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30 results on '"Caruso, Francesca P."'

1. Community assessment of methods to deconvolve cellular composition from bulk gene expression

Author

White, Brian S., de Reyniès, Aurélien, Newman, Aaron M., Waterfall, Joshua J., Lamb, Andrew, Petitprez, Florent, Lin, Yating, Yu, Rongshan, Guerrero-Gimenez, Martin E., Domanskyi, Sergii, Monaco, Gianni, Chung, Verena, Banerjee, Jineta, Derrick, Daniel, Valdeolivas, Alberto, Li, Haojun, Xiao, Xu, Wang, Shun, Zheng, Frank, Yang, Wenxian, Catania, Carlos A., Lang, Benjamin J., Bertus, Thomas J., Piermarocchi, Carlo, Caruso, Francesca P., Ceccarelli, Michele, Yu, Thomas, Guo, Xindi, Bletz, Julie, Coller, John, Maecker, Holden, Duault, Caroline, Shokoohi, Vida, Patel, Shailja, Liliental, Joanna E., Simon, Stockard, Saez-Rodriguez, Julio, Heiser, Laura M., Guinney, Justin, and Gentles, Andrew J.

Published
2024
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2. Epigenetic remodeling to improve the efficacy of immunotherapy in human glioblastoma: pre-clinical evidence for development of new immunotherapy approaches

Author

Lofiego, Maria Fortunata, Piazzini, Francesca, Caruso, Francesca Pia, Marzani, Francesco, Solmonese, Laura, Bello, Emma, Celesti, Fabrizio, Costa, Maria Claudia, Noviello, Teresa, Mortarini, Roberta, Anichini, Andrea, Ceccarelli, Michele, Coral, Sandra, Di Giacomo, Anna Maria, Maio, Michele, and Covre, Alessia

Published
2024
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4. Integrated molecular and multiparametric MRI mapping of high-grade glioma identifies regional biologic signatures

Author

Hu, Leland S., D’Angelo, Fulvio, Weiskittel, Taylor M., Caruso, Francesca P., Fortin Ensign, Shannon P., Blomquist, Mylan R., Flick, Matthew J., Wang, Lujia, Sereduk, Christopher P., Meng-Lin, Kevin, De Leon, Gustavo, Nespodzany, Ashley, Urcuyo, Javier C., Gonzales, Ashlyn C, Curtin, Lee, Lewis, