bluuebunny/crossref_metadata_2025_split huggingface dataset:
National and state models for relationships between social vulnerability and mammography rates.
Authors: Aijazuddin Ismail , Alloghbi Abdurahman , Sukari Ammar 
Published: June 2024

1573 Background: Health disparities arise from the confluence of medical and non-medical factors that affect measures of prevention, treatment, and outcomes. One crucial preventative measure is mammography rate. Neighborhood-level analysis using tools such as the CDC’s Social Vulnerability Index (SVI) may identify correlates of disparity in mammography access and utilization. Such investigation may reveal drivers of disparity in communities with lower screening. Methods: Self-reported mammography rates among women aged 50-74 were obtained from the CDC’s 2018 PLACES dataset at the Census Tract level and merged with the CDC’s 2018 SVI release. Data were available for 72,075 Census Tracts across all states and Washington, D.C. National univariate and multivariate regressions were performed between mammography rates and percentiles for SVI percentiles. State-specific multivariate regressions were performed for each state's Census Tracts. Results: In the national analysis, significant correlations with non-negligible effect size (correlation coefficient > 0.20 or < -0.20) were found between mammography rate and the following: Theme 2 - Household Composition & Disability (R = -0.22, p < 0.0001), Mobile Homes (R = -0.36, p < 0.0001), Civilians with a Disability (R = -0.24, p < 0.0001), and Minority Status (R = 0.25, p < 0.0001). The national multivariate model achieved Multiple R of 0.54 and Significance F < 0.001. The variables with the most negative associations (lower mammography rates with increased vulnerability) were Income (coefficient = -4.05, p < 0.001) and Speaks English Less than Well (coefficient = -2.33, p < 0.001). Across the state multivariate models, mean Multiple R was 0.70 (95% CI 0.67-0.73), with Significance F < 0.05 in all states (Table). The variables with the most negative mean coefficients across models were Income (-3.20) and No High School Diploma (-2.98); the most positive was Minority status (6.11). Conclusions: Neighborhood-level social determinants correlate meaningfully with mammography rates. Although lower income, limited English proficiency, and lower educational attainment are most strongly associated with lower mammography, the effect sizes vary across geographies, and additional factors have meaningful influence in certain states. The stronger performance of most state-specific models than the national model reinforces this finding. It demonstrates the need for further analysis at the level of state and within narrower geographies. Ultimately, targeted interventions should address those disparities that are most relevant to specific neighborhoods. [Table: see text]
Niraparib efficacy in patients with newly-diagnosed glioblastoma: Clinical readout of a phase 0/2 "trigger" trial.
Authors: Sanai Nader , Umemura Yoshie , Margaryan Tigran , Molloy Jennifer , Zhang Hualin , Knight William , Harmon Jocelyn , Hong Amy , Wanebo John , Braun Kelly , Kennedy William R. , Garcia Michael A. , Barani Igor J. , Yoo Wonsuk , Tien An-Chi , Tovmasyan Artak , Mehta Shwetal 
Published: June 2024

2002 Background: Poly (ADP-ribose) polymerase (PARP) mediates DNA damage response; niraparib is an investigational PARP1/2-selective inhibitor. This Phase 0 study evaluates newly-diagnosed glioblastoma (GBM) tumor pharmacokinetics (PK) and pharmacodynamics (PD), graduating patients with O6-methylguanine methyltransferase (MGMT) unmethylated tumors into a therapeutic regimen of niraparib plus fractionated radiotherapy when PK threshold is met. Methods: Presumed newly-diagnosed GBM patients received 4 days of niraparib (300/200 mg QD) prior to planned resection 3-5 (cohort 1) or 8-10 hours (cohort2) following the last dose. Tumor tissue (Gadolinium enhancing and non-enhancing regions), cerebrospinal fluid (CSF), and plasma were collected. Total and unbound niraparib concentrations were measured using validated LC-MS/MS methods. PARP inhibition was assessed by quantification of PAR induction after ex vivo irradiation of surgical vs non-irradiated tissue. A PK ‘trigger’ determined eligibility for the Phase 2 component of the study and was defined as unbound [niraparib] > 5-fold biochemical IC50 (i.e., 19 nM) in non-enhancing tumor. Patients with MGMT unmethylated tumors in excess of the PK threshold were eligible for Phase 2 dosing of niraparib plus radiotherapy followed by a maintenance phase of niraparib monotherapy. Results: All Phase 0 patients (n=46) met the PK threshold. In non-enhancing tumor regions, the mean unbound concentration of niraparib was 335.1 nM (n=43) for cohort 1 and 331.9 nM (n=3) for cohort 2. PAR suppression after ex vivo radiation was observed in 73% of the patients (24/33). Nineteen of 27 (70.3%) patients with unmethylated tumors were enrolled into Phase 2. Five patients in Phase 2 experienced Grade 4 thrombocytopenia related to niraparib. All adverse events resolved without sequelae. At time of data cutoff, median progression-free survival was 11.7 months. Mature overall survival (OS) data will be reported for the first time. Conclusions: Niraparib achieves pharmacologically relevant concentrations in non-enhancing, newly-diagnosed GBM tissue in excess of any other studied PARP inhibitor. Accompanying PD effects were observed in patient tumor tissue. For the first time, we report on the clinical efficacy of the study. A global Phase 3, open-label, randomized 2-arm study comparing niraparib versus temozolomide in adult patients with newly diagnosed, MGMT unmethylated glioblastoma is being planned. Clinical trial information: NCT05076513 .
