Organelle resolved proteomics uncovers PLA2R1 as a novel cell surface marker required for chordoma growth

Chordomas are clinically aggressive tumors with a high rate of disease progression despite maximal therapy. Given the limited therapeutic options available, there remains an urgent need for the development of novel therapies to improve clinical outcomes. Cell surface proteins are attractive therapeutic targets yet are challenging to profile with common methods. Four chordoma cell lines were analyzed by quantitative proteomics using a differential ultracentrifugation organellar fractionation approach. A subtractive proteomics strategy was applied to select proteins that are plasma membrane enriched. Systematic data integration prioritized PLA2R1 (secretory phospholipase A2 receptor-PLA2R1) as a chordoma-enriched surface protein. The expression profile of PLA2R1 was validated across chordoma cell lines, patient surgical tissue samples, and normal tissue lysates via immunoblotting. PLA2R1 expression was further validated by immunohistochemical analysis in a richly annotated cohort of 25-patient tissues. Immunohistochemistry analysis revealed that elevated expression of PLA2R1 is correlated with poor prognosis. Using siRNA- and CRISPR/Cas9-mediated knockdown of PLA2R1, we demonstrated significant inhibition of 2D, 3D and in vivo chordoma growth. PLA2R1 depletion resulted in cell cycle defects and metabolic rewiring via the MAPK signaling pathway, suggesting that PLA2R1 plays an essential role in chordoma biology. We have characterized the proteome of four chordoma cell lines and uncovered PLA2R1 as a novel cell-surface protein required for chordoma cell survival and association with patient outcome.

Fractionated radiotherapy for surgically resected intracranial meningiomas: A multicentre retrospective cohort study

BACKGROUND

Aside from surgical resection, the only standard of care treatment modality for meningiomas is radiotherapy (RT). Despite this, few studies have focused on identifying clinical covariates associated with failure of fractionated RT following surgical resection (fRT), and the timing of fRT following surgery still remains controversial (adjuvant versus salvage fRT). We assessed the outcomes of the largest, multi-institutional cohort of surgically resected meningiomas treated with subsequent adjuvant and salvage fRT to identify factors associated with local freedom from recurrence (LFFR) over 3-10 years post-fRT and to determine the optimal timing of fRT.

METHODS

Patients with intracranial meningiomas who underwent surgery and fRT between 1997 and 2018 were included. Primary endpoints were radiographic recurrence/progression and time to progression from the completion of fRT.

RESULTS

404 meningiomas were included for analysis. Of these, 167 (41.3%) recurred post-fRT. Clinical covariates independently associated with worse PFS post-fRT included receipt of previous RT to the meningioma, having a WHO grade 3 meningioma or recurrent meningioma, the meningioma having a higher MIB1-index or brain invasion on pathology, and older patient age at diagnosis. Subgroup analysis identified higher MIB1-index as a histological factor associated with poorer LFFR in WHO grade 2 meningiomas. 179 patients underwent adjuvant RT shortly after surgery whereas 225 patients had delayed, salvage fRT after recurrence/progression. Following propensity score matching, patients that underwent adjuvant fRT had improved LFFR post-fRT compared to those that received salvage fRT.

CONCLUSION

There is a paucity of clinical factors that can predict a meningioma's response to fRT following surgery. Adjuvant fRT may be associated with improved PFS post-fRT compared to salvage fRT. Molecular biomarkers of RT-responsiveness are needed to better inform fRT treatment decisions.

Financial Toxicity and Patient Experience Outcomes on a Multi-Institutional Phase I Single Fraction Stereotactic Partial Breast Irradiation Protocol for Early-Stage Breast Cancer

PURPOSE/OBJECTIVE(S)

Given the demonstrated financial toxicity (FT) of radiation treatment on breast cancer patients shown in both conventional and our recent 5 fraction stereotactic APBI (S-PBI) study, we assessed the FT, as well as patient-reported utility, quality-of-life and patient experience measures, on patients treated in our phase I single fraction S-PBI trial.

MATERIALS/METHODS

A phase I single fraction dose escalation trial of S-PBI for early-stage breast cancer was conducted. Women with in-situ or stage I-II (AJCC 6) invasive breast cancer following breast conserving surgery were treated with S-PBI in 1 fraction to a total dose of 22.5, 26.5 or 30 Gy (Clinical trials.gov ID NCT02685332). At one month follow-up, patients were asked to complete our novel "Patient Perspective Cost and Convenience of Care Questionnaire". Patients also completed the EQ-5D-5L, including the visual analogue scale of overall health (VAS), at enrollment, 6, 12-, 24-, 36-, and 48-month follow-up.

RESULTS

Of 29 patients enrolled and treated, questionnaire data was available for all patients. Our trial encompassed a wide range of annual household incomes, education, and employment status. Overall, 44.8% (n = 13/29) of patients reported that radiation treatment presented a financial burden. Interestingly, no demographic information, such as patient race, marital status, education, household income, or employment during treatment predicted perceived FT. Patients reporting FT trended towards younger age (median 64 vs 70.5) and having a cancer related co-pay similar to our 5 fraction S-PBI FT trial; however, due to the small size of this study, this did not reach significance (p = 0.24 and 0.10, respectively). VAS and utility scores were calculated per the EQ-5D-5L and remained unchanged from baseline through 4-year follow-up. Likewise, there was no difference in the utility or VAS between patients who reported FT and those who did not. Interestingly, while patient reported cosmesis was similar for all patients at enrollment, patients who reported FT noted significantly worse cosmesis scores (fair/poor vs good/excellent) at 6 month and 2-year follow-ups (p = 0.01 and 0.04, respectively). Finally, patients were surveyed on treatment related disruption to their daily activities and enjoyment of life. The median values were 0 (scale 0-10, with 0 being no disruption) regardless of perceived FT. Patients were also uniformly satisfied with treatment time with a median score of 10 (scale 0-10, 10 being most satisfied).

CONCLUSION

Here, we show that despite using SPBI in a single fraction, nearly half of the patients treated still reported FT of treatment. Importantly, single fraction S-PBI has no negative impact on patient VAS or utility scores, and all patients were uniformly satisfied with treatment time without significant disruption to their life.

