-published overexpression of ZIC1/4 early development genes in thalamic tumours and an enrichment of HOX-cluster genes in those of brainstem origin. Within DMGs of the thalamus, we further observed a significant overexpression and hypomethylation of NR2E1, a regulator of bivalent promoters via LSD1-H3K4, and essential for stem cell renewal; and CD96, an immune checkpoint blockade target in NK/T-cells. We confirmed differential immune response expression between tumour location by GSEA as well as deconvolution by methylation CIBERSORT from bulk samples, which we were able to characterise further by by single-cell RNA-sequencing. We report unique copy-number and differentially methylated loci as well as differential expression that recapitulates previously reported single-cell metaprogrammes. We also highlight involvement of neural stem cell development programme in thalamus-type tumours as well as evidence of these tumours as being potential targets for immune therapeutic targeting.
DIPG-38. PATIENT-DERIVED THREE-DIMENSIONAL AVATARS REVEAL CELL-AUTONOMOUS MECHANISMS DRIVING INVASION AND METASTATIC PROGRESSION IN DIFFUSE MIDLINE GLIOMAS
Authors: Bruschi Marco , Midjek Lilia , Ajlil Yassine , Vairy Stephanie , Lancien Manon , Ghermaoui Samia , Kergrohen Thomas , Verreault Maïté , Idbaih Ahmed , Beccaria Kévin , Blauwblomme Thomas , Puget Stéphanie , Tauziede-Espariat Arnault , Varlet Pascale , Dangouloff-Ros Volodia , Boddaert Nathalie , Teuff Gwenael Le , Grill Jacques , Montagnac Guillaume , Elkhatib Nadia , Debily Marie-Anne , Castel David
Published: June 2023

Diffuse midline gliomas H3K27-altered are pediatric tumors associated with dismal survival after diagnosis that are characterized by their ability to infiltrate the entire central nervous system. We show that the extent of tumor invasion and metastatic progression represent critical adverse prognostic factors affecting the survival of DMG patients. Yet, no genetic alterations associate to the tumor progression patterns. We therefore used glioma stem cells collected at diagnosis to create patient-specific 3D avatars. We found that their invasive behaviour faithfully predicts metastatic relapse in patients, thus proving DMG spread is mainly an autonomous ability of tumor cells. This relevant modelling strategy revealed the existence of phenotypic entities associated with distinct migration modalities and capacities. Using transcriptomics of both organoids and primary tumors, we identified the biological programs associated with variable invasiveness. Importantly, we show that Bone Morphogenetic Protein 7 (BMP7) signalling is a crucial tumour-autonomous regulator of DMG invasiveness via the control of a phenotypic switch. We further deciphered effectors downstream of BMP7 stimulation as actionable targets to reduce invasion.

These findings have two possible therapeutic applications. First, glioma stem cell 3D models represent a tool for tumor phenotypic stratification to rapidly predict patients with exacerbated invasiveness and increased risk of metastatic progression. This may allow to propose whole-brain or cranio-spinal irradiation within weeks after diagnosis to prevent the appearance of distant foci. Second, targeting autocrine and short-range BMP7-related signalling may become a useful adjunct to the current therapeutics, which are mainly directed to control the disease locally.
DIPG-47. DISCOVERING A MOLECULAR BASIS FOR VULNERABILITY OF H3K27M-DMG TO HISTONE DEACETYLASE INHIBITORS
Authors: Paine Danyelle , Hao Yue , Tang Nanyun , Biery Matt , Vitanza Nicholas , Berens Michael
Published: June 2023

