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Automated digital TIL analysis (ADTA) adds prognostic value to standard assessment of depth and ulceration in primary melanoma

Moore, Michael R; Friesner, Isabel D; Rizk, Emanuelle M; Fullerton, Benjamin T; Mondal, Manas; Trager, Megan H; Mendelson, Karen; Chikeka, Ijeuru; Kurc, Tahsin; Gupta, Rajarsi; Rohr, Bethany R; Robinson, Eric J; Acs, Balazs; Chang, Rui; Kluger, Harriet; Taback, Bret; Geskin, Larisa J; Horst, Basil; Gardner, Kevin; Niedt, George; Celebi, Julide T; Gartrell-Corrado, Robyn D; Messina, Jane; Ferringer, Tammie; Rimm, David L; Saltz, Joel; Wang, Jing; Vanguri, Rami; Saenger, Yvonne M
Accurate prognostic biomarkers in early-stage melanoma are urgently needed to stratify patients for clinical trials of adjuvant therapy. We applied a previously developed open source deep learning algorithm to detect tumor-infiltrating lymphocytes (TILs) in hematoxylin and eosin (H&E) images of early-stage melanomas. We tested whether automated digital (TIL) analysis (ADTA) improved accuracy of prediction of disease specific survival (DSS) based on current pathology standards. ADTA was applied to a training cohort (n = 80) and a cutoff value was defined based on a Receiver Operating Curve. ADTA was then applied to a validation cohort (n = 145) and the previously determined cutoff value was used to stratify high and low risk patients, as demonstrated by Kaplan-Meier analysis (p ≤ 0.001). Multivariable Cox proportional hazards analysis was performed using ADTA, depth, and ulceration as co-variables and showed that ADTA contributed to DSS prediction (HR: 4.18, CI 1.51-11.58, p = 0.006). ADTA provides an effective and attainable assessment of TILs and should be further evaluated in larger studies for inclusion in staging algorithms.
PMID: 33531581
ISSN: 2045-2322
CID: 4789702

An integrative approach identifies dysregulated long non-coding RNAs as microRNA decoys during nevus to melanoma transformation

Chang, Li-Wei; Badal, Brateil; Lu, Ching-Jung; Solovyov, Alexander; Greenbaum, Benjamin D; Celebi, Julide Tok
Mounting evidence supports a role for dysregulated long non-coding RNAs (lncRNA) in the development of many cancers. A recently discovered function of lncRNAs is to act as microRNA (miR) decoys or competing endogenous RNAs, which sequester specific miRs and relieve negative regulation of mRNA expression by miRs. Although a large number of non-coding RNAs are thought to function as competing endogenous RNAs, miR-sequestering lncRNAs involved in nevus to melanoma transformation remain largely unknown. In this study, we applied a bioinformatics approach to a unique dataset of benign melanocytic nevi and primary melanomas of the skin in order to fill this research gap. We modified a previously published miR target prediction algorithm, RNAhybrid, and improved its search efficiency. We reported the presence of many lncRNAs and miRs deregulated when transitioning from a senescence-like state of nevi to melanoma. We provided evidence of a relatively new and understudied mechanism of gene regulation during this process and identified for the first time lncRNAs (n = 122) that may potentially function as miR decoys as well as their target miRs during nevus to melanoma transformation. The knowledge presented here can be employed for developing biomarkers for diagnostic and risk stratification purposes.
PMID: 32976222
ISSN: 1473-5636
CID: 5181292

Genomic analysis of metastatic melanoma in an adult with giant congenital melanocytic nevus [Letter]

Chang, Li-Wei; Iqbal, Ramiz; Badal, Brateil; Bernstein, Daniel; Mendelson, Karen; Solovyov, Alexander; Friedlander, Philip; Phelps, Robert; Goodheart, Herbert; Desman, Garrett; Greenbaum, Benjamin D; Tok Celebi, Julide
PMID: 32096295
ISSN: 1755-148x
CID: 5181392

FBXW7 regulates a mitochondrial transcription program by modulating MITF

Abbate, Franco; Badal, Brateil; Mendelson, Karen; Aydin, Iraz T; Serasinghe, Madhavika N; Iqbal, Ramiz; Mohammed, Jarvier N; Solovyov, Alexander; Greenbaum, Benjamin D; Chipuk, Jerry E; Celebi, Julide T
FBXW7 is well characterized as a tumor suppressor in many human cancers including melanoma; however, the mechanisms of tumor-suppressive function have not been fully elucidated. We leveraged two distinct RNA sequencing datasets: human melanoma cell lines (n = 10) with control versus silenced FBXW7 and a cohort of human melanoma tumor samples (n = 51) to define the transcriptomic fingerprint regulated by FBXW7. Here, we report that loss of FBXW7 enhances a mitochondrial gene transcriptional program that is dependent on MITF in human melanoma and confers poor patient outcomes. MITF is a lineage-specific master regulator of melanocytes and together with PGC-1alpha is a marker for melanoma subtypes with dependence for mitochondrial oxidative metabolism. We found that inactivation of FBXW7 elevates MITF protein levels in melanoma cells. In vitro studies examining loss of FBXW7 and MITF alone or in combination showed that FBXW7 is an upstream regulator for the MITF/PGC-1 signaling.
PMID: 29665239
ISSN: 1755-148x
CID: 5181282