HAVOC: Small-scale histomic mapping of cancer biodiversity across large tissue distances using deep neural networks

Intratumoral heterogeneity can wreak havoc on current precision medicine strategies because of challenges in sufficient sampling of geographically separated areas of biodiversity distributed across centimeter-scale tumor distances. To address this gap, we developed a deep learning pipeline that leverages histomorphologic fingerprints of tissue to create "Histomic Atlases of Variation Of Cancers" (HAVOC). Using a number of objective molecular readouts, we demonstrate that HAVOC can define regional cancer boundaries with distinct biology. Using larger tumor specimens, we show that HAVOC can map biodiversity even across multiple tissue sections. By guiding profiling of 19 partitions across six high-grade gliomas, HAVOC revealed that distinct differentiation states can often coexist and be regionally distributed within these tumors. Last, to highlight generalizability, we benchmark HAVOC on additional tumor types. Together, we establish HAVOC as a versatile tool to generate small-scale maps of tissue heterogeneity and guide regional deployment of molecular resources to relevant biodiverse niches.

Oncolytic DNX-2401 virotherapy plus pembrolizumab in recurrent glioblastoma: a phase 1/2 trial

Immune-mediated anti-tumoral responses, elicited by oncolytic viruses and augmented with checkpoint inhibition, may be an effective treatment approach for glioblastoma. Here in this multicenter phase 1/2 study we evaluated the combination of intratumoral delivery of oncolytic virus DNX-2401 followed by intravenous anti-PD-1 antibody pembrolizumab in recurrent glioblastoma, first in a dose-escalation and then in a dose-expansion phase, in 49 patients. The primary endpoints were overall safety and objective response rate. The primary safety endpoint was met, whereas the primary efficacy endpoint was not met. There were no dose-limiting toxicities, and full dose combined treatment was well tolerated. The objective response rate was 10.4% (90% confidence interval (CI) 4.2-20.7%), which was not statistically greater than the prespecified control rate of 5%. The secondary endpoint of overall survival at 12 months was 52.7% (95% CI 40.1-69.2%), which was statistically greater than the prespecified control rate of 20%. Median overall survival was 12.5 months (10.7-13.5 months). Objective responses led to longer survival (hazard ratio 0.20, 95% CI 0.05-0.87). A total of 56.2% (95% CI 41.1-70.5%) of patients had a clinical benefit defined as stable disease or better. Three patients completed treatment with durable responses and remain alive at 45, 48 and 60 months. Exploratory mutational, gene-expression and immunophenotypic analyses revealed that the balance between immune cell infiltration and expression of checkpoint inhibitors may potentially inform on response to treatment and mechanisms of resistance. Overall, the combination of intratumoral DNX-2401 followed by pembrolizumab was safe with notable survival benefit in select patients (ClinicalTrials.gov registration: NCT02798406).

Increased mRNA expression of CDKN2A is a transcriptomic marker of clinically aggressive meningiomas

Homozygous deletion of CDKN2A/B was recently incorporated into the World Health Organization classification for grade 3 meningiomas. While this marker is overall rare in meningiomas, its relationship to other CDKN2A alterations on a transcriptomic, epigenomic, and copy number level has not yet been determined. We therefore utilized multidimensional molecular data of 1577 meningioma samples from 6 independent cohorts enriched for clinically aggressive meningiomas to comprehensively interrogate the spectrum of CDKN2A alterations through DNA methylation, copy number variation, transcriptomics, and proteomics using an integrated molecular approach. Homozygous CDKN2A/B deletions were identified in only 7.1% of cases but were associated with significantly poorer outcomes compared to tumors without these deletions. Heterozygous CDKN2A/B deletions were identified in 2.6% of cases and had similarly poor outcomes as those with homozygous deletions. Among tumors with intact CDKN2A/B (without a homozygous or heterozygous deletion), we found a distinct difference in outcome based on mRNA expression of CDKN2A, with meningiomas that had elevated mRNA expression (CDKN2A^high) having a significantly shorter time to recurrence. The expression of CDKN2A was independently prognostic after accounting for copy number loss and consistently increased with WHO grade and more aggressive molecular and methylation groups irrespective of cohort. Despite the discordant and mutually exclusive status of the CDKN2A gene in these groups, both CDKN2A^high meningiomas and meningiomas with CDKN2A deletions were enriched for similar cell cycle pathways but at different checkpoints. High mRNA expression of CDKN2A was also associated with gene hypermethylation, Rb-deficiency, and lack of response to CDK inhibition. p16 immunohistochemistry could not reliably differentiate between meningiomas with and without CDKN2A deletions but appeared to correlate better with mRNA expression. These findings support the role of CDKN2A mRNA expression as a biomarker of clinically aggressive meningiomas with potential therapeutic implications.

DNAR-09. THE IMPACT OF MISMATCH REPAIR DEFICIENCY ON HIGH GRADE GLIOMAS IN CHILDREN, ADOLESCENTS AND YOUNG ADULTS; A REPORT FROM THE IRRDC AND THE GLIOMA TASKFORCE

Mismatch repair deficiency (MMRD) is a pan-cancer mechanism resulting in universal hypermutation and aggressive cancers that are resistant to chemoradiation yet sensitive to immunotherapy. MMRD mutations can occur somatically or be inherited as a part of Lynch Syndrome or Constitutional Mismatch Repair Deficiency (CMMRD). Although MMRD affects children, adolescents and young adults (CAYA, ages 0-40) with gliomas, its prevalence and impact of germline inheritance is unknown. Given that high microsatellite instability (MSI) is a key characteristic of MMRD, we previously developed a robust low-coverage whole genome-based tool to quantify MSI, which allows for accurate MMRD detection. We are therefore performing a large-scale MMRD screen of CAYA high grade gliomas (HGGs) and utilizing data from the International Replication Repair Deficiency Consortium (IRRDC) to determine the impact of germline mutations in MMRD gliomas. Ongoing data on 346 HGGs from CAYA patients reveals that MMRD is identified in 6% of HGGs and is not present in tumors with pediatric type alterations. Moreover, of MMRD tumors with IDH1 mutations, none harbor 1p/19q co-deletions. Of patients with available information, all are diagnosed with Lynch Syndrome (69%) or CMMRD (31%), with all Lynch Syndrome diagnoses occurring in patients above 18 years of age. Complementary data from the IRRDC on 113 MMRD patients with gliomas reveal that the median age of glioma is 9.7 and 17.5 years in CMMRD and Lynch Syndrome, respectively (p < 0.001). Strikingly, CMMRD gliomas are enriched for secondary polymerase mutations (60%, p < 0.001) and exhibit ultra-hypermutation, while MMRD gliomas with Lynch Syndrome are enriched for IDH1 mutations (32%, p < 0.025) and harbor a lower mutational burden. Our data reveal a high prevalence of MMRD in CAYA HGGs with alarming impact of germline predisposition. These data can support universal screening for MMRD in high grade glioma diagnostics and identify patients for precision therapeutics.

