Faculty Bibliography

Purpose To identify MR imaging features of melanoma brain metastases (MBM) that correlate with genetic profile of melanoma and patient survival. Materials and methods Patients with newly diagnosed melanoma metastases were identified from institutional database A retrospective review of brain MRI was performed focusing on lesion number, size, T1-, T2- and diffusion-weighted signal characteristics, hemorrhage, necrosis, enhancement pattern and edema. Genomic (BRAF status), treatment and survival data was collected. Results 98 patients were included in final analysis. A strong correlation was found between size of the largest lesion and the percent of lesions with T1-weighted hyperintense signal (R = 0.49), percent of lesions with size >1 cm (0.55), and the lesions that are clearly hemorrhagic (0.43). The analyzed imaging parameters were found to be independent of BRAF mutation status. The median survival of subjects with single lesion (9.1 months) was significantly higher than the median survival of subjects with more than 1 lesion (4.9 months) (p = 0.002). Patients with 2-18 lesions had significantly longer survival (5.6 months) than with >18 lesions (2 months) (p < 0.001). Other imaging parameters such as lesion size, T1-weighted hyperintensity, number of lesions with edema and hemorrhage were not found to be significantly related to survival. BRAF inhibitor treatment was found to be the most significant prognostic factor (p = 0.002) among patients with multiple lesions. Conclusion There is a statistically significant correlation between number of brain metastases and survival. In patients with multiple lesions, BRAF inhibitor treatment was the most significant prognostic factor.

BACKGROUND:The frequency with which targeted tumor sequencing results will lead to implemented change in care is unclear. Prospective assessment of the feasibility and limitations of using genomic sequencing is critically important. METHODS:A prospective clinical study was conducted on 100 patients with diverse-histology, rare, or poor-prognosis cancers to evaluate the clinical actionability of a Clinical Laboratory Improvement Amendments (CLIA)-certified, comprehensive genomic profiling assay (FoundationOne), using formalin-fixed, paraffin-embedded tumors. The primary objectives were to assess utility, feasibility, and limitations of genomic sequencing for genomically guided therapy or other clinical purpose in the setting of a multidisciplinary molecular tumor board. RESULTS:Of the tumors from the 92 patients with sufficient tissue, 88 (96%) had at least one genomic alteration (average 3.6, range 0-10). Commonly altered pathways included p53 (46%), RAS/RAF/MAPK (rat sarcoma; rapidly accelerated fibrosarcoma; mitogen-activated protein kinase) (45%), receptor tyrosine kinases/ligand (44%), PI3K/AKT/mTOR (phosphatidylinositol-4,5-bisphosphate 3-kinase; protein kinase B; mammalian target of rapamycin) (35%), transcription factors/regulators (31%), and cell cycle regulators (30%). Many low frequency but potentially actionable alterations were identified in diverse histologies. Use of comprehensive profiling led to implementable clinical action in 35% of tumors with genomic alterations, including genomically guided therapy, diagnostic modification, and trigger for germline genetic testing. CONCLUSION/CONCLUSIONS:Use of targeted next-generation sequencing in the setting of an institutional molecular tumor board led to implementable clinical action in more than one third of patients with rare and poor-prognosis cancers. Major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access. Early and serial sequencing in the clinical course and expanded access to genomically guided early-phase clinical trials and targeted agents may increase actionability. IMPLICATIONS FOR PRACTICE/CONCLUSIONS:Identification of key factors that facilitate use of genomic tumor testing results and implementation of genomically guided therapy may lead to enhanced benefit for patients with rare or difficult to treat cancers. Clinical use of a targeted next-generation sequencing assay in the setting of an institutional molecular tumor board led to implementable clinical action in over one third of patients with rare and poor prognosis cancers. The major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access both on trial and off label. Approaches to increase actionability include early and serial sequencing in the clinical course and expanded access to genomically guided early phase clinical trials and targeted agents.

Antibodies that target the immune checkpoint receptor programmed cell death protein 1 (PD-1) have resulted in prolonged and beneficial responses toward a variety of human cancers. However, anti-PD-1 therapy in some patients provides no benefit and/or results in adverse side effects. The factors that determine whether patients will be drug sensitive or resistant are not fully understood; therefore, genomic assessment of exceptional responders can provide important insight into patient response. Here, we identified a patient with endometrial cancer who had an exceptional response to the anti-PD-1 antibody pembrolizumab. Clinical grade targeted genomic profiling of a pretreatment tumor sample from this individual identified a mutation in DNA polymerase epsilon (POLE) that associated with an ultramutator phenotype. Analysis of The Cancer Genome Atlas (TCGA) revealed that the presence of POLE mutation associates with high mutational burden and elevated expression of several immune checkpoint genes. Together, these data suggest that cancers harboring POLE mutations are good candidates for immune checkpoint inhibitor therapy.