Dual suppression of inner and outer mitochondrial membrane functions augments apoptotic responses to oncogenic MAPK inhibition

Serasinghe, Madhavika N; Gelles, Jesse D; Li, Kent; Zhao, Lauren; Abbate, Franco; Syku, Marie; Mohammed, Jarvier N; Badal, Brateil; Rangel, Cuahutlehuanitzin A; Hoehn, Kyle L; Celebi, Julide Tok; Chipuk, Jerry Edward
Mitogen-activated protein kinase (MAPK) pathway inhibitors show promise in treating melanoma, but are unsuccessful in achieving long-term remission. Concordant with clinical data, BRAFV600E melanoma cells eliminate glycolysis upon inhibition of BRAFV600E or MEK with the targeted therapies Vemurafenib or Trametinib, respectively. Consequently, exposure to these therapies reprograms cellular metabolism to increase mitochondrial respiration and restrain cell death commitment. As the inner mitochondrial membrane (IMM) is sub-organellar site of oxidative phosphorylation (OXPHOS), and the outer mitochondrial membrane (OMM) is the major site of anti-apoptotic BCL-2 protein function, we hypothesized that suppressing these critical mitochondrial membrane functions would be a rational approach to maximize the pro-apoptotic effect of MAPK inhibition. Here, we demonstrate that disruption of OXPHOS with the mitochondria-specific protonophore BAM15 promotes the mitochondrial pathway of apoptosis only when oncogenic MAPK signaling is inhibited. Based on RNA-sequencing analyses of nevi and primary melanoma samples, increased pro-apoptotic BCL-2 family expression positively correlates with high-risk disease suggesting a highly active anti-apoptotic BCL-2 protein repertoire likely contributes to worse outcome. Indeed, combined inhibition of the anti-apoptotic BCL-2 repertoire with BH3-mimetics, OXPHOS, and oncogenic MAPK signaling induces fulminant apoptosis and eliminates clonogenic survival. Altogether, these data suggest that dual suppression of IMM and OMM functions may unleash the normally inadequate pro-apoptotic effects of oncogenic MAPK inhibition to eradicate cancer cells, thus preventing the development of resistant disease, and ultimately, supporting long-term remission.
PMID: 29348439
ISSN: 2041-4889
CID: 5181272

Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation

Badal, Brateil; Solovyov, Alexander; Di Cecilia, Serena; Chan, Joseph Minhow; Chang, Li-Wei; Iqbal, Ramiz; Aydin, Iraz T; Rajan, Geena S; Chen, Chen; Abbate, Franco; Arora, Kshitij S; Tanne, Antoine; Gruber, Stephen B; Johnson, Timothy M; Fullen, Douglas R; Raskin, Leon; Phelps, Robert; Bhardwaj, Nina; Bernstein, Emily; Ting, David T; Brunner, Georg; Schadt, Eric E; Greenbaum, Benjamin D; Celebi, Julide Tok
BACKGROUND:Melanoma is a heterogeneous malignancy. We set out to identify the molecular underpinnings of high-risk melanomas, those that are likely to progress rapidly, metastasize, and result in poor outcomes. METHODS:We examined transcriptome changes from benign states to early-, intermediate-, and late-stage tumors using a set of 78 treatment-naive melanocytic tumors consisting of primary melanomas of the skin and benign melanocytic lesions. We utilized a next-generation sequencing platform that enabled a comprehensive analysis of protein-coding and -noncoding RNA transcripts. RESULTS:Gene expression changes unequivocally discriminated between benign and malignant states, and a dual epigenetic and immune signature emerged defining this transition. To our knowledge, we discovered previously unrecognized melanoma subtypes. A high-risk primary melanoma subset was distinguished by a 122-epigenetic gene signature ("epigenetic" cluster) and TP53 family gene deregulation (TP53, TP63, and TP73). This subtype associated with poor overall survival and showed enrichment of cell cycle genes. Noncoding repetitive element transcripts (LINEs, SINEs, and ERVs) that can result in immunostimulatory signals recapitulating a state of "viral mimicry" were significantly repressed. The high-risk subtype and its poor predictive characteristics were validated in several independent cohorts. Additionally, primary melanomas distinguished by specific immune signatures ("immune" clusters) were identified. CONCLUSION/CONCLUSIONS:The TP53 family of genes and genes regulating the epigenetic machinery demonstrate strong prognostic and biological relevance during progression of early disease. Gene expression profiling of protein-coding and -noncoding RNA transcripts may be a better predictor for disease course in melanoma. This study outlines the transcriptional interplay of the cancer cell's epigenome with the immune milieu with potential for future therapeutic targeting. FUNDING/BACKGROUND:National Institutes of Health (CA154683, CA158557, CA177940, CA087497-13), Tisch Cancer Institute, Melanoma Research Foundation, the Dow Family Charitable Foundation, and the Icahn School of Medicine at Mount Sinai.
PMID: 28469092
ISSN: 2379-3708
CID: 5181252

