Faculty Bibliography

PURPOSE OF REVIEW/OBJECTIVE:Patent foramen ovale (PFO) is widely prevalent and studies have suggested an association with ischemic stroke. In this review, we aim to highlight current management of patients with ischemic stroke in the setting of PFO and discuss some areas of controversy. RECENT FINDINGS/RESULTS:Upon reviewing the literature, we have found that the evidence regarding the management of patients with cryptogenic stroke and PFO has come a long way in the past several years, and many uncertainties remain in clinical practice. The Risk of Paradoxical Embolism (RoPE) score helps to predict the probability of a pathogenic PFO, and recent trial data confirms the benefit of closure in carefully selected patients. The benefit of closure in older patients and in patients with alternate, competing mechanisms is still uncertain, and the long-term risks of closure are not known. Finally, the efficacy of direct oral anticoagulants (DOACs) in this patient population as compared to other medical therapy or mechanical closure has not yet been investigated. Randomized data is needed to help answer these questions. PFO closure is a safe and effective strategy in reducing stroke risk in carefully selected patients with cryptogenic stroke in the setting of a PFO. More studies are needed to test optimal medical treatment strategies and the safety and efficacy of PFO closure in patient subgroups not included in prior PFO closure trials.

BACKGROUND:Over the past 2 decades, a growing number of large-scale clinical trials have helped expand the toolkit for emergency management of acute ischemic stroke. This article is intended to be an up-to-date resource to aid nonstroke specialist neurology providers and ophthalmologists in identifying situations and patient populations in which urgent stroke evaluation should be completed with options for emergent reperfusion therapy considered. EVIDENCE ACQUISITION/METHODS:The literature forming the foundation of the guidelines for early management of patients with acute ischemic stroke was reviewed, annotated, and summarized. RESULTS:Data from both initial and follow-up trials investigating the benefits and indications for use of intravenous thrombolysis and endovascular intervention for stroke are reviewed systematically, with an emphasis on new updates to qualifying patient populations and time periods for treatment. CONCLUSIONS:Recent studies underscore the conclusion that timely reperfusion in acute ischemic stroke is the most effective available treatment and that there are a growing number of new scenarios and patients for which interventions maybe applied.

Background: TERT promoter mutations in various reports have been associated with poor patient survival in early stage melanomas emphasizing it as a separate subset of melanoma. Thus far, no studies investigated whether the immune composition of the tumor microenvironment (TME) in TERT (HS) mutant melanomas differs from TERT WT melanomas. Furthermore, the mechanism underlying the worse outcome in early stage TPHS melanomas remains unclear. Herein, we aim to characterize the tumor microenvironment (TME) of TERT promoter hotspot (TPHS) mutant melanomas & compare them to TERT WT melanomas in a cohort of early and advanced stage melanomas. We also aim to elucidate the clinical significance of the TME composition.
Design(s): We analyzed tissue from a cohort of 93 melanoma patients. DNA and RNA were extracted from primary and metastatic tumor tissue, resected prior to treatment with immune checkpoint inhibitors. The extracted DNA was genotyped using a customized next generation sequencing high throughput panel that targets 580 cancer-related genes to determine TPHS mutation status. Gene expression analysis was performed on the RNA from 52 patients using a customized 770-gene expression panel combining markers 48 biologically significant signatures with the N-counter system. Differential gene expression (DGE) and Gene set enrichment analysis (GSEA) were performed using R package [(p<0.01; FDR<0.01; FDR<0.30 for GSEA] using TERT WT as a reference.
Result(s): Table 1 illustrates the clinicopathological characteristics of the cohort. TPHS mutant melanoma was associated with downregulation of melanoma-associated antigens (MAGES) and endothelial cells/angiogenesis signature (p<0.01). Notably, MAGEA4, MAGEA1, CTAG1B, PALMD & KDR were among the most downregulated genes in the (lg2fc= -3.2; -2.2; -2.66, -1.23; - 0.66, respectively). GSEA showed a significant enrichment for NOD-like receptor (NLR) signaling pathway including NFKB1, TNF & NLR3P in TPHS mutant melanoma (Figure 1). Within TPHS mutant melanoma, high endothelial cells/angiogenesis signature (score >3.85/median) was more prevalent in stage (I/II) melanomas (p=0.025). No significant association between TERT mutational status, outcome nor histologic subtype were noted. (Table presented)
Conclusion(s): Our findings show that TPHS mutant melanoma and TERT WT have distinct TME composition. The higher endothelial/angiogenesis signature seen in early stage TPHS mutant melanoma compared to stage III/IV TPHS mutant melanomas could contribute to the poor outcome reported in the former group