Using two H3K27M-DMG treatment-naive preclinical models (PBT22 and PBT29), we detected a 20-fold differential response to the histone deacetylase inhibitor, Quisinostat. PBT-22 harbors mutations in H3F3A, TP53, and ASXL2, while PBT-29 has mutations in H3F3A, TP53, PIK3CA and FGFR1. Acetylation and deacetylation of wtH3 alter chromatin structure as part of normal regulation of gene expression. The methionine substitution for Lysine in H3K27M removes this histone from participating in acetylation/deacetylation regulated gene expression. Concomitantly, H3K27M induces a marked reduction in global acetylation of histone tails on wtH3. In the native state of H3K27M DMG with hypoacetylated H3, we posit that the specific pattern of nucleosome integration with genes responsible for cell survival/death underlies the differential vulnerability of DMGs to HDACi. Additionally, the nucleosome integration pattern with cell survival/death genes may be based on the relative abundance of wtH3wt versus H3K27M- histones. Following Quis treatment (48 hrs) in both preclinical models, total wtH3ac protein abundance increased 3-fold, suggesting HDACi stabilizes or impedes K27 acetylated H3 histone turnover. Comparison of differentially expressed genes (DEGs) from control and Quis-treated PBT22 and PBT29 will seed gene ontology analysis focusing on chromatin remodeling, cell death, and growth arrest pathways accounting for differential vulnerability. Findings will be validated by measuring transcripts and proteins (qRT-PCR and ELISA or mass spectrometry) from analytes from a larger panel of DMG cell lines. The data depicts DMG preclinical models with large differential sensitivity to Quis. The long-term goal is to discover a molecular profile of DMGs predictive of the vulnerability to HDACi. The discovery exercise is also likely to yield insight into the development of resistance to HDAC inhibitors.
EPEN-10. SPINAL EPENDYMOMA WITH MYCN-AMPLIFICATION – A DISEASE OF CHILDHOOD AND YOUNG ADULTHOOD WITH DISMAL PROGNOSIS
Authors: Ghasemi David R , Sill Martin , Okonechnikov Konstantin , Shatara Margaret , Yip Stephen , Reisz Zita , Plate Karl-Heinz , Scheie David , Hasselbalch Benedikte , Dohmen Hildegard , Chaouch Amel , Jabado Nada , den Dunnen Wilfred F A , Wesseling Pieter , Fröhling Stefan , Donson Andrew , Capper David , Schüller Ulrich , Pfister Stefan M , Reuss David E , Pajtler Kristian W
Published: June 2023

Spinal ependymoma (EPN) with MYCN-amplification (SP-EPN-MYCN) was recently recognized as a distinct tumor type within the 2021 WHO classification of CNS tumors. To date, information about the epidemiological, clinical, and biological features of SP-EPN-MYCN remain sparse. Using DNA-methylation profiling, we collected a cohort of n = 71 (54 primaries, 17 relapses) SP-EPN-MYCNs. Based on the Heidelberg Methylation Brain Tumor Classifier V12.5, 95.6% (68/71) reached a classifier score of ≥ 0.9. In 68/71 cases, focal amplifications of MYCN were detected by copy number variation (CNV) analysis. Two tumors of pediatric patients harbored MYC-amplifications. Other repeated CNVs amongst the primary cases included gains of chromosomes 5 (5/54) and 18 (5/54), loss of chromosome 10 (14/51), and combined 17p loss and 17q gain (5/54). FISH (n = 17) and immunohistochemistry (n = 19) provided positive results for the detection of the MYCN-amplification. Epidemiological data was available for 63% (34/54) of all patients, showing an even sex distribution (17 female patients). Twenty-four percent (8/34) were children and adolescents younger than 20 years. The rest of the cohort consisted of an AYA-population with an overall median age of 31.5 years. Primary lesions were predominantly located in the thoracic (72%) and/or cervical (55%) spinal cord. Two patients showed extra-CNS metastasis to the humerus and the paraspinal musculature, respectively. At the point of analysis, 38% (10/26) of all patients had died, and 10/16 alive patients had already developed disseminated disease. Of patients with available information, 90% (18/20) had relapsed, whereas 10% (2/20) showed stable disease with leptomeningeal spread. Median PFS (n = 17) and OS (n = 25) were 15,5 (12 – 34) and 85 (61 – NA) months. In summary, SP-EPN-MYCN is a disease with dismal prognosis that can disseminate outside of the CNS and affects mainly children and AYA. Currently, comprehensive multi-omics analyses are ongoing.
METB-01. EXTRACHROMOSOMAL DNA IS ASSOCIATED WITH ONCOGENE AMPLIFICATION AND POOR SURVIVAL ACROSS MULTIPLE PEDIATRIC CANCER TYPES
Authors: Sridhar Sunita , Chapman Owen , Dutta Aditi , Wang Shanqing , Chavez Lukas
Published: June 2023