Longitudinal tumor-wide sampling of glioblastoma reveals diverse genomic drivers of the earliest clonal expansion at diagnosis and recurrence.
Authors: Lerman Benjamin Joshua , Hong Chibo , Chen Lee , Smirnov Ivan V , Phillips Joanna J. , Shai Anny , Lupo Janine , Costello Joseph 
Published: June 2024

2009 Background: Despite decades of clinical trials, glioblastoma (GBM) remains a rapidly fatal disease. Much of therapy resistance in GBM is attributed to intratumoral heterogeneity in which subclones rapidly evolve and treatment-resistant cell populations emerge. Understanding heterogeneity at diagnosis and its relationship to the origins of recurrence are critical to selecting therapies that are efficacious across the entire tumor. However, few genomic studies go beyond analyzing single tumor samples per patient. Methods: A spatially oriented, whole tumor sampling approach was used to obtain 43 biopsies from 3 GBMs at diagnosis and recurrence. Pyclone and ClonEvol were applied to whole exome sequencing to reconstruct clonal evolution, FACETs identified copy number variations and HATCHet estimated tumor purity. Candidate driver mutations were evaluated in relation to the Catalogue of Somatic Mutations In Cancer. Results: A single founding clone and multiple subclones were identified for each diagnosis-recurrence pair. Tumor-wide clonal alterations representing initial clonal expansions of these GBMs included both canonical changes (Chr 7 gain, Chr 10 loss, CDKN2A deletion, EGFR amplification) and a diverse set of large-scale copy number variations (Chr 19, 20 gain), driver mutations (PTEN, KDR, CDH11, CNTNAP2), and fusions (LIMCH1::UCHL1, KANK::DOCK8). A second subset of alterations (Chr 8 gain, ATRX mutation), appeared to be tumor wide at diagnosis but were not identified at recurrence. Cancer drivers were also present subclonally, including CDKN2A deletion, MDM2 amplification, and mutations in NF1, and GRM3. Evolutionary trees consisted of 5 generations of clones in Patient 323 (P323), 3 in P454, and 4 in P534. Divergence of the recurrent tumors from their matched primary occurred in the second generation in P454 and P534 and in the third in P323. As a result, an average of 37% of potential drivers of oncogenesis and clonal expansion across the cohort appear after divergence. Furthermore, each recurrent tumor contained at least one tumor wide driver alteration that was subclonal or undetected at diagnosis. Conclusions: Whole-tumor sampling of three GBM patients at both diagnosis and recurrence identified a diversity of genomic drivers and deeper and more complex genetic roots of individual GBM than previously seen in single-biopsy studies. Tumor recurrences consistently arose from a single subclone that diverged early in evolution of the primary tumor and contained clonal drivers either not detected or subclonal in the primary—suggesting a role for these drivers in persistence and expansion. In the age of personalized medicine, our study highlights the clinical potential of tumor wide sampling in identifying therapeutic targets that could avoid heterogeneity-related therapeutic failures.
Primary intracranial germ cell tumors in adolescents and adults: Results of an international, multicenter, retrospective cohort study.