Background: As hepatocellular carcinoma (HCC) develops from premalignant lesions (low and high grade dysplastic nodules; LGDN and HGDN), there is a corresponding accumulation of molecular alterations, some of which have been well described. However, the molecular features of lesions comprising the hepatocellular dysplasia-carcinoma sequence as they relate to different etiologies have not yet been explored. Herein, we characterize the molecular landscape of such lesions in cirrhotic explants with alcohol-related liver disease (ALD) and chronic hepatitis C (CHC).
Design(s): Tissue was assessed from 27 liver explants (14 CHC, 13 ALD) including 10 LGDNs (5 CHC, 5 ALD), 8 HGDNs (3 CHC, 5 ALD), 10 HCCs arising from HGDNs (5 CHC, 5 ALD), and 10 small HCCs defined as HCC < 2 cm (5 CHC, 5 ALD), as well as non-lesional cirrhotic parenchyma and matched normal non-liver tissue (e.g. porta hepatis structures). DNA was extracted from FFPE tissue for next generation sequencing (NGS) using a customized NGS580 panel targeting all exonic and select intronic areas in 580 cancer related genes. Data was analyzed using customized bioinformatics pipelines with an R package.
Result(s): TERT promoter HS C228T mutations were identified in 6 of 10 (60%) CHC related HCCs and only 1 of 9 (11%) alcohol related HCC (Figure 1). There was a significant association between TERT promoter HS C228T mutations and CHC related HCCs (p<0.02). In contrast, ALD related lesions showed deleterious events affecting tumor suppressor genes (NF1, BRCA1; CDKN2C) and histone methylation/chromatin remodeling genes (KMT2A; KMT2C; ASXL1; RAD21), which were found in 6 of 13 ALD related lesions (46.2% [3 of 5 small HCCs, 2 of 4 HGDNs, and 1 of 4 HCCs arising in HGDNs]). These events only occurred in 3 of 14 (21.4%) CHC related lesions (Figures 1 and 2). Within the CHC group, 1 HCC arising in HGDN showed copy number gains (CNG) in MARK4, ERCC2, FGFR4 and FLT4 and two HGDNs showed CNGs in NOTCH1 and TERT, respectively. No differences in the tumor mutational burden (TMB) were noted between CHC related and ALD related lesions, nor across the DN-HCC sequence. Non-lesional liver and LGDNs did not show recurrent mutations pertaining to a specific pathway. (Figure presented)
Conclusion(s): Our findings suggest that the pathways of hepatocarcinogenesis are distinct in ALD and CHC. While upregulation of telomerase activity (TA) and cancer cell immortalization play a pivotal role in CHC related HCC, defective chromatin remodeling appears to contribute to tumorigenesis in ALD related HCC

