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Genomic and transcriptomic analyses of NF1-mutant melanoma identify potential targeted approach for treatment

Jour, George; Illa-Bochaca, Irineu; Ibrahim, Milad; Donnelly, Douglas; Zhu, Kelsey; Vega-Saenz de Miera, Eleazar; Vasudevaraja, Varshini; Mezzano, Valeria; Ramswami, Sitharam; Yeh, Yu-Hsin; Winskill, Carolyn; Betensky, Rebecca A; Mehnert, Janice; Osman, Iman
There is currently no targeted therapy to treat NF1-mutant melanomas. Herein, we compared the genomic and transcriptomic signatures of NF1-mutant and NF1-WT melanoma to reveal potential treatment targets for this subset of patients. Genomic alterations were verified using qPCR, and differentially expressed genes were independently validated using TCGA data, and immunohistochemistry (IHC). Digital spatial profiling (DSP) with multiplex IHC and immunofluorescence (IF) were used to validate the signatures. The efficacy of combinational regimens driven by these signatures was tested through in vitro assays using low-passage cell lines. Pathogenic NF1 mutations were identified in 27% cases. NF1-mutant melanoma expressed higher proliferative markers MK167 and CDC20 compared to NF1-WT (P=0.008), which was independently validated both in the TCGA dataset (P=0.01, P=0.03) and with IHC (P=0.013, P=0.036), respectively. DSP analysis showed upregulation of LY6E within the tumor cells [FDR<0.01, lg2FC>1], confirmed with multiplex IF showing co-localization of LY6E in melanoma cells. The combination of MEK and CDC20 co-inhibition induced both cytotoxic and cytostatic effects, decreasing CDC20 expression in multiple NF1-MUT cell lines. In conclusion, NF1-mutant melanoma is associated with a distinct genomic and transcriptomic profile. Our data support investigating CDC20 inhibition with MAPK pathway inhibitors as a targeted regimen in this melanoma subtype.
PMID: 35988589
ISSN: 1523-1747
CID: 5338052

Erdheim-Chester Disease with BRAF V600E Mutation and a Concomitant Myeloid Malignancy Sharing NRAS and IDH2 Mutations [Case Report]

Prabhakaran, Nitya; Jour, George; Balar, Arjun; Ward, Nicholas
Erdheim-Chester disease (ECD) is a rare clonal histiocytic process that is characterized by a foamy (xanthomatous) proliferation often associated with Touton giant cells. The diagnosis is often challenging and not exclusively a histologic diagnosis, as it requires correlation with unique clinical, radiographic and recently described molecular findings. Activating mutations involving the MAPK pathway including BRAF, ARAF, N/KRAS and MEK are recurrent in the disease. However, it is increasingly being described that mutations associated with clonal hematopoiesis are also found in bone marrow specimens of patients with Erdheim-Chester disease (ECD), as well as higher frequency of overt concomitant myeloid malignancy including acute myeloid leukemia, myeloproliferative neoplasms, myelodysplastic syndromes, and mixed myeloproliferative neoplasms/myelodysplastic syndromes. Herein, we report a unique case of a patient presenting with BRAF-V600E-positive ECD with with peripheral blood findings consistent with a concurrent myeloid malignancy featuring co-occurrence of NRAS and IDH-2 mutations.
PMID: 36754028
ISSN: 1421-9662
CID: 5431072

Case Report: Giant Thyroid Angiolipoma-Challenging Clinical Diagnosis and Novel Genetic Alterations

Wilkins, Reid; Zan, Elcin; Leonardi, Olga; Patel, Kepal N; Jacobson, Adam S; Jour, George; Liu, Cheng Z; Zhou, Fang
BACKGROUND:A 64-year-old man presented with a 7.8 cm lipomatous thyroid mass discovered on magnetic resonance imaging. METHODS:After two non-diagnostic fine needle aspirations (FNAs) were performed, computed tomography (CT) revealed features concerning for malignancy including central necrosis and infiltrative borders. A third FNA was still non-diagnostic. Total thyroidectomy was performed. RESULTS:Upon pathologic examination, the final diagnosis was primary thyroid angiolipoma. The lesion contained central fat necrosis with ischemic features, attributable to the FNAs. CONCLUSION/CONCLUSIONS:Ours is the third published case report of this rare entity. To date, no lipomatous thyroid tumor has undergone extensive genomic testing. Next-generation sequencing of our case revealed multiple genetic alterations, supporting the concept of angiolipomas being true neoplasms. Whereas the two previously reported cases in the literature were radiographically much smaller and appeared indolent, the large tumor in our case exhibited radiographic features concerning for liposarcoma, which belied the benign final pathologic diagnosis. Our case demonstrates that conservative surgical management (partial thyroidectomy) may be considered for lipomatous thyroid tumors, with further interventions to be determined only after final pathologic diagnosis.
PMID: 36255668
ISSN: 1936-0568
CID: 5360392

