Transcription factors are frequent cancer driver genes, exhibiting noted specificity based on the precise cell of origin. We demonstrate that ZIC1 exhibits loss-of-function (LOF) somatic events in group 4 (G4) medulloblastoma through recurrent point mutations, subchromosomal deletions and mono-allelic epigenetic repression (60% of G4 medulloblastoma). In contrast, highly similar SHH medulloblastoma exhibits distinct and diametrically opposed gain-of-function mutations and copy number gains (20% of SHH medulloblastoma). Overexpression of ZIC1 suppresses the growth of group 3 medulloblastoma models, whereas it promotes the proliferation of SHH medulloblastoma precursor cells. SHH medulloblastoma ZIC1 mutants show increased activity versus wild-type ZIC1, whereas G4 medulloblastoma ZIC1 mutants exhibit LOF phenotypes. Distinct ZIC1 mutations affect cells of the rhombic lip in diametrically opposed ways, suggesting that ZIC1 is a critical developmental transcriptional regulator in both the normal and transformed rhombic lip and identifying ZIC1 as an exquisitely context-dependent driver gene in medulloblastoma.

Table S1. Sequence of targeted amplification primers. Table S2. Sequence of ddPCR primer and probes. Table S3. Cellularity and location of bone metastases.

PDF file - 439K, Additional representative images of HLA Class I and CD8 immunohistochemistry.

PDF file - 96K, Summary of specificity of anti-HLA Class I antibodies.

ABSTRACTLimited ancestral diversity has impaired our ability to detect risk variants more prevalent in non-European ancestry groups in genome-wide association studies (GWAS). We constructed and analyzed a multi-ancestry GWAS dataset in the Alzheimer’s Disease (AD) Genetics Consortium (ADGC) to test for novel shared and ancestry-specific AD susceptibility loci and evaluate underlying genetic architecture in 37,382 non-Hispanic White (NHW), 6,728 African American, 8,899 Hispanic (HIS), and 3,232 East Asian individuals, performing within-ancestry fixed-effects meta-analysis followed by a cross-ancestry random-effects meta-analysis. We identified 13 loci with cross-ancestry associations including known loci at/nearCR1,BIN1,TREM2,CD2AP,PTK2B,CLU,SHARPIN,MS4A6A,PICALM,ABCA7,APOEand two novel loci not previously reported at 11p12 (LRRC4C) and 12q24.13 (LHX5-AS1). Reflecting the power of diverse ancestry in GWAS, we observed theSHARPINlocus using 7.1% the sample size of the original discovering single-ancestry GWAS (n=788,989). We additionally identified three GWS ancestry-specific loci at/near (PTPRK(P=2.4×10-8) andGRB14(P=1.7×10-8) in HIS), andKIAA0825(P=2.9×10-8in NHW). Pathway analysis implicated multiple amyloid regulation pathways (strongest withPadjusted=1.6×10-4) and the classical complement pathway (Padjusted=1.3×10-3). Genes at/near our novel loci have known roles in neuronal development (LRRC4C, LHX5-AS1, andPTPRK) and insulin receptor activity regulation (GRB14). These findings provide compelling support for using traditionally-underrepresented populations for gene discovery, even with smaller sample sizes.

PDF file - 75K, Microsatellite markers on chromosome 6.

Table S1. Clinicopathological characteristics and sample distribution by site Table S2. Primers/probes design for ddPCR (ESR1, EIF2C, AP3P1) Table S3. Raw nanoString counts Table S4. Normalized copy number calls (ER+ samples) Table S5. Normalized copy number calls (ER- samples) Table S6. DdPCR analysis of cell lines Table S7. NanoString raw counts (cell lines) Table S8. NanoString copy number calls (cell lines) Table S9. Nanostring log2 normalized counts (cell lines) Table S10. ESR1 CN amplifications by site in ER- samples Table S11. Multiple Fisher exact comparisons Table S12. ESR1 5`-3` copy number imbalance Table S13. Correlation matrix of ESR1 copy number calls by the different exons and mRNA expression Table S14. Normalized copy number calls for other genes (ER+ samples) Table S15. Normalized copy number calls other genes (ER- samples)

Supplementary Figure 1 from COX-2 Blockade Suppresses Gliomagenesis by Inhibiting Myeloid-Derived Suppressor Cells

PDF file - 67K, Characteristics of patients who underwent standard of care.