EPID-25. THE CLINICAL AND MOLECULAR LANDSCAPE OF GLIOMAS IN ADOLESCENTS AND YOUNG ADULTS

OBJECTIVE

Gliomas in adolescents and young adults (AYA) are commonly treated with a standard chemo-radiation approach. Molecular alterations have not been comprehensively described to date.

METHODS

We compiled a multi-institutional cohort of patients diagnosed with glioma between 15-39.9 years over 20 years. Molecular analysis, therapeutic data and outcome was collected. For specific alterations, analysis included patients aged 0-39.9 years.

RESULTS

A total of 1900 patients with 876 AYA gliomas were included. Ongoing analysis reveals genetic alterations in 95% of available tumours. IDH p.R132H was found in 49% of tumours, while non-canonical IDH mutations were found in 7%. Paediatric-type mutations were found in 33% of AYA tumours with IDH-WT GBM accounting for the remaining 11%. The most common paediatric alterations in AYAs included BRAF p.V600E (11%) and FGFR alterations (7%) while BRAF fusions, H3 p.K27M and H3.3 p.G34R were rarely observed (4%, 4% and 1% respectively). BRAF fused tumours with non-canonical binding partners were enriched in AYAs. Analysis of BRAF-V600E gliomas between ages 0-40 revealed increased tendency for malignant tumours in patients > 20 years suggesting malignant transformation possibly due to higher rate of secondary hits. This resulted in worse overall-survival for AYA patients with BRAF-V600E glioma when compared to children under 20 years (p=0.0032). Ten-year OS of 100%, 90% and 95% was seen for BRAF fused, BRAF-V600E and FGFR-altered AYA low grade glioma respectively, compared to 14% and 25% for BRAF-V600E and FGFR-altered high grade glioma. In contrast, continuous decline was observed in the IDH-mutant gliomas with 10-year OS of 50% which declined to 29% at 15 years.

CONCLUSIONS

Gliomas in AYA often have non-canonical alterations that may evade standard molecular analysis. They are enriched for paediatric-type alterations with distinct molecularly-based outcomes. These tumours may respond to targeted inhibitors and would benefit from comprehensive diagnostic and therapeutic approaches.

TMIC-73. HIGH-DIMENSIONAL HISTOPATHOLOGIC EVALUATION OF THE HYPOXIC MICROENVIRONMENT IN GLIOBLASTOMA

Rapidly growing solid tumors such as glioblastoma (GBM) are characteristically hypoxic, displaying large areas of necrosis surrounded by hyperproliferative pseudopalisading cells. Intra-tumoral hypoxia develops over time in the three-dimensional space and the degree of tissue oxygenation is a dynamic process that varies continuously. Combined with the extensive inter- and intra-tumoral heterogeneity associated with GBM at the bulk and single cell level, hypoxia contributes to a gradient of molecular alterations that are specific to the different cell populations that make up the bulk of the tumor and reside in specific niches. To date, high dimensional histopathologic analyses of the hypoxic regions within GBM tissue have not been performed. Here, we took a combined spatial and single-cell proteomic profiling approach to investigate the histopathologic features of hypoxia by leveraging a unique clinical study where the exogenous hypoxia marker pimonidazole (PIMO) is administered to patients with GBM prior to surgery. Tissue specimens were subjected to imaging mass cytometry and serial immunohistochemistry using a panel of 27 markers associated with cellular hallmarks of hypoxia, metabolism, proliferation, stemness, angiogenesis, and immune cell types. We took high-resolution imaging and statistical approaches to explore the interplay of the different markers within hypoxic regions of primary and recurrent GBMs, in addition to IDH-mutant gliomas. Our findings elucidate the expression pattern of key biological markers relative to one another, altered composition of different cell types, along with differential proliferative, transcriptional, and translational activation states associated with each cell type within the hypoxic regions of GBM.

Molecular testing for adolescent and young adult central nervous system tumors: A Canadian guideline

The 2021 World Health Organization (WHO) classification of CNS tumors incorporates molecular signatures with histology and has highlighted differences across pediatric vs adult-type CNS tumors. However, adolescent and young adults (AYA; aged 15–39), can suffer from tumors across this spectrum and is a recognized orphan population that requires multidisciplinary, specialized care, and often through a transition phase. To advocate for a uniform testing strategy in AYAs, pediatric and adult specialists from neuro-oncology, radiation oncology, neuropathology, and neurosurgery helped develop this review and testing framework through the Canadian AYA Neuro-Oncology Consortium. We propose a comprehensive approach to molecular testing in this unique population, based on the recent tumor classification and within the clinical framework of the provincial health care systems in Canada.

LGG-41. The clinical and molecular landscape of gliomas in adolescents and young adults