Authors: Zschaebitz Stefanie , Heck Clarissa K , Kasim Rega , Seidel Christoph Alexander , Blum Veronika , Paffenholz Pia , Hentrich Marcus , Cathomas Richard , Augustin Marinela , Timmer Marco , Schäfers Christoph , Schäfer Sophia , Harrabi Semi , Jaeger Dirk , Beyer Joerg , Lorch Anja , Ochsenreither Sebastian 
Published: June 2024

2061 Background: Primary Intracranial Germ Cell Tumors (iGCT) are rare. Previous prospective and retrospective studies mainly included pediatric patients (pts) with a median age of 10-14 years. The aim of this retrospective analysis was to evaluate characteristics, treatment and outcome of adolescents and adults with iGCT. Methods: Data were collected from 10 institutions in Germany and Switzerland. Pts aged >/= 16 years at first diagnosis or at relapse with a primary iGCT were included. Objective responses were evaluated by local investigators. Statistics (Cox proportional hazard model, progression-free survival (PFS) and overall survival (OS) analyzed by Kaplan-Meier method) were performed with SPSS v29. Results: We identified 75 pts (92.0% male) with a median age of 23 years (range 16-60, 94.7% >/= 18 years). At first diagnosis, histology was pure germinoma in 70.7%, pure teratoma in 10.7%, other non-germinomatous GCT (NGGCT) in 13.3%, unknown in 5.3% of pts. Localized, bifocal, and metastatic disease was found in 72.0, 6.7, and 21.3% of pts. As part of their first line (1L) treatment, 69.3%, 80.0%, and 62.7% received surgery, radiotherapy, and chemotherapy, respectively. High dose chemotherapy/ autologous stem cell transplantation (HDCT/ASCT) was part of 1L treatment in n=3 pts with NGGCT. Trimodal and bimodal treatment was performed in 48.0% and 32.0% of pts. Response to 1L therapy was complete remission (CR) in 61.3%, partial remission tumor marker negative (PRm-) in 16.0%, PRm+ in 4.0%, PR with tumor marker status unknown in 4.0%, progressive disease (PD) in 2.7%, and unknown in 12.0%. Relapse occurred in 13/75 pts (17.3%) with unknown histology (n=4), teratoma (n=2), other NGGCT (n=4), and germinoma (n=3). In 2 pts. in whom germinoma was diagnosed at time of first diagnosis, at time of recurrence PNET and Yolk sac tumor were histologically proven. Median time to relapse was 19.0 months (mo.; range 3-223). HDCT/ASCT as salvage treatment was performed in 5 pts with NGGCT and in one pt with germinoma as 2L (n=5) or 3L (n=1). NGGCT histology was associated with increased risk for recurrence or death (p=0.012 and 0.039).3-year PFS was 90.7% (germinoma: 98.1%, NGGCT: 73.9%) and 5-year OS was 92.0% (germinoma: 98.1%; NGGCT: 78.3%). Median follow-up time was 60 mo (range 0-339). Conclusions: Disease characteristics, treatment and outcomes of adolescent/ adult iGCT pts are comparable to those reported in pediatric pts. High cure rates are achieved in pts with pure germinoma and current treatment concepts. In pts with NGGCT further investigation is needed to improve survival outcomes.
A phase 0/1 trigger trial of BDTX-1535 in patients with recurrent high-grade glioma (HGG) with EGFR alterations or fusions.
Authors: Sanai Nader , Umemura Yoshie , Karapetyan Vahuni , Margaryan Tigran , Huttenlocher Dylan , Harmon Jocelyn , Hong Amy , Yoo Wonsuk , Tien An-Chi , Tovmasyan Artak , Mehta Shwetal 
Published: June 2024

2069 Background: This Phase 0/1 clinical trial evaluates the pharmacokinetic (PK), pharmacodynamic (PD), and clinical response of recurrent high-grade glioma (HGG) patients with EGFR alterations and/or fusions to the ATP-competitive, irreversible EGFR inhibitor, BDTX-1535. Methods: Recurrent HGG patients with EGFR alterations (Arm A) or EGFR fusions (Arm B) received 5 days of BDTX-1535 (200 mg) prior to planned resection at 2-4 hours following the final dose. In the Phase 0 component of the study, total and unbound drug concentrations were measured in tumor tissue (Gadolinium enhancing and non-enhancing regions), cerebrospinal fluid (CSF), and plasma using validated LC-MS/MS methods. A PK ‘trigger’, defined as unbound drug concentration above 5-fold biochemical IC50 in Gadolinium (Gd)-nonenhancing tumor, determined eligibility for Phase 1. PD response was assessed by quantification of percentage of positive pEGFR, pERK and MIB-1 cells in the surgical tumor tissue compared to baseline pre-treatment tissue. Patients with tumors exceeding the PK threshold for unbound drug concentration were eligible for expansion phase therapeutic dosing of BDTX-1535. Results: A total of 7 patients with recurrent glioblastoma (Arm A) were enrolled in the Phase 0 component of the study. Two patients were excluded from PK analysis due to pseudoprogression. The mean unbound concentrations of BDTX-1535 in Gd-enhancing and nonenhancing tumor regions were 16.0 nM and 10.5 nM respectively. Four of five (80%) evaluable patients exceeded the PK threshold. The suppression of pEGFR and MIB1 was observed in 40% and 60% of patients, respectively. No serious adverse events were observed among patients in the Phase 1 component of the study and a clinical readout is planned in Q2 2024. Conclusions: BDTX-1535 is well-tolerated in recurrent HGG patients, achieves pharmacologically relevant concentrations in Gd-nonenhancing tumor tissue and is associated with suppression of EGFR signaling. Clinical trial information: NCT06072586 .