Circular extrachromosomal DNA (ecDNA) is an important driver of aggressive cancers. Its frequency and impact on the spectrum of pediatric cancers has yet to be fully described. To determine the ecDNA prevalence in various pediatric cancer types, we accessed whole genome sequencing (WGS) data in the Children’s Brain Tumor Network (CBTN) and St. Jude cancer cloud genomics platforms and utilized the bioinformatics tools Amplicon Architect (AA) and Amplicon Classifier (AC) to reconstruct ecDNA sequence structures. We then identified which genes were amplified on the ecDNA and the association of ecDNA with survival using Kaplan Meier curves. In total, we analyzed a retrospective cohort of over 1600 tumor biopsies from 1400 different patients, spanning 69 different tumor types. We identified ecDNA in 14 tumor types. The incidence of ecDNA within these 14 tumors was 16% with the highest percentage in osteosarcoma (47%), pineoblastoma (40%) and rhabdomyosarcoma (40%). The overall incidence of ecDNA across the patient cohort was 10%. In analyzing matched diagnostic/relapse and relapse/progression pairs, ecDNA was noted to evolve over time with progression of disease. Across the cohort, ecDNA was found to be significantly associated with poor survival. Our preliminary results demonstrate that ecDNA is prevalent in pediatric cancer, can contain known and potentially novel oncogenes and can be associated with poorer outcomes across many different pediatric cancer types.
HGG-12. INFANT HEMISPHERIC GLIOMA: CLINICAL AND MOLECULAR CHARACTERISTICS AND RESULTS OF TARGETED THERAPY
Authors: Papusha Ludmila , Druy Alexander , Zaytseva Margarita , Salnikova Ekaterina , Panferova Agnesa , Samarin Alexey , Novichkova Galina , Hwang Eugene , Packer Roger
Published: June 2023

We analyzed an infant cohort consisting of 14 patientswith hemispheric gliomas (hHGG, n=10 and DIGG, n=4) diagnosed at D. Rogachev Center between 2017and 2022.

The hHGG cohort included nine females and one male ranging in age from one week to 22 months. RTK-fusions were detected in all (ROS1 - 4, ALK - 2,NTRK1 – 2, NTRK3 - 1, and EGFR - 1). In one of thesecases, the diagnosis was made retrospectively in a patient initially diagnosed with anaplastic ependymoma who died during treatment. Out of the nine remaining hHGG patients, four (ROS1 - 3, NTRK3-1) experienced rapid progressive disease (PD) duringconventional chemotherapy and one pt (ROS1) after RT. These five pts received targeted therapy with entrectinib with initial good responses in all cases (CR-2, PR-3); one of these patients (ROS1) experienced PD after 7 months of targeted therapy and died of disease. Molecular genetic analysis after the second operationin this case revealed an acquired ROS1 G2032R mutation. Treatment-related adverse events on entrectinib therapy were detected in two patients and included bone fractures and neutrophil count decrease in one case and decrease left ventricular ejection fraction in another patient. Median duration of targeted therapy was 7 months (range, 3-33). From those pts who received only chemotherapy – 2 pts are alive with CR and 1 pt died from complication of CT.

All patients with DIGG are alive without signs of progression after surgery alone. Median follow-up time is 19 months (range, 5-64). Molecular genetic analysis revealed MAPK-pathway alterations in each case (rearrangements of NTRK1-1, ROS-1, RAF1-1, BRAF-1), respectively.

Patients with infant hHGG demonstrate an aggressive course on conventional therapy, especially in cases with ROS1-positive tumors. Targeted therapy may be an effective treatment option but required close monitoring for toxicity and resistance.
HGG-15. HIGH-GRADE GLIOMAS OCCURRING IN TEENAGERS AND YOUNG ADULT PATIENTS COMPRISE NOVEL MOLECULAR SUBGROUPS
Authors: Clarke Matthew , Pereira Rita , Mackay Alan , Grabovska Yura , Clarke Amelia , Nicoll James , Procter John , Moore Andrew , Schagen Joanna , Walker Liam , Roncaroli Federico , Ogunbigi Olumide , Jacques Thomas , Marshall Lynley , Carceller Fernando , Reisz Zita , Al-Sarraj Safa , Vinci Maria , Kurian Kathreena , Ng H K , Brandner Sebastian , Jones Chris
Published: June 2023