Cutaneous Inflammatory Myofibroblastic Tumor with CARS-ALK Fusion: Case Report and Literature Review [Case Report]

McCollum, Kasey J; Jour, George; Al-Rohil, Rami N
Cutaneous inflammatory myofibroblastic tumors (IMT) constitute a rare entity, generating a diagnostic pitfall when diagnosing spindle cell proliferation within the dermis. Raising awareness of this tumor among dermatopathologists remains vital in differentiating it from common cutaneous tumors such as fibrous histiocytoma, atypical fibroxanthoma, melanoma, poorly differentiated carcinoma, and other more aggressive tumors. Accurate diagnosis of IMT aid in ensuring appropriate management and follow-up for patients while preventing unnecessary harm and overtreatment. Here we report a case of a 38-year-old female with a painless, slow-growing nodule of the left posterior scalp initially diagnosed as a dermatofibroma. The histological examination revealed an ill-defined dermal nodule of spindled cells without connection or infiltration of the epidermis. At high power, the cells were arranged in fascicles with a prominent background of lymphocytic infiltrate. Immunohistochemical analysis showed strong diffuse immunoreactivity for anaplastic lymphoma kinase (ALK), targeted RNA sequencing identified a CARS-ALK fusion ultimately confirming the accurate diagnosis of a cutaneous IMT. This article is protected by copyright. All rights reserved.
PMID: 35560368
ISSN: 1600-0560
CID: 5214932

Deep learning and pathomics analyses reveal cell nuclei as important features for mutation prediction of BRAF-mutated melanomas

Kim, Randie H; Nomikou, Sofia; Coudray, Nicolas; Jour, George; Dawood, Zarmeena; Hong, Runyu; Esteva, Eduardo; Sakellaropoulos, Theodore; Donnelly, Douglas; Moran, Una; Hatzimemos, Aristides; Weber, Jeffrey S; Razavian, Narges; Aifantis, Iannis; Fenyo, David; Snuderl, Matija; Shapiro, Richard; Berman, Russell S; Osman, Iman; Tsirigos, Aristotelis
Image-based analysis as a method for mutation detection can be advantageous in settings when tumor tissue is limited or unavailable for direct testing. Here, we utilize two distinct and complementary machine learning methods of analyzing whole slide images (WSI) for predicting mutated BRAF. In the first method, WSI of melanomas from 256 patients were used to train a deep convolutional neural network (CNN) in order to develop a fully automated model that first selects for tumor-rich areas (Area Under the Curve AUC=0.96) then predicts for mutated BRAF (AUC=0.71). Saliency mapping was performed and revealed that pixels corresponding to nuclei were the most relevant to network learning. In the second method, WSI were analyzed using a pathomics pipeline that first annotates nuclei and then quantifies nuclear features, demonstrating that mutated BRAF nuclei were significantly larger and rounder nuclei compared to BRAF WT nuclei. Lastly, we developed a model that combines clinical information, deep learning, and pathomics that improves the predictive performance for mutated BRAF to AUC=0.89. Not only does this provide additional insights on how BRAF mutations affect tumor structural characteristics, machine learning-based analysis of WSI has the potential to be integrated into higher order models for understanding tumor biology.
PMID: 34757067
ISSN: 1523-1747
CID: 5050512

Detection of gene fusions, cryptic rearrangements, and gene regulatory interactions in brain tumors by whole-genome Hi-C [Meeting Abstract]

