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Predicting BRAF and NRAS Mutations Using Deep Learning on Histopathology Images of Melanoma [Meeting Abstract]
Kim, Randie; Nomikou, Sofia; Dawood, Zarmeena; Coudray, Nicolas; Jour, George; Moran, Una; Razavian, Narges; Osman, Iman; Tsirigos, Aristotelis
ISI:000478081100486
ISSN: 0023-6837
CID: 4048332
Long Noncoding RNAs (LncRNAs) Signatures in Prostate Cancer: External Validation with The Cancer Genome Atlas (TCGA) database [Meeting Abstract]
Parimi (Parini), Vamsi; Vasudevaraja, Varshini; Xia, Yuhe; Selvaraj, Shanmugapriya; Mezzano, Valeria; Jour, George; Snuderl, Matija; Tsirigos, Aristotelis; Deng, Fangming; Melamed, Jonathan
ISI:000478081101390
ISSN: 0023-6837
CID: 4048392
Comparative Study of Lower Limit of Detection of EGFRvIII Variant Detection Using Amplicon-Based NGS Testing and RT-PCR [Meeting Abstract]
Shen, G.; Vougiouklakis, T.; Snuderl, M.; Cotzia, P.; Park, K.; Jour, G.; Feng, X.
ISI:000496996500419
ISSN: 1525-1578
CID: 4222302
Dermal xanthomatous infiltrates after brentuximab vedotin therapy in mycosis fungoides with large cell transformation: a novel histologic finding [Case Report]
Buchely, Natalia; Al-Rohil, Rami; Aung, Phyu P; Jour, George; Torres-Cabala, Carlos; Prieto, Victor G; Ivan, Doina
Mycosis fungoides (MF) is the most common variant of cutaneous T-cell lymphomas (CTCL). Large cell transformation of MF has been associated with disease progression and overall poor outcome. The expression of CD30, which defines anaplastic large cell lymphoma (ALCL) and lymphomatoid papulosis (LyP), might also occur in a subset of patients with MF, with or without large cell transformation. Brentuximab vedotin is an anti-CD30 monoclonal antibody which has been proven to be a safe and effective therapeutic agent in the treatment of CD30-positive lymphomas, such as Hodgkin lymphoma and ALCL. Recently, brentuximab vedotin has been shown to have a significant clinical activity in treatment-refractory or advanced MF or Sezary syndrome (SS) with a wide-range of CD30 expression levels. We report a patient with MF tumor stage with large cell transformation and low CD30 expression with good response to brentuximab vedotin and unusual extensive xanthomatous changes in the follow-up biopsy.
PMID: 29806104
ISSN: 1600-0560
CID: 3135922
Novel enriched pathways in superficial malignant peripheral nerve sheath tumours and spindle/desmoplastic melanomas
Jour, George; Andeen, Nicole K; Al-Rohil, Rami; Aung, Phyu P; Mehrotra, Meenakshi; Duose, Dzifa; Hoch, Benjamin; Argenyi, Zolt; Luthra, Rajyalakshmi; Wistuba, Ignacio I; Prieto, Victor G
Superficial malignant peripheral nerve sheath tumour (MPNST) is a rare, soft tissue neoplasm that shares morphological features and some molecular events with spindle/desmoplastic melanoma (SDM). Herein, we sought to identify molecular targets for therapy by using targeted RNA/DNA sequencing and gene expression of key immunological players. DNA and RNA from formalin-fixed paraffin-embedded tissue were extracted and processed. Massive high-throughput deep parallel sequencing was performed with the Oncomine comprehensive panel, enabling detection of relevant single-nucleotide variants, copy number variations, gene fusions and indels for 143 unique genes on the Ion torrent sequencer for clinical trial research programmes. Gene expression analysis was carried out with a customized 770-gene expression panel combining markers for 24 different immune cell types and 30 common cancer antigens, including key checkpoint blockade genes analysed with the Ncounter system. Fifty-one patients (SDM, 16/11; MPNST, 24; male, n = 37; female, n = 16) had sufficient DNA and RNA for testing. NF1 deleterious mutations and/or deep/homozygous deletions were identified in 73% of MPNSTs and 67% of SDMs, with 50% of the mutations involving the RAS-binding domain. Inactivating/deleterious mutations of TSC1/TSC2 were identified in 40% and 41% of MPNSTs and SDMs, respectively. Activating mutations affecting the EGFR-like and the negative regulatory domains of NOTCH1 and KDR (VEGFR2) were identified in 45% and 40% of SDMs and in 30% and 8% of MPNSTs, respectively. Differential gene expression and gene clustering analysis showed significantly perturbed immune pathway components, including nuclear factor-κB (NF-κB), JAK-STAT, and CXCL12-CXCR4, and differentially expressed CD274 and CTLA4, in both SDM and MPNST. Angiogenesis (KDR and NOTCH1) and mammalian target of rapamycin complex (mTORC) pathways offer a rationale for anti-angiogenic and selective mTORC inhibition as treatment strategies for MPNST and SDM. Cytokines and the JAK-STAT, TNF and NF-κB axes were perturbed in both SDM and MPNST. These pathways have been targeted in haematological malignancies and present promising targets for these tumours.