OBJECTIVE: Gliomas in adolescents and young adults (AYA) are commonly treated with a standard chemo-radiation approach based on data from adults. The clinical impact of paediatric-type alterations in these tumours is unknown. METHODS: We compiled a multi-institutional cohort of patients diagnosed with glioma between 15-39.9 years over 20 years. Complete molecular analysis, therapeutic data and outcome was collected. For specific alterations, analysis included patients aged 0-39.9 years. RESULTS: A total of 1900 patients with 876 AYA gliomas were included. Ongoing analysis reveals genetic alterations in 95% of available tumours. IDH-mutant tumours account for only 53%, while paediatric-type mutations were found in 35% of AYA tumours with IDH-WT GBM accounting for the remaining 12%. The most common paediatric alterations in AYAs included BRAF p.V600E (11%) and FGFR alterations (6%) while BRAF fusions, H3 p.K27M and H3.3 p.G34R were rarely observed (4%, 4% and 1% respectively). BRAF fused tumours with non-canonical binding partners were enriched in AYAs. Analysis of BRAF-V600E gliomas between ages 0-40 revealed increased tendency for malignant tumours in patients >20 years suggesting malignant transformation possibly due to higher rate of secondary hits including TP53, CDKN2A and ATRX mutations. This resulted in worse overall-survival for AYA patients with BRAF-V600E glioma when compared to children under 20 years (p=0.0032). Ten-year OS of 100%, 90% and 95% was seen for BRAF fused, BRAF-V600E and FGFR-altered AYA low grade glioma respectively, compared to 14% and 25% for BRAF-V600E and FGFR-altered high grade glioma. In contrast, continuous decline was observed in the IDH-mutant gliomas with 10-year OS of 50% which declined to 29% at 15 years. CONCLUSIONS: Gliomas in AYA are enriched for paediatric-type alterations with distinct molecularly-based outcomes. As these tumours carry different outcomes than childhood glioma and may respond to targeted inhibitors, AYA gliomas would benefit from comprehensive diagnostic and therapeutic approaches.

Machine-Learning-Based Virtual Screening to Repurpose Drugs for Treatment of Candida albicans Infection

BACKGROUND

Approximately 30% of Candida genus isolates are resistant to all currently available antifungal drugs and it is highly important to develop new treatments. Additionally, many current drugs are toxic and cause unwanted side effects. 1,3-beta-glucan synthase is an essential enzyme that builds the cell walls of Candida.

OBJECTIVES

Targeting CaFKS1, a subunit of the synthase, could be used to fight Candida.

METHODS

In the present study, a machine-learning model based on chemical descriptors was trained to recognize drugs that inhibit CaFKS1. The model attained 96.72% accuracy for classifying between active and inactive drug compounds. Descriptors for FDA-approved and other drugs were calculated and the model was used to predict the potential activity of these drugs against CaFKS1.

RESULTS

Several drugs, including goserelin and icatibant, were detected as active with high confidence. Many of the drugs, interestingly, were gonadotrophin-releasing hormone (GnRH) antagonists or agonists. A literature search found that five of the predicted drugs inhibit Candida experimentally.

CONCLUSIONS

This study yields promising drugs to be repurposed to combat Candida albicans infection. Future steps include testing the drugs on fungal cells in vitro.

Calpain activation and progression of inflammatory cycles in Parkinson's disease

Parkinson's disease (PD) is a progressive, neurodegenerative condition of the central nervous system (CNS) affecting 6.3 million people worldwide with no curative treatments. Current therapies aim to mitigate PD's effects and offer symptomatic relief for patients. Multiple pathways are involved in the pathogenesis of PD, leading to neuroinflammation and the destruction of dopaminergic neurons in the CNS. This review focuses on PD pathology and the role of calpain, a neutral protease, as a regulator of various immune cells such as T-cells, microglia and astrocytes which lead to persistent neuroinflammatory responses and neuronal loss in both the brain and spinal cord (SC). Calpain plays a significant role in the cleavage and aggregation of toxic α-synuclein (α-syn), a presynaptic neural protein, and other organelles, contributing to mitochondrial dysfunction and oxidative stress. α-Syn aggregation results in the formation of Lewy bodies (LB) that further contribute to neuronal damage through lipid bilayer penetration, calcium ion (Ca2+) influx, oxidative stress and damage to the blood brain barrier (BBB). Dysfunctional mitochondria destabilize cytosolic Ca2+ concentrations, raising intracellular Ca2+; this leads to excessive calpain activation and persistent inflammatory responses. α-Syn aggregation also results in the disruption of dopamine synthesis through phosphorylation of tyrosine hydroxylase (TH), a key enzyme involved in the conversion of tyrosine to levodopa (L-DOPA), the amino acid precursor to dopamine. Decreased dopamine levels result in altered dopamine receptor (DR) signaling, ultimately activating pro-inflammatory T-cells to further contribute to the inflammatory response. All of these processes, together, result in neuroinflammation, degeneration and ultimately neuronal death seen in PD. 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP-a prodrug to the neurotoxin 1-methyl-4-phenylpyridinium (MPP+)), rotenone (an environmental neurotoxin), and 6-hydroxydopamine (6-OHDA - a neurotoxic synthetic organic compound) induce PD-like conditions when injected into rodents. All three agents work through similar mechanisms and lead to degeneration of dopaminergic neurons in the substantia nigra (SN) and more recently discovered in motor neurons of the spinal cord (SC). These neurotoxins also increase calpain activity, furthering the neuroinflammatory response. Hence, calpain inhibitors have been posited as potential therapeutics for PD to prevent calpain-related inflammation and neurodegenerative responses in not only the SN but the SC as well.

Integrating morphologic and molecular histopathological features through whole slide image registration and deep learning

Background

Modern molecular pathology workflows in neuro-oncology heavily rely on the integration of morphologic and immunohistochemical patterns for analysis, classification, and prognostication. However, despite the recent emergence of digital pathology platforms and artificial intelligence-driven computational image analysis tools, automating the integration of histomorphologic information found across these multiple studies is challenged by large files sizes of whole slide images (WSIs) and shifts/rotations in tissue sections introduced during slide preparation.

Methods

To address this, we develop a workflow that couples different computer vision tools including scale-invariant feature transform (SIFT) and deep learning to efficiently align and integrate histopathological information found across multiple independent studies. We highlight the utility and automation potential of this workflow in the molecular subclassification and discovery of previously unappreciated spatial patterns in diffuse gliomas.

Results

First, we show how a SIFT-driven computer vision workflow was effective at automated WSI alignment in a cohort of 107 randomly selected surgical neuropathology cases (97/107 (91%) showing appropriate matches, AUC = 0.96). This alignment allows our AI-driven diagnostic workflow to not only differentiate different brain tumor types, but also integrate and carry out molecular subclassification of diffuse gliomas using relevant immunohistochemical biomarkers (IDH1-R132H, ATRX). To highlight the discovery potential of this workflow, we also examined spatial distributions of tumors showing heterogenous expression of the proliferation marker MIB1 and Olig2. This analysis helped uncovered an interesting and unappreciated association of Olig2 positive and proliferative areas in some gliomas (r = 0.62).