A novel liquid biopsy assay with an 88% detection rate of genomic alterations across CNS tumors.
Authors: Varga Matthew Gordon , Klosowski Christian , Bower Xavier , Tsao David , Palmer Gary A. , Kesari Santosh 
Published: June 2024

2077 Background: Diagnosis and treatment decisions for CNS tumors rely upon imaging with subsequent histological and genomic analyses of tissue to identify appropriate courses of therapy. Genomic profiling of tumor tissue for informative alterations is used to guide treatment, however contemporaneous tissue can sometimes be unavailable, inconclusive or overlook possible actionable alterations given the high amount of spatial heterogeneity in certain tumor types such as glioblastomas GBMs. Liquid biopsies may pose a possible solution, as they are readily accessible and provide a holistic snapshot of the tumoral genomic landscape. However, detection of ctDNAs from CNS tumors is impeded by its inherently low shedding biology and poor permeability across the BBB resulting in low plasma variant allele fractions (VAFs), with alteration detection rates ranging 27-55%. Thus, current assays do not yet have the sensitivity to be clinically useful in aiding decision making for CNS tumors. Methods: 62 cases of primary CNS tumors were submitted commercially for assessment with Northstar Select, a tumor-naive, plasma-based ctDNA liquid biopsy assay. Cases were obtained from a single clinic dating from January-December 2023. Results: See table. Conclusions: There remains an unmet clinical need for a highly sensitive liquid biopsy assay for use in determining the genomic landscape of CNS tumors to aid in clinical decision making. Current assays do not have a low enough limit of detection (LoD) to accurately detect ctDNAs at low VAFs. Herein, we demonstrate that Northstar Select has a detection rate of 88.7% in all cases and 91.4% in GBMs, nearly doubling current rates. This is due to the assay’s uniquely low LoD of 0.13-0.16% VAF, which is below the 0.17% median VAF demonstrated across CNS tumors in this study, allowing for more low-abundance alterations to be detected. Given the increased total variant detection rate, nearly 50% of which were actionable when alterations were detected, these data support the clinical utility of Northstar Select to inform clinical decisions either as a complement to imaging and tissue analyses or independently when tissue biopsies are infeasible. These data further suggest that the clinical utility of Northstar Select may be expanded into metastatic brain disease and other low ctDNA shedding tumors. [Table: see text]
Unraveling the immunologic vulnerabilities of diffuse hemispheric glioma, H3 G34-mutant.
Authors: Galvin Robert Thomas , Sadeghipour Negar , Xiu Joanne , Ashley David M. , Ahluwalia Manmeet Singh , Aulakh Sonikpreet , Huang R. Stephanie , Largaespada David A 
Published: June 2024

2082 Background: Recent insights into the molecular basis of diffuse hemispheric glioma, H3 G34-mutant (DHG-G34), an incurable high-grade glioma, have opened new therapeutic possibilities. The oncohistone mutation in DHG-G34 impairs the epigenetic regulator SETD2, which normally orchestrates DNA-mismatch-repair and negatively regulates the transcriptional silencing activity of the Polycomb Repressive Complex 2 (PRC2). In DHG-G34, a mismatch-repair-deficiency phenotype is predicted, but an anti-tumor immune response is notably absent in clinical observations, which we posit is linked to the aberrant transcriptional repression by PRC2. Here, we investigate DHG-G34 immunosuppression mechanisms in a large real-world multi-omics cohort and human cell lines. Methods: Clinical, molecular, and immunologic characteristics of a DHG-G34 cohort, sequenced (DNA and RNA) at Caris Life Sciences (Phoenix, AZ), are contrasted against diffuse midline glioma (DMG) and pediatric low-grade glioma (LGG). A significant difference between genomic subgroups was defined as fold-change > 1.2. Statistical significance was determined using chi-square, Fishers-exact, and Mann Whitney U tests with corrections for multiple hypothesis testing (q < 0.05).Hazard ratio (HR) was calculated using the Cox proportional hazards model. KNS-42 DHG-G34 cell line was exposed in triplicate to 1 µM valemetostat (an EZH1/2 inhibitor) or DMSO in vitro. Flow cytometry and RNA-sequencing were utilized to determine differential immunologic characteristics. Results: 29 