Limited ancestral diversity has impaired our ability to detect risk variants more prevalent in non-European ancestry groups in genome-wide association studies (GWAS). We constructed and analyzed a multi-ancestry GWAS dataset in the Alzheimer Disease (AD) Genetics Consortium (ADGC) to test for novel shared and ancestry-specific AD susceptibility loci and evaluate underlying genetic architecture in 37,382 non-Hispanic White (NHW), 6,728 African American, 8,899 Hispanic (HIS), and 3,232 East Asian individuals, performing within-ancestry fixed-effects meta-analysis followed by a cross-ancestry random-effects meta-analysis. We identified 13 loci with cross-ancestry associations including known loci at/near CR1, BIN1, TREM2, CD2AP, PTK2B, CLU, SHARPIN, MS4A6A, PICALM, ABCA7, APOE and two novel loci not previously reported at 11p12 (LRRC4C) and 12q24.13 (LHX5-AS1). Reflecting the power of diverse ancestry in GWAS, we observed the SHARPIN locus using 7.1% the sample size of the original discovering single-ancestry GWAS (n=788,989). We additionally identified three GWS ancestry-specific loci at/near (PTPRK (P=2.4E10-8) and GRB14 (P=1.7E10-8) in HIS), and KIAA0825 (P=2.9E10-8 in NHW). Pathway analysis implicated multiple amyloid regulation pathways (strongest with Padjusted=1.6E10-4) and the classical complement pathway (Padjusted=1.3E10-3). Genes at/near our novel loci have known roles in neuronal development (LRRC4C, LHX5-AS1, and PTPRK) and insulin receptor activity regulation (GRB14). These findings provide compelling support for using traditionally-underrepresented populations for gene discovery, even with smaller sample sizes.

Figure S1: Genomic organization of ESR1 nanoString probes Figure S2: Correlation of ESR1 amplification with mRNA expression Figure S3: ESR1 copy number status in ER+ primary-metastasis pairs Figure S4: Oncoprint visualization of copy number alterations in clinical samples Figure S5: eSNP-Karyotyping analysis of ERBB2 amplified samples Figure S6: Oncoprint visualization of copy number alterations in ER+ vs ER+ brain metastases Figure S7: Oncoprint visualization of copy number alterations in paired primary-met samples

Supplementary Figure S1A. Pre-amplification preserves mutant allele frequency and maintains sensitivity of ESR1-D538G mutation detection by ddPCR. Supplementary Figure S1B. Pre-amplification preserves mutant allele frequency and maintains sensitivity of PIK3CA-E545K mutation detection by ddPCR. Supplementary Figure S2. ESR1 Y537C/N/S and D538G mutation probes are specific to their corresponding mutations. Supplementary Figure S3. Specificity of Probes Supplementary Figure S4. LLoD determination of ddPCR on A) Frozen tissues, B) cfDNA, and C) FFPE tissues. Supplementary Figure S5. Mutant allele frequency of PIK3CA H1047R mutation in 12 bone metastases. Supplementary Figure S6. The D538G ER mutation in 3 brain mets was confirmed by Sanger sequencing. Supplementary Figure S7. ESR1 Y537S and D538G observed in the same specimens are not mutated on the same alleles. Supplementary Figure S8. Clinical timelines and allele frequency of ESR1 mutations in multiple blood draws and matched metastatic lesions from two patients.

Supplementary Figure 1. T2-Flair MRI images of 2 cases (Patient 9 in Cohort 1 and Patient 1 in Cohort 2)

Background and Objective: Transmural inflammation of the temporal artery on biopsy is considered strongly suggestive of giant cell arteritis (GCA). Occasionally other inflammation patterns are seen. It is controversial whether these findings predict GCA-like disease. Our objective was to describe the clinicopathologic features in a cohort of patients with temporal artery biopsies to examine outcomes of patients with non-transmural inflammation. Methods: We examined through retrospective chart review the clinical course from 2010-2020 of patients with temporal artery biopsies from 2010-2012. Biopsy results were divided into 3 groups: GCA transmural inflammation, non-GCA perivascular inflammation and negative. Non-GCA perivascular inflammation included small vessel, vasa vasorum and adventitial inflammation. Endpoints included constitutional and craniofacial symptoms, CRP and ESR levels, ASCVD, large vessel complications, and length of steroid treatment. Results: 95 patients were included. Transmural patients had more visual loss compared with perivascular patients (55.5% vs 15.7%, p=0.004). Transmural patients had more jaw claudication or headache/jaw claudication compared with perivascular patients (44.5% vs 12.6%, p=0.01). Weight loss was more common in transmural patients compared with perivascular (27.8% vs 3.1%, p=0.02). Night sweats, PMR symptoms, and temporal artery tenderness were similar between groups. CRP was higher in transmural patients though not significantly. ESR levels were similar between groups. Transmural patients had a longer steroid duration with a median of 24 months vs 1.5 for perivascular, p=0.001. Conclusion: Patients with non-transmural inflammation on temporal artery biopsies had improved outcomes when compared with transmural patients. This raises the question of whether steroids should be continued after a biopsy returns with perivascular inflammation.

Sonic hedgehog medulloblastoma encompasses a clinically and molecularly diverse group of cancers of the developing central nervous system. Here, we use unbiased sequencing of the transcriptome across a large cohort of 250 tumors to reveal differences among molecular subtypes of the disease, and demonstrate the previously unappreciated importance of non-coding RNA transcripts. We identify alterations within the cAMP dependent pathway (GNAS, PRKAR1A) which converge on GLI2 activity and show that 18% of tumors have a genetic event that directly targets the abundance and/or stability of MYCN. Furthermore, we discover an extensive network of fusions in focally amplified regions encompassing GLI2, and several loss-of-function fusions in tumor suppressor genes PTCH1, SUFU and NCOR1. Molecular convergence on a subset of genes by nucleotide variants, copy number aberrations, and gene fusions highlight the key roles of specific pathways in the pathogenesis of Sonic hedgehog medulloblastoma and open up opportunities for therapeutic intervention.

Over the past decade, wingless-activated (WNT) medulloblastoma has been identified as a candidate for therapy de-escalation based on excellent survival; however, a paucity of relapses has precluded additional analyses of markers of relapse. To address this gap in knowledge, an international cohort of 93 molecularly confirmed WNT MB was assembled, where 5-year progression-free survival is 0.84 (95%, 0.763-0.925) with 15 relapsed individuals identified. Maintenance chemotherapy is identified as a strong predictor of relapse, with individuals receiving high doses of cyclophosphamide or ifosphamide having only one very late molecularly confirmed relapse (p = 0.032). The anatomical location of recurrence is metastatic in 12 of 15 relapses, with 8 of 12 metastatic relapses in the lateral ventricles. Maintenance chemotherapy, specifically cumulative cyclophosphamide doses, is a significant predictor of relapse across WNT MB. Future efforts to de-escalate therapy need to carefully consider not only the radiation dose but also the chemotherapy regimen and the propensity for metastatic relapses.

Medically intractable temporal lobe epilepsy is a devastating disease, for which surgical removal of the seizure onset zone is the only known cure. Multiple studies have found evidence of abnormal dentate gyrus network circuitry in human mesial temporal lobe epilepsy (MTLE). Principal neurons within the dentate gyrus gate entorhinal input into the hippocampus, providing a critical step in information processing. Crucial to that role are GABA-expressing neurons, particularly parvalbumin (PV)-expressing basket cells (PVBCs) and chandelier cells (PVChCs), which provide strong, temporally coordinated inhibitory signals. Alterations in PVBC and PVChC boutons have been described in epilepsy, but the value of these studies has been limited due to methodological hurdles associated with studying human tissue. We developed a multilabel immunofluorescence confocal microscopy and a custom segmentation algorithm to quantitatively assess PVBC and PVChC bouton densities and to infer relative synaptic protein content in the human dentate gyrus. Using en bloc specimens from MTLE subjects with and without hippocampal sclerosis, paired with nonepileptic controls, we demonstrate the utility of this approach for detecting cell-type specific synaptic alterations. Specifically, we found increased density of PVBC boutons, while PVChC boutons decreased significantly in the dentate granule cell layer of subjects with hippocampal sclerosis compared with matched controls. In contrast, bouton densities for either PV-positive cell type did not differ between epileptic subjects without sclerosis and matched controls. These results may explain conflicting findings from previous studies that have reported both preserved and decreased PV bouton densities and establish a new standard for quantitative assessment of interneuron boutons in epilepsy. NEW & NOTEWORTHY A state-of-the-art, multilabel immunofluorescence confocal microscopy and custom segmentation algorithm technique, developed previously for studying synapses in the human prefrontal cortex, was modified to study the hippocampal dentate gyrus in specimens surgically removed from patients with temporal lobe epilepsy. The authors discovered that chandelier and basket cell boutons in the human dentate gyrus are differentially altered in mesial temporal lobe epilepsy.