Conclusion

This efficient neuropathologist-inspired workflow provides a generalizable approach to help automate a variety of advanced immunohistochemically compatible diagnostic and discovery exercises in surgical neuropathology and neuro-oncology.

BAP1-deficient meningioma presenting with trabecular architecture and cytokeratin expression: a report of two cases and review of the literature

AIMS

BRCA (BReast CAncer gene)-associated protein 1 (BAP1), encoded by the BAP1 gene, a tumour suppressor that is lost in several cancers. Importantly, such mutations have been shown to be susceptible to poly (ADP-ribose) polymerase (PARP) inhibition in preclinical studies, offering hope for targeted therapy. While rare, BAP1 loss has been observed in a subset of rhabdoid and papillary meningioma and is associated with earlier recurrence. We seek to add to the literature on this rare disease and advocate for more routine BAP1 testing.

METHODS

We present a report of two cases of BAP1-deficient meningioma and review the available literature on this rare entity.

RESULTS

Both cases present with a distinct trabecular architecture without rhabdoid or papillary features. Interestingly, both also presented with radiographic and histopathological findings unusual for meningioma. While immunohistochemistry and genetic sequencing confirmed BAP1 loss, DNA methylation analysis was required to confirm the final diagnosis.

CONCLUSIONS

We suggest that BAP1-deficient meningioma should be considered in the differential diagnosis of extra-axial central nervous system (CNS) tumours with atypical imaging or histopathological features and that BAP1 loss may constitute a clinically important meningioma subtype with opportunities for targeted therapy.

The centrally restricted diffusion sign on MRI for assessment of radiation necrosis in metastases treated with stereotactic radiosurgery

Purpose

Differentiation of radiation necrosis from tumor progression in brain metastases treated with stereotactic radiosurgery (SRS) is challenging. For this, we assessed the performance of the centrally restricted diffusion sign.

Methods

Patients with brain metastases treated with SRS who underwent a subsequent intervention (biopsy/resection) for a ring-enhancing lesion on preoperative MRI between 2000 and 2020 were included. Excluded were lesions containing increased susceptibility limiting assessment of DWI. Two neuroradiologists classified the location of the diffusion restriction with respect to the post-contrast T1 images as centrally within the ring-enhancement (the centrally restricted diffusion sign), peripherally correlating to the rim of contrast enhancement, both locations, or none. Measures of diagnostic accuracy and 95% CI were calculated for the centrally restricted diffusion sign. Cohen's kappa was calculated to identify the interobserver agreement.

Results

Fifty-nine patients (36 female; mean age 59, range 40 to 80) were included, 36 with tumor progression and 23 with radiation necrosis based on histopathology. Primary tumors included 34 lung, 12 breast, 5 melanoma, 3 colorectal, 2 esophagus, 1 head and neck, 1 endometrium, and 1 thyroid. The centrally restricted diffusion sign was seen in 19/23 radiation necrosis cases (sensitivity 83% (95% CI 63 to 93%), specificity 64% (95% CI 48 to 78%), PPV 59% (95% CI 42 to 74%), NPV 85% (95% CI 68 to 94%)) and 13/36 tumor progression cases (difference p < 0.001). Interobserver agreement was substantial, at 0.61 (95% CI 0.45 to 70.8).

Conclusion

We found a low probability of radiation necrosis in the absence of the centrally restricted diffusion sign.

A clinically applicable integrative molecular classification of meningiomas

Meningiomas are the most common primary intracranial tumour in adults1. Patients with symptoms are generally treated with surgery as there are no effective medical therapies. The World Health Organization histopathological grade of the tumour and the extent of resection at surgery (Simpson grade) are associated with the recurrence of disease; however, they do not accurately reflect the clinical behaviour of all meningiomas2. Molecular classifications of meningioma that reliably reflect tumour behaviour and inform on therapies are required. Here we introduce four consensus molecular groups of meningioma by combining DNA somatic copy-number aberrations, DNA somatic point mutations, DNA methylation and messenger RNA abundance in a unified analysis. These molecular groups more accurately predicted clinical outcomes compared with existing classification schemes. Each molecular group showed distinctive and prototypical biology (immunogenic, benign NF2 wild-type, hypermetabolic and proliferative) that informed therapeutic options. Proteogenomic characterization reinforced the robustness of the newly defined molecular groups and uncovered highly abundant and group-specific protein targets that we validated using immunohistochemistry. Single-cell RNA sequencing revealed inter-individual variations in meningioma as well as variations in intrinsic expression programs in neoplastic cells that mirrored the biology of the molecular groups identified.

Loss of H3K27me3 in meningiomas

BACKGROUND

There is a critical need for objective and reliable biomarkers of outcome in meningiomas beyond WHO classification. Loss of H3K27me3 has been reported as a prognostically unfavorable alteration in meningiomas. We sought to independently evaluate the reproducibility and prognostic value of H3K27me3 loss by immunohistochemistry (IHC) in a multicenter study.

METHODS

IHC staining for H3K27me3 and analyses of whole slides from 181 meningiomas across three centers was performed. Staining was analyzed by dichotomization into loss and retained immunoreactivity, and using a 3-tiered scoring system in 151 cases with clear staining. Associations of grouping with outcome were performed using Kaplan-Meier survival estimates.

RESULTS

A total of 21 of 151 tumors (13.9%) demonstrated complete loss of H3K27me3 staining in tumor with retained endothelial staining. Overall, loss of H3K27me3 portended a worse outcome with shorter times to recurrence in our cohort, particularly for WHO grade 2 tumors which were enriched in our study. There were no differences in recurrence-free survival (RFS) for WHO grade 3 patients with retained vs loss of H3K27me3. Scoring by a 3-tiered system did not add further insights into the prognostic value of this H3K27me3 loss. Overall, loss of H3K27me3 was not independently associated with RFS after controlling for WHO grade, extent of resection, sex, age, and recurrence status of tumor on multivariable Cox regression analysis.

CONCLUSIONS

Loss of H3K27me3 identifies a subset of WHO grade 2 and possibly WHO grade 1 meningiomas with increased recurrence risk. Pooled analyses of a larger cohort of samples with standardized reporting of clinical definitions and staining patterns are warranted.

