Faculty Bibliography

Brain metastasis is a significant cause of morbidity and mortality in multiple cancer types and represents an unmet clinical need. The mechanisms that mediate metastatic cancer growth in the brain parenchyma are largely unknown. Melanoma, which has the highest rate of brain metastasis among common cancer types, is an ideal model to study how cancer cells adapt to the brain parenchyma. Our unbiased proteomics analysis of melanoma short-term cultures revealed that proteins implicated in neurodegenerative pathologies are differentially expressed in melanoma cells explanted from brain metastases compared to those derived from extracranial metastases. We showed that melanoma cells require amyloid beta (AB) for growth and survival in the brain parenchyma. Melanoma-secreted AB activates surrounding astrocytes to a pro-metastatic, anti-inflammatory phenotype and prevents phagocytosis of melanoma by microglia. Finally, we demonstrate that pharmacological inhibition of AB decreases brain metastatic burden.

PURPOSE/OBJECTIVE:-truncating mutations. Conversely, the molecular underpinnings of the rare juvenile granulosa cell tumor (JGCT) have not been well elucidated. To this end, we applied a tumor-only integrated approach to investigate the genomic, transcriptomic, and epigenomic landscape of 31 JGCTs to identify putative oncogenic drivers. EXPERIMENTAL DESIGN/METHODS:Multipronged analyses of 31 JGCTs were performed utilizing a clinically validated next-generation sequencing (NGS)-panel targeting 580 cancer-related genes for genomic interrogation, in addition to targeted RNA NGS for transcriptomic exploration. Genome-wide DNA methylation profiling was conducted using an Infinium Methylation EPIC array targeting 866,562 CpG methylation sites. RESULTS:non-rearranged JGCTs under direct promoter control. Genome-wide DNA methylation rendered a clear delineation between AGCTs and JGCTs at the epigenomic level further supporting its diagnostic utility in distinguishing among these tumors. CONCLUSIONS:rearrangements in a subset of tumors. Our findings further offer insights into possible targeted therapies in a rare entity.

Primary sarcomas of the lung are extremely uncommon. A diverse group of round cell sarcomas has been reported to originate in this location, including Ewing sarcoma, desmoplastic small round cell tumor, rhabdomyosarcoma, and poorly differentiated synovial sarcoma. The rarity of these tumors presents a potential pitfall; without careful study, they may easily be misidentified as the significantly more common poorly differentiated carcinoma. While histomorphology is a key aspect of correctly identifying a sarcoma, ancillary testing has become increasingly important in making a definitive diagnosis, as more and more recurrent genetic alterations are discovered and new entities are defined. We present three cases of primary round cell sarcomas of the lung that proved diagnostically challenging, describe the features and ancillary testing that led to the correct diagnoses, and discuss classic and evolving entities among sarcomas with round cell morphology.

Background: Digital papillary adenocarcinoma (DPAC) is a rare but aggressive cutaneous malignant sweat gland neoplasm that occurs on acral sites and mimics other benign entities leading to diagnostic dilemmas. We investigate genomic and transcriptomic signatures unique to DPAC that would help differentiate it from other benign entities and aim to unveil unique transcriptomic signatures inherent to its biology.
Design(s): 9 DPAC and 10 hidradenoma (HD) cases were selected (Table 1). DNA analysis used targeted 607 gene FDA validated panel (clinically validated). Customized RNA panel targeting 104 genes (FusionSeeqer) was used for fusion analysis. All pipelines used are clinically validated. Transcriptomic analysis used nCounter Pan Cancer IO 360TM panel (770 genes) with subsequent analysis using our own pipelines n R studio. Accurate transcript quantification (lg2FC) was performed after normalization to standard housekeeping genes. DESEQ2 was used for the gene level differential gene expression (DGE) analysis after normalization to reference group benign HDs (FDR<0.01, fold change: > 2 or < -2) with subsequent KEGG pathway analysis.
Result(s): DPAC cases showed very low tumor mutational burden on genomic analysis (range 0-1 mut/mb). Gene rearrangements were more frequent in HD compared to DPAC (4/4 vs 2/7, p= 0.03). Mastermind-like family of protein genes (MAML2) rearrangements were more frequent in HD, while DPAC showed novel zinc finger gene (PLAG1) rearrangements (TRPS1- PLAG1; n=1) (Fig 1A). Unsupervised clustering analysis and subsequent DGE analysis revealed 100 significantly differentially expressed genes between DPAC and HD. MAGEA4, IL2, IFNG, and COL11A2 showed a significant upregulation in DPAC (lg2FC =2.6, 2.93, 2.98, 3.04, FDR range = 0.0001 to 0.00004) respectively (Fig 1B). Pathway analysis identified enrichment of JAK/STAT pathway, which is triggered by the upregulated cytokines in DPAC (Fig 1C).
Conclusion(s): While morphologically overlapping, DPAC and HD are biologically distinct. MAGEA4 upregulation seen in DPAC could serve as potential marker for both diagnostic and therapeutic purposes, since it could be potentially targeted with adoptive Tcell therapy (ADP-A2M4). Validation of the findings on a larger cohort is underway

Background: There is paucity of transcriptomic data concerning primary cutaneous CD8+ lymphoproliferative disorders. Herein we aim to investigate the transcriptomic profile of CD8+ mycosis fungoides (CD8+ MF) and type D lymphomatoid papulosis (Type D LyP), in order to better characterize them at and assess whether the two entities are biologically related.
Design(s): Adequate RNA was successfully extracted from formalin-fixed paraffin embedded sections derived from 7 CD4+ MF, 8 CD8+ MF and 4 type D LyP. After passing quality control, whole transcriptome sequencing (WTS) was performed. Fusion detection was performed using star-fusion (version 1.10.0). Accurate transcript quantification from RNASEQ data was performed using RSEM (version 1.3.1). DESEQ2 was used for differential gene expression (DGE) analysis, comparing CD8+ MF vs CD4+MF, CD8+ MF vs type D LyP groups, after normalization against normal skin controls.
Result(s): Unsupervised clustering classified CD4+ MF and CD8+ MF into two distinct groups and identified 100 genes that were differentially expressed at a significant level between both entities (Figure 1 a). CD8+ MF shows a profound down regulation of skin-homing chemokine receptors, immune signaling-related molecules or transcription factors and upregulation of long non-coding RNAs (lncRNAs) and small nuclear RNAs (snRNAs) (Figure 1a). KEGG pathway analysis showed an upregulation of pathways related to linoleic acid metabolism, as well as retinoid acid, PPAR and adipocytokine signaling in CD8+ MF (Figure 1b). Unsupervised clustering did not segregate CD8+ MF and Type D LyP. Nevertheless, DGE analysis identified 546 genes that were differentially expressed between both (FDR<0.01, fold change: > 1 or < -1, Figure 1c). KEGG pathway analysis showed that Wnt signaling is significantly upregulated in CD8+ MF compared to Type D LyP. A recurrent mRNA-lncRNA fusion secondary to interstitial deletion involving RP11-367G6.3-FAM65B (Figure 1d) was identified in 5 cases from 4 unique patients, including 2 type D LyP and 2 CD8+ MF patients.
Conclusion(s): WTS shows that CD8+ MF has unique signatures compared to CD4+MF pertaining to lncRNAs and snRNAs. Type D LyP and CD8+ MF display similar genomic rearrangements, yet pathway analysis highlights different genes contributing to their pathogenesis