Galbraith, K; Yang, Y; Mohamed, H; Movahed-Ezazi, M; Tran, I; Zeck, B; Chiriboga, L; Sikkink, K; Schmitt, A; Tsirigos, A; Jour, G; Snuderl, M
Introduction: Gene rearrangements play a critical role in the development of brain tumors. RNA next-generation sequencing (NGS) panels cover a limited number of genes, are rarely successful in FFPE samples > 5 years old, and cannot detect rearrangements between genes and non-coding regulatory regions. We evaluated whole genome Hi-C NGS for detection of gene fusions and cryptic rearrangements.
Method(s): DNA was extracted from FFPE scrolls of 55 glial and non-glial brain tumors and processed using Arima-HiC+ FFPE Sample protocol, consisting of chromatin fragmentation, labeling, and re-ligation, followed by DNA purification and library preparation for paired-end Illumina sequencing with an average of 10X genome coverage (100M PE reads per sample). Data were analyzed using the Arima-SV pipeline using Juicer and HiCUP, SV detection using HiC-Breakfinder, loop calling using Juicer Tools, and integrative data visualization using Juicebox. Overexpression of putative driver genes was confirmed by immunohistochemistry.
Result(s): Hi-C libraries were prepared and sequenced from FFPE tissues including samples that failed RNA NGS. Hi-C successfully detected gene-gene fusions including actionable EML4-NTRK3, ETV6-NTRK3, fusions. We detected rearrangements missed by RNA NGS (i.e., complex MYBL1 rearrangement) or between non-coding regions and known cancer genes (i.e. PDL1, PAX5, NRAS, TERT, KAT6A, GATA6, and ARID1B). Since Hi-C data captures 3D genome structural features such as chromatin loops and topological domains, datasets were of high quality and capable of detecting up to 13,000 chromatin loops per tumor.
Conclusion(s): Genome-wide Hi-C NGS is successful in detecting gene fusions and cryptic rearrangements between coding and non-coding regions in archival FFPE tissue including degraded samples. Because Hi-C data captures 3D genome structures, these datasets simultaneously inform gene regulatory mechanisms that may play a role in oncogenesis or tumor progression. Whole-genome Hi-C NGS expands our ability to detect actionable and novel drivers, and potentially new therapeutic targets in a single NGS workflow
ISSN: 1554-6578
CID: 5292482

Melanoma-secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis

Kleffman, Kevin; Levinson, Grace; Rose, Indigo V L; Blumenberg, Lili M; Shadaloey, Sorin A A; Dhabaria, Avantika; Wong, Eitan; Galan-Echevarria, Francisco; Karz, Alcida; Argibay, Diana; Von Itter, Richard; Floristan, Alfredo; Baptiste, Gillian; Eskow, Nicole M; Tranos, James A; Chen, Jenny; Vega Y Saenz de Miera, Eleazar C; Call, Melissa; Rogers, Robert; Jour, George; Wadghiri, Youssef Zaim; Osman, Iman; Li, Yue-Ming; Mathews, Paul; DeMattos, Ronald; Ueberheide, Beatrix; Ruggles, Kelly V; Liddelow, Shane A; Schneider, Robert J; Hernando, Eva
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.
PMID: 35262173
ISSN: 2159-8290
CID: 5183542

Integrated analysis of ovarian juvenile granulosa cell tumors reveals distinct epigenetic signatures and recurrent TERT rearrangements

Vougiouklakis, Theodore; Zhu, Kelsey; Vasudevaraja, Varshini; Serrano, Jonathan; Shen, Guomiao; Linn, Rebecca L; Feng, Xiaojun; Chiang, Sarah; Barroeta, Julieta E; Thomas, Kristen M; Schwartz, Lauren E; Shukla, Pratibha S; Malpica, Anais; Oliva, Esther; Cotzia, Paolo; DeLair, Deborah F; Snuderl, Matija; Jour, George
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.
PMID: 35031544
ISSN: 1557-3265
CID: 5119182

Primary Pulmonary Round Cell Sarcomas: Multiple Potential Pitfalls for the Pathologist

Richards, Ryland; Jour, George; Tafe, Laura J; Pinto, Andre; Brčić, Iva; Linos, Konstantinos; Kerr, Darcy A
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.
PMID: 35404156
ISSN: 1940-2465
CID: 5204262

Multi-omics Analysis of Digital Papillary Adenocarcinoma Reveals Upregulation of MAGEA4 and Infrequent Zinc Finger Genes Rearrangements [Meeting Abstract]

Aung, P; Gill, P; Lai, Z; Zhu, K; Vasudevaraja, V; Ivan, D; Nagarajan, P; Cheal, Cho W; Ballester, L; Curry, J; Torres-Cabala, C; Prieto, V; Jour, G
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
ISSN: 1530-0285
CID: 5252092