Adult isocitrate dehydrogenase-mutant brainstem glioma: illustrative case

BACKGROUND

Adult brainstem gliomas are rare entities that demonstrate heterogeneous biology and appear to be distinct from both their pediatric counterparts and adult supratentorial gliomas. Although the role of histone 3 mutations is being increasingly understood in this disease, the effect of isocitrate dehydrogenase (IDH) mutations remains unclear, largely because of limited data.

OBSERVATIONS

The authors present the case of a 29-year-old male with an IDH1-mutant, World Health Organization grade III anaplastic astrocytoma in the dorsal medulla, and they provide a review of the available literature on adult IDH-mutant brainstem glioma. The authors have amassed a cohort of 15 such patients, 7 of whom have survival data available. Median survival is 56 months in this small cohort, which is similar to that for IDH wild-type adult brainstem gliomas.

LESSONS

The authors' work reenforces previous literature suggesting that the role of IDH mutation in glioma differs between brainstem and supratentorial lesions. Therefore, the authors advocate that adult brainstem gliomas be studied in terms of major molecular subgroups (including IDH mutant) because these gliomas may exhibit fundamental differences from each other, from pediatric brainstem gliomas, and from adult supratentorial gliomas.

LGG-13. THE CLINICAL AND MOLECULAR LANDSCAPE OF GLIOMAS IN ADOLESCENTS AND YOUNG ADULTS

OBJECTIVE

Pediatric low grade gliomas are typically driven by MAPK upregulation with excellent long-term survival. In contrast, adult lower grade gliomas commonly harbor IDH-1 mutations and undergo malignant transformation. Gliomas in adolescents and young adults (AYA) are an orphan group of tumors that have been poorly described. We aim to determine the clinical and molecular landscape of AYA gliomas.

METHODS

A multi-institutional population based cohort of 839 patients diagnosed with glioma between 15–40 years has been identified. Complete molecular analysis, long term outcome and therapeutic data are being collected.

RESULTS

Of 364 AYA gliomas analyzed, the prevalence of WHO grade I tumors was highest in those <21 years (54%), while the prevalence of higher grade tumors increased with age. Interestingly, only 38% harbor IDH-1 mutations while 23% harbor pediatric mutations, including 8% with BRAF p.V600E, and 4% with KIAA1549:BRAF fusion. The median age for IDH-1 mutation is 32 years, with highest frequency in WHO grade II and III tumors. In contrast, BRAF alterations were most frequently observed in WHO grade I and II tumors and enriched in those less than 20 years. Five-year progression-free survival for BRAF fusion, p.V600E and IDH-1 p.R132H were 81%, 78% and 26% respectively. No survivors were observed in H3 p.K27M and p.G34R gliomas (p<0.0001).

CONCLUSIONS

Gliomas in AYA overlap pediatric and adult classification and exhibit enrichment for pediatric alterations. As the latter are associated with improved PFS and are amenable to targeted therapies, this should be considered in the work up of these tumors.

Bovine leukemia virus relation to human breast cancer: Meta-analysis

Bovine leukemia virus (BLV) is a virus that infects cattle around the world and is very similar to the human T-cell leukemia virus (HTLV), which causes adult T-cell leukemia/lymphoma (ATL). Recently, presence of BLV DNA and protein was demonstrated in commercial bovine products and in humans. BLV DNA is generally found at higher rates in humans who have or will develop breast cancer, according to research done with subjects from several countries. These findings have led to a hypothesis that BLV transmission plays a role in breast cancer oncogenesis in humans. Here we summarize the current knowledge in the field.

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DNA of BLV is found at higher rates in humans who have or will develop breast cancer.

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Global analysis links the frequency of breast cancer cases to consumption of milk and beef in the countries studied.

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These findings have led to a hypothesis that BLV transmission plays a role in breast cancer oncogenesis.

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There are contradicting results in majority of cases can be explained by different experimental methods used.

Ultralow Acoustic Loss Micromachined Butterfly Lamb Wave Resonators on AlN Plates

This study reports the design of a novel Butterfly Lamb wave resonator (LWR) employing the S₀ mode in the AlN plate, and for the first time, its ultrahigh parallel-resonance quality factor ( Q_p ) of 4,021 is demonstrated, indicating an ultralow acoustic loss. Although the series resonance quality factor ( Q_s ) is widely used for various loss comparisons, it is inconclusive since Q_s is always dominated by the routing resistance ( R_s ), which is normally huge without the thick metal rewiring. Instead, Q_p is a precise representation of the acoustic loss level for its independence of R_s and as it is closer to Q_max of the Bode Q -curve in the IDT-excited devices. A butterfly-shaped resonance cavity, theoretically predicted to reduce the anchor loss and suppress the transverse spurious mode, has been applied to the AlN LWR and experimentally shown to boost the Q_p by 2.3 times. In addition, a directly measured Bode- Q curve for the LWR is reported for the first time, showing superior Q profile for the Butterfly-LWR than the conventional-LWR and good agreement with the 3 dB- Q_p 's.

Neuropathologic description of CHCHD10 mutated amyotrophic lateral sclerosis

Objective

To present the postmortem neuropathologic report of a patient with a CHCHD10 mutation exhibiting an amyotrophic lateral sclerosis (ALS) clinical phenotype.

Methods

A 54-year-old man without significant medical history or family history presented with arm weakness, slowly progressed over 19 years to meet the El Escorial criteria for clinically probable ALS with bulbar and respiratory involvement, and was found to have a CHCHD10 p.R15L mutation. Postmortem neuropathologic examination took place including immunohistochemical staining with CHCHD10, and double immunofluorescence combining CHCHD10 with TDP43 and neurofilament was performed and the results were compared with normal controls and sporadic ALS cases.

Results

Postmortem examination of the CHCHD10 mutation carrier showed severe loss of hypoglossal and anterior horn motor neurons, mild corticospinal tract degeneration, and a relative lack of TDP43 immunopathology. CHCHD10 immunohistochemistry for the 3 controls and the 5 sporadic ALS cases showed strong neuronal cytoplasmic and axonal labeling, with the CHCHD10 mutation carrier also having numerous CHCHD10 aggregates within their anterior horns. These aggregates may be related to the CHCHD10 aggregates recently described to cause mitochondrial degeneration and disease in a tissue-selective toxic gain-of-function fashion in a CHCHD10 knock-in mouse model. The CHCHD10 aggregates did not colocalize with TDP43 and were predominantly extracellular on double immunofluorescence labeling with neurofilament.