DHG-G34, 51 DMG, and 52 LGG were identified in Caris database. Median OS among DHG-G34 was 15.4 mo., similar to DMG (HR = 1.1, 95% CI: 0.70-1.73, p = 0.686). Most frequent alterations in DHG-G34 were TP53 (93.1%), ATRX (69.0%), PDGFRA (31.0%). Tumor mutational burden (TMB) was high, >=10mt/MB, in 10% of DHG-G34 and 0/51 in DMG and 0/52 LGG (p < 0.01, q > 0.05), but immune fractions including dendritic cells, T cells, macrophages, microglia, and antigen-presenting genes were decreased (fold-change: 0.19 – 0.83, q < 0.05). In KNS-42, PRC2 inhibition upregulated MHC class 1 (p < 0.001). Of 402 KNS-42 missense variants, transcription of 43 were upregulated following EHZ2 inhibition, and 4 were downregulated (q < 0.05). Among immunostimulatory genes, P2RX7, which engages T-cells and stimulates an inflammatory response, was downregulated in patient samples (q < 0.001) and upregulated in KNS-42 following EZH2 inhibition (q < 0.001). Conclusions: DHG-G34 has an increased propensity for high TMB but remains immunologically cold. Our pilot experiment suggests inhibiting PRC2’s unique role in DHG-G34 may sensitize DHG-G34 to an immune response by inducing MHC class 1 expression and transcriptional readthrough of mutated transcripts. Understanding whether treatment induces TMB in DHG-G34 may affect timing of an immunotherapeutic intervention.
NFKBIA deletions reshape the epigenome antithetical to the IDH mutation and indication of prognosis in diffuse gliomas.
Authors: Bredel Markus , Espinosa Lluis , Pugh Stephanie L. , Chakravarti Arnab ,   NRG Oncology
Published: June 2024

2083 Background: Genetic alterations help predict the clinical behavior of diffuse gliomas, but some variability remains uncorrelated. The NFKBIA gene at 14q13.2 encodes IkBa, a protein that regulates the activity of NF-kB in the cytoplasm. Evidence that, in chromatin, nuclear NFKBIA dynamically interacts with histones H2A and H4 to regulate polycomb-dependent transcriptional repression and, thus, stem cell maturation and lineage specification and our characterization of NFKBIA as a tumor suppressor in glioblastoma prompted our investigation of the relationship of NFKBIA deletions to other genetic markers, alterations in the methylome, and the clinical course of gliomas. Methods: We analyzed the genetic profiles of 2,343 WHO grade 2 to 4 diffuse gliomas in multiple clinically well-characterized patient populations, including national randomized phase III consortium trial RTOG 9802, to determine whether incorporation of NFKBIA deletions could enhance the prognostic value of current molecular descriptions. Results: We demonstrate that haploinsufficient deletions of NFKBIA display distinct patterns of occurrence in relation to other genetic markers, including driver mutations IDH, TERT, ATRX, and PTEN, 1p19q codeletion, and CDKN2A/B deletion, and are disproportionally present at recurrence. NFKBIA haploinsufficiency is associated with unfavorable patient outcomes, independent of genetic and clinicopathologic predictors. NFKBIA deletions reshape the DNA and histone methylome antipodal to the IDH mutation. The methylome changes facilitated through NFKBIA deletions engender a transcriptome landscape partly reminiscent of H3K27M mutant pediatric gliomas and are highly enriched for neural stem cell and neurogenesis genes bearing repressive H3K27 marks. Our findings imply that the NFKBIA deletion in adult gliomas and the H3K27M mutation in pediatric diffuse midline gliomas define aggressive disease subtypes that may share an epigenetic state reflecting a common PRC2 loss-of-function phenotype antipodal to the quasi PRC2 gain-of-function phenotype of IDH mutant gliomas and their favorable clinical course. Lower-grade gliomas harboring NFKBIA deletions behave much like high-grade gliomas. In IDH mutant gliomas, NFKBIA deletions are common in tumors with a clinical course similar to that of IDH wildtype tumors. A sparse, easily interpretable, and externally validated nomogram model for estimating individual patient survival in IDH mutant gliomas, incorporating NFKBIA deletion and current best-established genetic and clinicopathologic factors, confirms that NFKBIA deletions predict comparatively brief survival. Conclusions: NFKBIA haploinsufficiency aligns with distinct epigenome changes, portends a poor prognosis, and should be incorporated into clinical models predicting the disease fate of diffuse gliomas.