INTRODUCTION:Abscesses associated with tumors are a rare entity. Imaging to differentiate abscess from other entities is often non-diagnostic, and often the source of infection is unknown. We present an unusual case of peritumoral abscess infected with both gram-negative and gram-positive bacteria.METHODS:A 70-year-old, previously healthy male presented with a 1-day history of right-sided facial weakness sparing the forehead, as well as concomitant right upper and lower extremity numbness. A homogenously enhancing mass with adjacent rim-enhancing lesion with diffusion restricting cavity seen on magnetic resonance imaging (MRI) raised the possibility of abscess.RESULTS:Separate biopsy specimens of both the tumor and adjacent fluid collection during drainage of the collection confirmed World Health Organization (WHO) grade I meningioma and bacterial abscess containing Streptococcus constellatus, Fusobacterium species, Prevotella dentalis, and Parvimonas micra. The histologic diagnosis therefore confirmed the preoperative radiologic findings of two different but associated lesions. Investigations to determine a definitive source of infection were inconclusive, including urinalysis, blood cultures, respiratory cultures, endoscopy, and an orthopantomogram.CONCLUSIONS:Gram-negative and gram-positive bacteria can both be culprits in the formation of peritumoral abscess. Although the source of infection is unconfirmed, the presence of oropharyngeal flora in the abscess suggests a subclinical odontogenic infection with hematogenous spread to the tumor and adjacent brain.

OBJECTIVE Recent large-cohort sequencing studies have investigated the genomic landscape of meningiomas, identifying somatic coding alterations in NF2, SMARCB1, SMARCE1, TRAF7, KLF4, POLR2A, BAP1, and members of the PI3K and Hedgehog signaling pathways. Initial associations between clinical features and genomic subgroups have been described, including location, grade, and histology. However, further investigation using an expanded collection of samples is needed to confirm previous findings, as well as elucidate relationships not evident in smaller discovery cohorts. METHODS Targeted sequencing of established meningioma driver genes was performed on a multiinstitution cohort of 3016 meningiomas for classification into mutually exclusive subgroups. Relevant clinical information was collected for all available cases and correlated with genomic subgroup. Nominal variables were analyzed using Fisher's exact tests, while ordinal and continuous variables were assessed using Kruskal-Wallis and 1-way ANOVA tests, respectively. Machine-learning approaches were used to predict genomic subgroup based on noninvasive clinical features. RESULTS Genomic subgroups were strongly associated with tumor locations, including correlation of HH tumors with midline location, and non-NF2 tumors in anterior skull base regions. NF2 meningiomas were significantly enriched in male patients, while KLF4 and POLR2A mutations were associated with female sex. Among histologies, the results confirmed previously identified relationships, and observed enrichment of microcystic features among "mutation unknown" samples. Additionally, KLF4-mutant meningiomas were associated with larger peritumoral brain edema, while SMARCB1 cases exhibited elevated Ki-67 index. Machine-learning methods revealed that observable, noninvasive patient features were largely predictive of each tumor's underlying driver mutation. CONCLUSIONS Using a rigorous and comprehensive approach, this study expands previously described correlations between genomic drivers and clinical features, enhancing our understanding of meningioma pathogenesis, and laying further groundwork for the use of targeted therapies. Importantly, the authors found that noninvasive patient variables exhibited a moderate predictive value of underlying genomic subgroup, which could improve with additional training data. With continued development, this framework may enable selection of appropriate precision medications without the need for invasive sampling procedures.