OBJECTIVES/OBJECTIVE:This study sought to assess the incidence, operator demographics, clinical characteristics, procedural factors, and prognosis of esophageal perforation and fistula after atrial fibrillation ablation. BACKGROUND:Esophageal injury is a feared complication of atrial fibrillation ablation. METHODS:An Internet-based global survey soliciting anonymous information regarding esophageal perforation and fistula was emailed to 3,080 physicians. Detailed information regarding physician, patient, and procedural characteristics related to esophageal perforation with or without fistula was collected. RESULTS:; p = 0.03), and lower left ventricular ejection fraction (55.1 ± 9.1% vs. 61.7 ± 5.4%; p = 0.04). Among analyzed patients, atrial-esophageal fistula was seen in 72%, pericardial-esophageal fistula in 14%, and esophageal perforation without fistula in 14%. Mortality was 79% with atrial-esophageal fistula and 13% in esophageal perforation without atrial-esophageal fistula. CONCLUSIONS:Esophageal perforation is rare but continues to occur with multiple catheter types despite esophageal monitoring during ablation. The prognosis of esophageal perforation is substantially improved if diagnosed and treated before development of atrial-esophageal fistula. An early surgical approach to esophageal perforation should be strongly considered regardless of evidence of fistula.

BACKGROUND: Age has been reported as an independent prognostic factor for melanoma-specific survival (MSS). We tested the hypothesis that age impacts the host anti-tumor immune response, accounting for age-specific survival outcomes in three unique melanoma patient cohorts. METHODS: We queried the U.S. population-based Surveillance, Epidemiology, and End Results Program (SEER), the prospective tertiary care hospital-based Interdisciplinary Melanoma Cooperative Group (IMCG) biorepository, and the Cancer Genome Atlas (TCGA) biospecimen database to test the association of patient age at time of melanoma diagnosis with clinicopathologic features and survival outcomes. Age groups were defined as 65 (older). Each age group in the IMCG and TCGA cohorts was stratified by tumor infiltrating lymphocyte (TIL) measurements and tested for association with MSS. Differential expression of 594 immunoregulatory genes was assessed in a subset of primary melanomas in the IMCG and TCGA cohorts using an integrative pathway analysis. RESULTS: We analyzed 304, 476 (SEER), 1241 (IMCG), and 292 (TCGA) patients. Increasing age at melanoma diagnosis in both the SEER and IMCG cohorts demonstrated a positive correlation with tumor thickness, ulceration, stage, and mortality, however age in the TCGA cohort did not correlate with mortality. Older age was associated with shorter MSS in all three cohorts. When the young age group in both the IMCG and TCGA cohorts was stratified by TIL status, there were no differences in MSS. However, older IMCG patients with brisk TILs and intermediate aged TCGA patients with high lymphocyte scores (3-6) had improved MSS. Gene expression analysis revealed top pathways (T cell trafficking, communication, and differentiation) and top upstream regulators (CD3, CD28, IFNG, and STAT3) that significantly changed with age in 84 IMCG and 43 TCGA primary melanomas. CONCLUSIONS: Older age at time of melanoma diagnosis is associated with shorter MSS, however age's association with clinicopathologic features is dependent upon specific characteristics of the study population. TIL as a read-out of the host immune response may have greater prognostic impact in patients older than age 45. Recognition of age-related factors negatively impacting host immune responses may provide new insights into therapeutic strategies for the elderly.

The next-generation sequencing data, called high-throughput sequencing data, are recorded as count data, which are generally far from normal distribution. Under the assumption that the count data follow the Poisson log-normal distribution, this article provides an L1-penalized likelihood framework and an efficient search algorithm to estimate the structure of sparse directed acyclic graphs (DAGs) for multivariate counts data. In searching for the solution, we use iterative optimization procedures to estimate the adjacency matrix and the variance matrix of the latent variables. The simulation result shows that our proposed method outperforms the approach which assumes multivariate normal distributions, and the log-transformation approach. It also shows that the proposed method outperforms the rank-based PC method under sparse network or hub network structures. As a real data example, we demonstrate the efficiency of the proposed method in estimating the gene regulatory networks of the ovarian cancer study.