Conclusions

The neuropathology of CHCHD10 mutated ALS includes predominantly lower motor neuron degeneration, absent TDP43 immunopathology, and aggregates of predominantly extracellular CHCHD10, which do not contain TDP43.

Validation of T2- and diffusion-weighted magnetic resonance imaging for mapping intra-prostatic tumour prior to focal boost dose-escalation using intensity-modulated radiotherapy (IMRT)

BACKGROUND AND PURPOSE

To assess the diagnostic accuracy and inter-observer agreement of T2-weighted (T2W) and diffusion-weighted (DW) magnetic resonance imaging (MRI) for mapping intra-prostatic tumour lesions (IPLs) for the purpose of focal dose-escalation in prostate cancer radiotherapy.

MATERIALS AND METHODS

Twenty-six men selected for radical treatment with radiotherapy were recruited prospectively and underwent pre-treatment T2W+DW-MRI and 5 mm spaced transperineal template-guided mapping prostate biopsies (TTMPB). A 'traffic-light' system was used to score both data sets. Radiologically suspicious lesions measuring ≥0.5 cm3 were classified as red; suspicious lesions 0.2-0.5 cm3 or larger lesions equivocal for tumour were classified as amber. The histopathology assessment combined pathological grade and tumour length on biopsy (red = ≥4 mm primary Gleason grade 4/5 or ≥6 mm primary Gleason grade 3). Two radiologists assessed the MRI data and inter-observer agreement was measured with Cohens' Kappa co-efficient.

RESULTS

Twenty-five of 26 men had red image-defined IPLs by both readers, 24 had red pathology-defined lesions. There was a good correlation between lesions ≥0.5 cm3 classified "red" on imaging and "red" histopathology in biopsies (Reader 1: r = 0.61, p < 0.0001, Reader 2: r = 0.44, p = 0.03). Diagnostic accuracy for both readers for red image-defined lesions was sensitivity 85-86%, specificity 93-98%, positive predictive value (PPV) 79-92% and negative predictive value (NPV) 96%. Inter-observer agreement was good (Cohen's Kappa 0.61).

CONCLUSIONS

MRI is accurate for mapping clinically significant prostate cancer; diffusion-restricted lesions ≥0.5 cm3 can be confidently identified for radiation dose boosting.

Synergistic O2-/Li+ Dual Ion Transportation at Atomic Scale

The ion migration during electrochemical process is a fundamental scientific issue for phase transition behavior and of technical importance for various functional devices, where cations or anions are active under electrical bias. Usually only one type of functional ion, O^2- or Li⁺, is activated due to their different migration energy barriers, cooperated by the valence change of other immobile ions in the host lattice matrix, e.g., Co²⁺/Co³⁺ and Mn³⁺/Mn⁴⁺ redox couples, owing to the charge neutralization. Here we select spinel Li₄Ti₅O₁₂ as anode and construct an all-solid-state battery under a transmission electron microscope; a synergistic transportation of O^2- and Li⁺ driven by an electrical bias was directly observed at the atomic scale. A small amount of oxygen anions was extracted firstly as a result of its lowest vacancy formation energy under 2.2 V, leading to the vertical displacement of oxygen. Up to 2.7 V, an ordered phase with both Li- and O- deficiency formed. The Li⁺ and O^2- ions are simultaneously extracted out from the [LiO₄] tetrahedra due to the electroneutrality principle. The migration paths of O and Li have been proposed and verified by first-principles calculations. These results reveal a brand new synergistic ion migration manner and may provide up-to-date insights on the transportation process of lithium ion conductors.

Leukemia cell infiltration causes defective erythropoiesis partially through MIP-1α/CCL3

Leukemia often results in severe anemia, which may significantly contribute to patient mortality and morbidity. However, the mechanisms underlying defective erythropoiesis in leukemia have not been fully elucidated. In this study, we demonstrated that insufficient erythropoiesis in an immunocompetent acute myeloid leukemia (AML) murine model was due to reduced proliferation of megakaryocyte erythroid progenitors and increased apoptosis of erythroblasts. Colony-forming cell assays indicated that the leukemic bone marrow (BM) plasma inhibited erythroid colony formation, whereas they had no inhibitory effect on other types of colonies. Cytokine array analysis demonstrated that the chemokine CCL3 was elevated in the plasma of AML mice and patients. CCL3 inhibited erythroid differentiation of hematopoietic stem cells, common myeloid progenitors and especially megakaryocytic-erythroid progenitors. Administration of the CCR1 antagonist partially recovered the yield of erythroid colonies in the presence of CCL3 or leukemic BM plasma. Mechanistically, we observed an increase of p38 phosphorylation and subsequent downregulation of GATA1 after CCL3 treatment. Furthermore, knockdown of CCL3 attenuated leukemic progression and alleviated anemia. Therefore, our results demonstrate that elevated CCL3 in the leukemic environment suppresses erythropoiesis via CCR1-p38 activation, suggesting a novel mechanism for the erythroid defects observed in leukemia.

Photoluminescence-based detection of particle contamination on extreme ultraviolet reticles

Here, we propose a comparison-free inspection technique to detect particle contamination on the reticle of extreme ultraviolet (EUV) lithography systems, based on the photoluminescence spectral characteristics of the contaminant particles and their elemental composition. We have analyzed the spectra from different particles found on reticles in EUV lithographic systems and have determined the minimum detectable particle size: 25 nm for organic particles and 100 nm for Al particles. Stainless steel coatings (50 nm thick and 50 × 50 μm(2) in area) exhibit detectable photoluminescence, and the estimated minimum detectable particle is 2 μm.

Colonic mucosal a-synuclein lacks specificity as a biomarker for Parkinson disease

OBJECTIVE

To determine the utility of detecting a-synuclein (aSyn) in colonic mucosal biopsy tissue as a potential diagnostic biomarker for Parkinson disease (PD).

METHODS

We used the paraffin-embedded tissue (PET) blot, which degrades physiologic nonaggregated aSyn using proteinase K and enhances antigen retrieval allowing sensitive and selective detection of remaining protein aggregates, to detect aSyn in colonic mucosal biopsies from 15 patients with early PD (,3 years), 7 patients with later PD (.5 years), and 11 individuals without PD. aSyn and serine 129–phosphorylated aSyn (Ser129p-aSyn) were assessed by PET blot and conventional immunohistochemistry.