BACKGROUND: Up to 20% of meningiomas are aggressive tumors with high recurrence rates and poor prognosis. Biomarkers predicting the risk of an unfavorable clinical course are lacking although aberrations in NF2, increased copy number variations and a hypomethylated phenotype have been associated with more aggressive behavior. Mutational signatures (MS) are characteristic patterns of somatic mutations seen in cancer genomes associated with aging, exposure to certain mutagens, or defective DNA repair. We aimed to identify MS patterns in clinically aggressive meningiomas.
METHOD(S): We performed whole exome sequencing of 18 de novo meningiomas (locally invasive and recurrent WHO I, n=6; atypical WHO II, n=4; anaplastic WHO III, n=8). Median PFS was 18.9 months. Copy numbers and DNA methylation phenotype were assessed by DNA methylation array analysis. Mutational signatures were identified using published signature algorithms (COSMIC).
RESULT(S): MS1 and MS5 (aging) were found in 18 (100%) cases. MS associated with defective DNA MMR were highly prevalent: MS20 and MS26 were detected in 18 (100%) and MS6 in 2 (12%) cases. MS12 (unknown etiology) was present in 14 (82%) cases. Despite the association with defective DNA MMR, none (0%) of the MS6 cases harbored somatic mutations associated with DNA MMR while MS12 tumors were enriched for mutations in DNA MMR (43%), chromatin remodeling (36%) and other cancer-associated genes (7%). MS6 tumors had significantly lower indels compared to non-MS6 tumors (p=0.01). Tumors with mutations in chromatin remodeling genes had a significantly higher rate of single nucleotide variants (SNVs) compared to cases without such mutations (p=0.02).
CONCLUSION(S): MS associated with defective DNA MMR were highly prevalent in this set of aggressive meningiomas. However, despite the association with DNA MMR, MS6 meningiomas harbored no somatic mutations associated with DNA MMR while MS12 tumors were enriched for mutations in DNA MMR, chromatin remodeling and cancerassociated genes

BACKGROUND:The potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measurement assurance are critical components of genome-scale measurements. Here, we evaluated the utility of a set of total RNA samples, designed with between-sample differences in the relative abundance of miRNAs, as process controls. RESULTS:Three pure total human RNA samples (brain, liver, and placenta) and two different mixtures of these components were evaluated as measurement assurance control samples on multiple measurement systems at multiple sites and over multiple rounds. In silico modeling of mixtures provided benchmark values for comparison with physical mixtures. Biomarker development laboratories using next-generation sequencing (NGS) or genome-scale hybridization assays participated in the study and returned data from the samples using their routine workflows. Multiplexed and single assay reverse-transcription PCR (RT-PCR) was used to confirm in silico predicted sample differences. Data visualizations and summary metrics for genome-scale miRNA profiling assessment were developed using this dataset, and a range of performance was observed. These metrics have been incorporated into an online data analysis pipeline and provide a convenient dashboard view of results from experiments following the described design. The website also serves as a repository for the accumulation of performance values providing new participants in the project an opportunity to learn what may be achievable with similar measurement processes. CONCLUSIONS:The set of reference samples used in this study provides benchmark values suitable for assessing genome-scale miRNA profiling processes. Incorporation of these metrics into an online resource allows laboratories to periodically evaluate their performance and assess any changes introduced into their measurement process.

Exsanguination from hemodialysis vascular sites may cause a rapid death. Due to extensive blood loss at the scene, investigators may initially suspect a homicide or suicide. We reviewed 100 deaths due to hemorrhage from hemodialysis shunt sites. The majority (81%) of these hemorrhages occurred at home and 44% subsequently died at home. Recognition of this medical complication at the scene is important to prevent the dispatch of the crime scene or homicide unit. In these instances, the common causes of kidney failure included hypertensive cardiovascular disease and diabetes mellitus. The manners of death were certified as therapeutic complication (93%), accident (5%), and suicide (2%). These fatal shunt hemorrhages are rapid and large due to their superficial subcutaneous locations and elevated shunt pressures from the arterial-venous anastamosis. The cause of death statement must include the proximate cause of death, which is usually the disease that resulted in kidney failure, if it is known.

Arthropod species diversity was compared between two human corpses confined to a small geographic area during the winter and summer of 2004 in Santa Clara County, California. One of the primary flies collected from the corpse in the summer (Compsomyiops callipes) as well as two silphid species (Nicrophorus nigritus and Necrophilus hydrophiloides) in the winter appear to be new collection records on human remains. Different arthropod species were collected from both corpses and, in general, arthropods were more numerous on the corpse found in the summer. These differences can most likely be attributed to seasonal variation. This comparison demonstrates how seasonality impacts arthropod succession, often an important indicator of postmortem interval.