PMID: 28991373
ISSN: 1096-9896
CID: 2835512
Differential expression of CCR4 in primary cutaneous gamma/delta (γâ„δ) T cell lymphomas and mycosis fungoides: Significance for diagnosis and therapy [Letter]
Jour, George; Aung, Phyu P; Merrill, E Dean; Curry, Jonathan L; Tetzlaff, Michael T; Nagarajan, Priyadharsini; Ivan, Doina; Prieto, Victor G; Duvic, Madeleine; Miranda, Roberto N; Torres-Cabala, Carlos A
PMID: 29030090
ISSN: 1873-569x
CID: 2835522
High amplification levels of MDM2 and CDK4 correlate with poor outcome in patients with dedifferentiated liposarcoma: A cytogenomic microarray analysis of 47 cases
Ricciotti, Robert W; Baraff, Aaron J; Jour, George; Kyriss, McKenna; Wu, Yu; Liu, Yuhua; Li, Shao-Chun; Hoch, Benjamin; Liu, Yajuan J
Dedifferentiated liposarcoma (DDLS) is characterized at the molecular level by amplification of genes within 12q13-15 including MDM2 and CDK4. However, other than FNCLCC grade, prognostic markers are limited. We aim to identify molecular prognostic markers for DDLS to help risk stratify patients. To this end, we studied 49 cases of DDLS in our institutional archives and performed cytogenomic microarray analysis on 47 cases. Gene copy numbers for 12 loci were evaluated and correlated with outcome data retrieved from our institutional electronic medical records. Using cut point analysis and comparison of Kaplan-Meier survival curves by log rank tests, high amplification levels of MDM2 (>38 copies) and CDK4 (>30 copies) correlated with decreased disease free survival (DFS) (P = .0168 and 0.0169 respectively) and disease specific survival (DSS) (P = .0082 and 0.0140 respectively). Additionally, MDM2 and CDK4 showed evidence of a synergistic effect so that each additional copy of one enhances the effect on prognosis of each additional copy of the other for decreased DFS (P = .0227, 0.1% hazard). High amplification of JUN (>16 copies) also correlated with decreased DFS (P = .0217), but not DSS. The presence of copy number alteration at 3q29 correlated with decreased DSS (P = .0192). The presence of >10 mitoses per 10 high power fields and FNCLCC grade 3 also correlated with decreased DFS (P = .0310 and 0.0254 respectively). MDM2 and CDK4 gene amplification levels, along with JUN amplification and copy alterations at 3q29, can be utilized for predicting outcome in patients with DDLS.
PMID: 29153098
ISSN: 2210-7762
CID: 3022912
Intraepidermal Merkel cell carcinoma: A case series of a rare entity with clinical follow up
Jour, George; Aung, Phyu P; Rozas-Muñoz, Eduardo; Curry, Johnathan L; Prieto, Victor; Ivan, Doina
BACKGROUND/BACKGROUND:Merkel cell carcinoma (MCC) is a rare but aggressive cutaneous carcinoma. MCC typically involves dermis and although epidermotropism has been reported, MCC strictly intraepidermal or in situ (MCCIS) is exceedingly rare. Most of the cases of MCCIS described so far have other associated lesions, such as squamous or basal cell carcinoma, actinic keratosis and so on. Herein, we describe 3 patients with MCC strictly in situ, without a dermal component. METHODS/METHODS:Our patients were elderly. 2 of the lesions involved the head and neck area and 1 was on a finger. All tumors were strictly intraepidermal in the diagnostic biopsies, and had histomorphologic features and an immunohistochemical profile supporting the diagnosis of MCC. Excisional biopsies were performed in 2 cases and failed to reveal dermal involvement by MCC or other associated malignancies. RESULTS AND CONCLUSION/CONCLUSIONS:Our findings raise the awareness that MCC strictly in situ does exist and it should be included in the differential diagnosis of Paget's or extramammary Paget's disease, pagetoid squamous cell carcinoma, melanoma and other neoplasms that typically show histologically pagetoid extension of neoplastic cells. Considering the limited number of cases reported to date, the diagnosis of isolated MCCIS should not warrant a change in management from the typical MCC.
PMID: 28543532
ISSN: 1600-0560
CID: 2835422
GNAS Mutations in Fibrous Dysplasia: A Comparative Study of Standard Sequencing and Locked Nucleic Acid PCR Sequencing on Decalcified and Nondecalcified Formalin-fixed Paraffin-embedded Tissues
Jour, George; Oultache, Alifya; Sadowska, Justyna; Mitchell, Talia; Healey, John; Nafa, Khedoudja; Hameed, Meera
It is well known that fibrous dysplasia (FD) is characterized by the presence of activating mutations involving G-nucleotide binding protein-α subunit (GNAS) involving codon R201 and rarely codon 227 with a mutation frequency between 45% and 93%. Herein, we investigate the sensitivity of detection of GNAS mutations in exons 8 and 9 using a standard and a highly sensitive locked nucleic acid polymerase chain reaction (LNA-PCR) sequencing in 52 cases of FD. In view of the recent report of GNAS mutations in a small number of low-grade osteosarcomas, we also tested in addition 12 cases of low-grade osteosarcomas. GNAS exon 8 mutations p.R201H (31%), p.R201C (15%), and p.R201S (2%) were identified in 50% of FD cases. LNA-PCR sequencing identified only 1 positive case within the mutation negative cases tested by standard PCR and Sanger sequencing. No mutations were identified in any of the low-grade osteosarcomas by standard and LNA-PCR sequencing. There was no association between age, site, size, specimen type, and mutational status. No exon 9 or codon 227 mutations were identified in any of tested cases. There was a significant difference in the sensitivity of the assay between decalcified and nondecalcified FDs (31% vs. 70%, P=0.002). LNA-PCR has no added value in enhancing detection sensitivity for GNAS mutations in FD. In addition to decalcification, innate somatic mosaicism contributes to the decreased sensitivity in mutation detection.
PMCID:5563825
PMID: 26574629
ISSN: 1533-4058
CID: 3022902
Autoimmune dermatologic toxicities from immune checkpoint blockade with anti-PD-1 antibody therapy: a report on bullous skin eruptions [Case Report]
Jour, George; Glitza, Isabella C; Ellis, Rachel M; Torres-Cabala, Carlos A; Tetzlaff, Michael T; Li, Janet Y; Nagarajan, Priyadharsini; Huen, Auris; Aung, Phyu P; Ivan, Doina; Drucker, Carol R; Prieto, Victor G; Rapini, Ronald P; Patel, Anisha; Curry, Jonathan L
Monoclonal antibodies against the immune checkpoint programmed cell death receptor 1 (PD-1) improve the hosts' antitumor immune response and have showed tremendous promise in the treatment of advanced solid tumors and hematologic malignancies. Reports of serious autoimmune dermatologic toxicities from immune checkpoint blockade therapy, however, are emerging. We report our experience with five patients who presented with pruritic vesicles and blisters on the skin while treated with anti-PD-1 antibody immunotherapy with either nivolumab or pembrolizumab. Four of the patients' skin biopsies revealed subepidermal bullae with immunohistochemical study for type IV collagen labeling the floor of the blister cavity and direct immunofluorescence studies (in three of the four patients tested) decorated linear IgG and C3 immune deposits on the blister roof, diagnostic of bullous pemphigoid. One patient developed bullous erythema multiforme. All patients had partial or complete resolution of skin lesions following treatment with systemic corticosteroid and cessation of checkpoint blockade. Recognition and treatment of rare immune-related bullous dermatologic toxicities will become increasingly important as more patients are treated with effective and newer immune checkpoint blockade therapy.
PMID: 27086658
ISSN: 1600-0560
CID: 2835372