RESULTS

PET blot–resistant aggregated aSyn and Ser129p-aSyn was present in 12 of 15 individuals with early PD, 7 of 7 individuals with later PD, and 11 of 11 control subjects. The number of biopsies positive by PET blot relative to conventional immunohistochemistry was significantly lower in both PD groups compared with the control group for both aSyn and Ser129p-aSyn,whereas routine immunohistochemistry was positive more often in PD, but was positive in as many as 9 of 11 control individuals.

CONCLUSION

Strong evidence of the presence of aggregated hyperphosphorylated aSyn in individuals with and without PD, using such a sensitive and specific method as the PET blot, suggests that colonic deposition of aSyn is not a useful diagnostic test for PD. The utility of detecting aSynin the colon as a biomarker in combination with other assessments remains to be determined.

Bone morphogenetic protein 7 attenuates epithelial-mesenchymal transition induced by silica

The epithelial-mesenchymal transition (EMT) is a critical process in the pulmonary fibrosis. It has been reported that bone morphogenetic protein 7 (BMP-7) was able to reverse EMT in proximal tubular cells. Therefore, we test the hypothesis that EMT contributes to silica-induced pulmonary fibrosis and BMP-7 inhibits EMT in silica-induced pulmonary fibrosis. Progressive silica-induced pulmonary fibrosis in the rat was used as a model of silicosis. Epithelial and mesenchymal markers were measured from rat fibrotic lungs. Then the effects of BMP-7 on the EMT were further confirmed in A549 cells. There are increases of vimentin as a mesenchymal marker and decreases of E-cadherin as an epithelial marker in the silica-exposed rat lungs, which is in agreement with the A549 cells data. However, BMP-7 treatment significantly reduced expression of vimentin in the rat pulmonary fibrosis model and in A549 cells. In conclusion, EMT contributes to silica-induced pulmonary fibrosis. Meanwhile, the treatment of BMP-7 can inhibit silica-induced EMT in vitro and in vivo.

Survival of Shiga toxin-producing Escherichia coli in broth as influenced by pH, water activity and temperature

This study examined the effects of and interactions between pH, aw and temperature on the survival of the top six non-O157 STECs and Escherichia coli O157:H7. All variables significantly affected the survival of all STEC serotypes. However, aw bore the most significant effect, followed by temperature and then pH. Examination of the effect of the interaction between these variables revealed that the interaction between aw and temperature was the most significant followed by the interaction between pH and temperature and then aw and pH. Decrease in aw resulted in population reduction of all serotypes studied. This reduction in population was significantly increased with the increase in temperature and was further significantly enhanced with decreasing pH. Examination of the differences in the survival among the individual serotypes revealed that the response of each serotype to aw or temperature changes was significantly different, while their response to pH changes was similar. Analysis of the relative survival of individual non-O157 STECs to O157:H7 revealed that the survival of O121 and O45 was not significantly different to O157:H7 while O103, O111, O145 and O26 showed less tolerance to the combined treatments, and their survival was significantly different from O157:H7.

SIGNIFICANCE AND IMPACT OF THE STUDY

Results of this study estimate the interaction between pH, aw and temperature on the survival of the top six non-O157 STECs relative to Escherichia coli O157:H7 and provide important growth and no-growth condition which will offer risk assessors a means of estimating the likelihood of these pathogens, if present, would grow in response to the interaction between the three variables assessed.

A 6-year follow-up of a randomized prospective trial comparing methimazole treatment with or without exogenous L-thyroxine in Chinese patients with Graves' disease

OBJECTIVE

Antithyroid drug therapy is one of the main medical treatments for Graves' disease. There have been conflicting reports as to whether the addition of exogenous L-thyroxine improves remission rates more than antithyroid drugs alone. This randomized, controlled and prospective clinical trial was undertaken to investigate the long-term outcome of methimazole treatment with or without exogenous L-thyroxine in Chinese patients.

METHODS

145 patients with Graves' disease were randomly divided into 3 groups and all patients initially received 30 mg of methimazole daily for at least 1 month and then followed the titration -regimen with or without L-thyroxine: group 1 (30 mg→20 mg→15 mg→10 mg→5 mg); group 2 (30 mg→20 mg→15 mg→10 mg+L-thyroxine→5 mg+L-thyroxine); group 3 (30 mg→20 mg→15 mg→10 mg+L-thyroxine→5 mg+L-thyroxine→2.5 mg+L-thyroxine). The drug therapy was discontinued after 5 months of the final dose.

RESULTS

16 out of 46 patients in group 1 (34.8%), 12 out of 47 in group 2 (25.5%) and 16 out of 52 in group 3 (30.8%) had a recurrence of Graves' disease within 6-year follow-up after drug withdrawal. Survival Analysis showed no significant differences in the remission rates between any 2 groups, despite the remission rates in group 2 and 3 were slightly higher than that in group 1.

CONCLUSIONS

The addition of L-thyroxine to methimazole treatment in patients with Graves' disease neither improves nor prevents the remission or recurrence of Graves' disease in China.

CT45A1 acts as a new proto-oncogene to trigger tumorigenesis and cancer metastasis

Cancer/testis antigen (CTA)-45 family (CT45) belongs to a new family of genes in phylogenetics and is absent in normal tissues except for testis, but is aberrantly overexpressed in various cancer types. Whether CT45 and other CTAs act as proto-oncogenes has not been determined. Using breast cancer as a model, we found that CT45A1, a representative CT45 family member, alone had a weak tumorigenic effect. However, its neoplastic potency was greatly enhanced in the presence of growth factors. Overexpression of CT45A1 in breast cancer cells markedly upregulated various oncogenic and metastatic genes, constitutively activated ERK and CREB signaling pathways, promoted epithelial-mesenchymal transition, and increased cell stemness, tumorigenesis, invasion, and metastasis, whereas silencing CT45A1 significantly reduced cancer cell migration and invasion. We propose that CT45A1 functions as a novel proto-oncogene to trigger oncogenesis and metastasis. CT45A1 and other CT45 members are therefore excellent targets for anticancer drug discovery and targeted tumor therapy, and valuable genes in the study of a molecular phylogenetic tree.