High-grade gliomas (HGG) arise in any central nervous system location, in adults and children, with a poor prognosis. HGGs in teenagers and young adults (TYA) are understudied; this project aimed to characterise these tumours and identify potential therapeutic targets. HGG samples (n=195, FFPE/FF, 13-30 years) were collected, excluding well-characterised entities (histone/IDH-mutant). DNA methylation profiling (Illumina EPIC BeadArrays, brain tumour classifier (MNP v12.5 R package), n=195) classified cases against a reference cohort. Calibrated scores guided workflows to characterise mutational landscapes including RNA-based ArcherDx fusion panel (n=112), whole exome sequencing (n=84), and histological reviews in parallel. Well-characterised entities (n=50, including IDH-mutant tumours (n=18), PXA (n=12)) were excluded. Of the cases scoring >0.6, 64% classified as paediatric-type subgroups (pedHGG-RTK1A/B/C (30%), pedHGG-MYCN (10%), pedHGG-A/B (7%), pedHGG-RTK2A (6%)). 29% classified as subgroups more frequently seen in adults (GBM-MES (12%), GBM-RTK1/2 (3%)). 54% classified with a score <0.6. 38% cases were assigned to novel, recently identified, poorly-characterised subgroups with distinct methylation profiles and molecular features (HGG-B, HGG-E, ANTCON, GBM-CBM). Frequency comparisons to publicly available methylation data showed GBM-MES-ATYP tumours are TYA age-specific, in contrast to adult age-specific GBM-MES-TYP. Copy number profiling identified frequent changes across the cohort, including chromosomal gains (chr1q (54%), chr2 (22%), chr7 (41%)) and losses (chr10 (40%), chr13 (64%)). Focal amplifications included PDGFRA (12%), CDK4 (7%), MYCN/ID2 (3%), MYC (2%) and EGFR (0.7%) and the most common focal deletion was CDKN2A/p16 (12%). The most frequent glioma-associated somatic variants included TP53, PDGFRA, EGFR, and NF1. BCOR alterations were enriched compared to adult and paediatric reference cohorts. 10% cases showed a hypermutator phenotype, enriched in HGG-E. CDK4 amplifications were recurrent in GBM-RTK1 and GBM-CBM. Histology showed variable cytological and architectural features within novel subgroups. TYA HGG comprise novel subgroups with distinct methylation profiles and molecular characteristics, representing opportunities to refine future treatment.
IMMU-06. SYSTEMIC MRNA VACCINES RESET IMMUNOGENICITY AGAINST DIFFUSE MIDLINE GLIOMA
Authors: McGuiness James , Weidert Frances , DeVries Anna , Ligon John , Zhang Dingpeng , Von Roemeling Christina , Grippin Adam , Karachi Aida , Qdaisat Sadeem , Thomas Nagheme , Castillo Paul , Huang Jianping , Silver Natalie , Rahman Maryam , Hwang Eugene , Mitchell Duane , Mendez-Gomez Hector , Sayour Elias
Published: June 2023

BACKGROUND

DIPG remains a uniformly fatal disease in dire need of new therapies. There are currently no systemic therapies with proven efficacy against these tumors. To overcome these barriers, we developed a systemic mRNA lipid particle (LP) vaccine that localizes to tumors and reticuloendothelial (RE) organs to modulate both innate and adaptive immunity against poorly immunogenic tumors like DIPG.

OBJECTIVE

We sought to assess whether RNA-LPs encoding for model antigens (e.g. H3K27M) would reprogram innate immunity and simultaneously elicit sustained adaptive immunity against diffuse midline glioma (DMG).

RESULTS

RNA-LP encoding for model antigens elicit massive recruitment of nearly all monocytes and lymphocytes to RE organs secondary to a danger response mediated by release of orchestrated cytokines (IL-12, TNF-α, IFN-α) and chemokines (CCL2, CCL4, CXCL9-10). This corresponds to increases in absolute numbers of activated DCs and T cells in the RE organs of mice and reprogramming the glioma tumor microenvironment in canines (pet dogs with spontaneous disease). In neonatal mice inoculated midline with established murine K2 gliomas, we observed that RNA-LP vaccines encoding for H3K27M (beginning at ~day 30) elicit significant long-term survivorship, which appears curative in the bulk of animals treated. While H3K27M specific constructs appeared superior, we observed improved survivorship with irrelevant mRNA species (i.e. pp65 and GFP) suggesting these tumors to be particularly sensitive to innate immune modulation. In mice with DMGs, we observed clinical symptomatology of edema/hydrocephalus followed by improvement in many animals suggesting pseudoprogression from intratumoral inflammation and remodeling.

CONCLUSION

RNA-LPs reprogram the tumor microenvironment of poorly immunogenic tumors in effect making them ‘hot.’ Treatment responses in murine models of advanced DMGs are encouraging. We are advancing a final RNA-LP formulation for FDA-IND submission and early phase clinical trials for DIPG through multi-institutional consortia.