Genomic Characterization of Dysplastic Nevi Unveils Implications for Diagnosis of Melanoma

Melamed, Rachel D; Aydin, Iraz T; Rajan, Geena Susan; Phelps, Robert; Silvers, David N; Emmett, Kevin J; Brunner, Georg; Rabadan, Raul; Celebi, Julide Tok
A well-defined risk factor and precursor for cutaneous melanoma is the dysplastic nevus. These benign tumors represent clonal hyperproliferation of melanocytes that are in a senescent-like state, but with occasional malignant transformation events. To portray the mutational repertoire of dysplastic nevi in patients with the dysplastic nevus syndrome and to determine the discriminatory profiles of melanocytic nevi (including dysplastic nevi) from melanoma, we sequenced exomes of melanocytic nevi including dysplastic nevi (n = 19), followed by a targeted gene panel (785 genes) characterization of melanocytic nevi (n = 46) and primary melanomas (n = 42). Exome sequencing revealed that dysplastic nevi harbored a substantially lower mutational load than melanomas (21 protein-changing mutations versus >100). Known "driver" mutations in genes for melanoma, including CDKN2A, TP53, NF1, RAC1, and PTEN, were not found among any melanocytic nevi sequenced. Additionally, melanocytic nevi including dysplastic nevi showed a significantly lower frequency and a different UV-associated mutational signature. These results show that although melanocytic nevi and dysplastic nevi harbor stable genomes with relatively few alterations, progression into melanomas requires additional mutational processes affecting key tumor suppressors. This study identifies molecular parameters that could be useful for diagnostic platforms.
PMID: 27890785
ISSN: 1523-1747
CID: 5181242

FBXW7 inactivation in a BrafV600E -driven mouse model leads to melanoma development [Letter]

Aydin, Iraz T; Abbate, Franco; Rajan, Geena Susan; Badal, Brateil; Aifantis, Iannis; Desman, Garrett; Celebi, Julide Tok
PMID: 28581198
ISSN: 1755-148x
CID: 5181262

Activation of the Mitochondrial Fragmentation Protein DRP1 Correlates with BRAF(V600E) Melanoma [Letter]

Wieder, Shira Y; Serasinghe, Madhavika N; Sung, Julie C; Choi, Daniel C; Birge, Miriam B; Yao, Jonathan L; Bernstein, Emily; Celebi, Julide T; Chipuk, Jerry E
PMID: 26032958
ISSN: 1523-1747
CID: 5181222

FBXW7 modulates cellular stress response and metastatic potential through HSF1 post-translational modification

Kourtis, Nikos; Moubarak, Rana S; Aranda-Orgilles, Beatriz; Lui, Kevin; Aydin, Iraz T; Trimarchi, Thomas; Darvishian, Farbod; Salvaggio, Christine; Zhong, Judy; Bhatt, Kamala; Chen, Emily I; Celebi, Julide T; Lazaris, Charalampos; Tsirigos, Aristotelis; Osman, Iman; Hernando, Eva; Aifantis, Iannis
Heat-shock factor 1 (HSF1) orchestrates the heat-shock response in eukaryotes. Although this pathway has evolved to help cells adapt in the presence of challenging conditions, it is co-opted in cancer to support malignancy. However, the mechanisms that regulate HSF1 and thus cellular stress response are poorly understood. Here we show that the ubiquitin ligase FBXW7alpha interacts with HSF1 through a conserved motif phosphorylated by GSK3beta and ERK1. FBXW7alpha ubiquitylates HSF1 and loss of FBXW7alpha results in impaired degradation of nuclear HSF1 and defective heat-shock response attenuation. FBXW7alpha is either mutated or transcriptionally downregulated in melanoma and HSF1 nuclear stabilization correlates with increased metastatic potential and disease progression. FBXW7alpha deficiency and subsequent HSF1 accumulation activates an invasion-supportive transcriptional program and enhances the metastatic potential of human melanoma cells. These findings identify a post-translational mechanism of regulation of the HSF1 transcriptional program both in the presence of exogenous stress and in cancer.
PMID: 25720964
ISSN: 1465-7392
CID: 1474022