Breast cancer has the second highest death toll in women worldwide, despite significant progress in early diagnosis and treatments. The main cause of death is metastatic disease. Matrix metalloproteinases (MMPs) are required for the initial steps of metastasis, and have therefore been considered as ideal pharmacological targets for anti-metastatic therapy. However, clinical trials of MMP inhibitors were unsuccessful. These trials were conducted in patients with advanced disease, beyond the stage when these compounds could have been effective. We hypothesized that early treatment with a selective MMP inhibitor between the time of diagnosis and definitive surgery, the so-called "window-of-opportunity," can inhibit metastasis and thereby improve survival. To investigate our hypothesis we used the 4T1 mouse model of aggressive mammary carcinoma. We treated the animals with SD-7300, an oral inhibitor of MMP-2, -9 and -13, starting after the initial detection of the primary tumor. Seven days later the primary tumors were excised and analyzed for MMP activity, and the SD-7300 treatment was discontinued. After four weeks the animals were sacrificed and their lungs analyzed histologically for number of metastases and metastatic burden (metastases' area / lung section area). SD-7300 treatment inhibited 70-80% of tumor-associated MMP activity (P = 0.0003), reduced metastasis number and metastatic burden by 50-60% (P = 0.002; P = 0.0082, respectively), and increased survival (92% vs. 66.7%; P = 0.0409), relative to control vehicle. These results show that treatment of early invasive breast cancer with selective MMP inhibitors can lower the risk of recurrence and increase long-term disease-free survival.

Tumor infiltrating lymphocytes (TILs) in primary melanomas are thought to represent the host anti-tumor immune response, but controversy exists over whether TILs offer independent prognostication of survival. We studied a cohort of 1241 primary melanoma patients to assess the association of absent, non-brisk, and brisk TIL grade with survival outcomes. We tested whether quantitative TIL counts using immunohistochemical lymphocyte markers CD3, CD45, and FOXP3 add prognostic value to TIL grading compared to histology alone in 15% of the cohort. To assess for inter-group immunologic heterogeneity among TIL grades, we investigated differential expression of 594 immunoregulatory genes in 67 primary melanomas. On histologic evaluation of 1241 primary melanomas, TILs were graded as absent (n=388, 31%), non-brisk (n=330, 27%), and brisk (n=523, 42%). Patients with brisk TILs had improved recurrence-free survival (RFS) (P=.025) and overall survival (OS) (P=.006) compared to patients with non-brisk and absent TILs, for which there were no differences in RFS (P=.40) or OS (P=.41). TIL quantitation by immunohistochemistry did not improve prognostication compared to TIL grading on hematoxylin and eosin stained sections. Melanomas with non-brisk and absent TILs share similar immunoregulatory gene expression profiles. In contrast, melanomas with brisk TILs demonstrate upregulation of T-cell activation pathways and inhibition of upstream immune checkpoint regulators. The presence of TILs in primary melanomas represents a heterogeneous group and caution in prognostic interpretation is warranted. Melanomas with brisk TILs are defined by an immunostimulatory gene expression profile and improved prognosis compared to melanomas with non-brisk or absent TILs.

Staphylococcus aureus is a formidable human pathogen that uses secreted cytolytic factors to injure immune cells and promote infection of its host. Of these proteins, the bicomponent family of pore-forming leukocidins play critical roles in S. aureus pathogenesis. The regulatory mechanisms governing the expression of these toxins are incompletely defined. In this work, we performed a screen to identify transcriptional regulators involved in leukocidin expression in S. aureus strain USA300. We discovered that a metabolic sensor-regulator, RpiRc, is a potent and selective repressor of two leukocidins, LukED and LukSF-PV. Whole-genome transcriptomics, S. aureus exoprotein proteomics, and metabolomic analyses revealed that RpiRc influences the expression and production of disparate virulence factors. Additionally, RpiRc altered metabolic fluxes in the trichloroacetic acid cycle, glycolysis, and amino acid metabolism. Using mutational analyses, we confirmed and extended the observation that RpiRc signals through the accessory gene regulatory (Agr) quorum-sensing system in USA300. Specifically, RpiRc represses the rnaIII promoter, resulting in increased repressor of toxins (Rot) levels, which in turn negatively affect leukocidin expression. Inactivation of rpiRc phenocopied rot deletion and increased S. aureus killing of primary human polymorphonuclear leukocytes and the pathogenesis of bloodstream infection in vivo. Collectively, our results suggest that S. aureus senses metabolic shifts by RpiRc to differentially regulate the expression of leukocidins and to promote invasive disease. IMPORTANCE: The bicomponent pore-forming leukocidins play pivotal roles in the ability of S. aureus to kill multiple host immune cells, thus enabling this pathogen to have diverse tissue- and species-tropic effects. While the mechanisms of leukocidin-host receptor interactions have been studied in detail, the regulatory aspects of leukocidin expression are less well characterized. Moreover, the expression of the leukocidins is highly modular in vitro, suggesting the presence of regulators other than the known Agr, Rot, and S. aureus exoprotein pathways. Here, we describe how RpiRc, a metabolite-sensing transcription factor, mediates the repression of two specific leukocidin genes, lukED and pvl, which in turn has complex effects on the pathogenesis of S. aureus Our findings highlight the intricacies of leukocidin regulation by S. aureus and demonstrate the involvement of factors beyond traditional virulence factor regulators.