Faculty Bibliography

Background: Over 250,000 breast cancer cases are diagnosed annually in the US, of which 15% (n=37,500) are triple negative breast cancers (TNBC). TNBC has an aggressive clinical course with limited therapeutic options. Some studies estimate that a small proportion of TNBCs defined by immunohistochemical (IHC) stains alone, i.e. estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2)-negative, can, in fact, show HER2 amplification by fluorescent in situ hybridization (FISH) and, therefore, be reclassified as HER2-enriched. If properly classified, these patients can benefit from anti-HER2 therapy. To capture this subset of patients, we performed a now four-year-long prospective study, in which TNBCs were reflexed to HER2 by FISH. Herein, we present our findings with detailed clinicopathologic analysis of the reclassified cases. Design: TNBC cases and ER/PR-positive, HER2-negative breast cancers from 2014 to 2017 with concurrent IHC and FISH results were analyzed. The pathology slides were reviewed by two pathologists. Stromal tumor infiltrating lymphocytes (sTILs) were defined as the percentage of all mononuclear cells within tumor stroma not in direct contact with tumor cells. Results: Of the 253 TNBCs in the past 4 years, 13 tumors (5%) showed HER2 amplification by FISH (6 surgical excisions and 7 core biopsies). Two patients have previously identified BRCA1 mutation. Twelve of 13 tumors (92%) were grade 3. All tumors were invasive ductal carcinoma of no special type. No apocrine morphology was noted. Notably, five tumors had >=50% sTILs, which can be classified as lymphocyte-predominant breast cancer based on some studies. In the same time period, 41 ER/PR-positive/HER2-negative breast cancers were reflexed to HER2 by FISH, none of which showed amplification. All tumors were fixed in formalin for comparable amount of time (6-72 hours). After reclassification, approximately 40% of patients received anti-HER2 therapy. (Table Presented) Conclusions: Pathologists may consider reflexing HER2 evaluation to FISH in TNBCs with grade 3, high ki67 and high sTILs. If 5% of TNBCs can be reclassified as HER2-enriched tumors, based on the national statistics, annually approximately 1875 patients with TNBCs by IHC may actually benefit from anti-HER2 therapy

Epigenetic patterns on the level of DNA methylation have already been shown to separate clinically relevant subgroups of meningiomas. We here set out to identify potential prognostic implications of epigenetic modification on the level of histones with focus on H3K27 trimethylation (H3K27me3). H3K27me3 was assessed by immunohistochemistry on 232 meningiomas from 232 patients. In 194 cases, trimethylation was detected in tumor cells. In 25 cases, staining was limited to vessels while all tumor cells were negative. Finally, 13 cases yielded equivocal staining patterns. Reduced abundance of H3K27me3 in cases with staining limited to vessels was confirmed by mass spectrometry on a subset of cases. Lack of staining for H3K27me3 in all tumor cells was significantly associated with more rapid progression (p = 0.009). In line, H3K27me3-negative cases were associated with a DNA methylation pattern of the more aggressive types among the recently introduced DNA methylation groups. Also, NF2 and SUFU mutations were enriched among cases with complete lack of H3K27me3 staining in tumor cells (p < 0.0001 and p = 0.029, respectively). H3K27me3 staining pattern added significant prognostic insight into WHO grade II cases and in the compound subset of WHO grade I and II cases (p = 0.04 and p = 0.007, respectively). However, it did not further stratify within WHO grade III cases. Collectively, these data indicate that epigenetic modifications beyond DNA methylation are involved in the aggressiveness of meningioma. It also suggests that H3K27me3 immunohistochemistry might be a useful adjunct in meningioma diagnostics, particularly for cases with WHO grade II histology or at the borderline between WHO grade I and II.

Purpose: Prior studies have shown correlation between relative cerebral blood volume (rCBV) and patient survival and tumor genomics. The purpose of this study was to determine whether rCBV values correlate with isocitrate dehydrogenase (IDH) mutation status, genome-wide CNV (copy number variation) and patient overall survival in diffuse gliomas. Materials & Methods: 107 treatment naive gliomas (62 patients from TCGA/TCIA dataset and 45 patients from our institute) (44 glioblastoma and 63 lower grade gliomas) with DSC T2* perfusion data were included. IDH mutation and survival data were assayed by the TCGA, and pre-surgical imaging collected by The Cancer Imaging Archive. CNVabundance plots obtained with Illumina 850k EPIC DNA methylation arrays were reviewed in 19 patients. The association of rCBV with tumor genomics, CNV and overall survival were analyzed. Results: IDH-wildtype gliomas (44.8%) demonstrated higher rCBV values (rCBV = 6.87 +/- 3.09) than IDH-mutated gliomas (55.2%, rCBV =2.21 +/- 1.71 for 1p/19q codeleted gliomas and 2.09 +/- 2.00 for non-codeleted gliomas, ANOVA, p<0.0001). rCBV is a significant predictor of overall survival (HR 1.23, p<0.0001). Gliomas with rCBV < 3.80 showed better survival (n = 54, median survival time unobserved) than gliomas with rCBV > 3.8 (n = 53, median 18 months; log-rank p<0.0001). IDHwt gliomas with high rCBV had the worst survival (10.6% surviving at 3 years, 95% CI (4%, 30%)). CNV-S IDHmut 1p19q noncodeleted gliomas demonstrated significantly lower mean rCBV (1.4 +/- 0.4) than CNV-U gliomas (4.0 +/- 1.1, p = 0.009). Conclusion: IDHwt gliomas show higher rCBV than IDHmut gliomas irrespective of the glioma grade. Higher rCBV measurements are associated with poorer survival in the entire cohort and also within IDHmut and IDHwt gliomas. IDHmut 1p19q noncodeleted gliomas with higher CNV abundance (CNV-U) also show higher CBV when compared with those with lesser degree of CNVabundance (CNV-S)

Sudden unexpected death in epilepsy (SUDEP) is the leading cause of epilepsy-related mortality in young adults. The exact mechanisms are unknown but death often follows a generalized tonic-clonic seizure. Proposed mechanisms include seizure-related respiratory, cardiac, autonomic, and arousal dysfunction. Genetic drivers underlying SUDEP risk are largely unknown. To identify potential SUDEP risk genes, we compared whole-exome sequences (WES) derived from formalin-fixed paraffin embedded surgical brain specimens of eight epilepsy patients who died from SUDEP with seven living controls matched for age at surgery, sex, year of surgery and lobe of resection. We compared identified variants from both groups filtering known polymorphisms from publicly available data as well as scanned for epilepsy and candidate SUDEP genes. In the SUDEP cohort, we identified mutually exclusive variants in genes involved in µ-opiod signaling, gamma-aminobutyric acid (GABA) and glutamate-mediated synaptic signaling, includingARRB2,ITPR1,GABRR2,SSTR5,GRIK1,CTNAP2,GRM8,GNAI2andGRIK5. In SUDEP patients we also identified variants in genes associated with cardiac arrhythmia, includingKCNMB1,KCNIP1,DPP6,JUP,F2, andTUBA3D, which were not present in living epilepsy controls. Our data shows that genomic analysis of brain tissue resected for seizure control can identify potential genetic biomarkers of SUDEP risk.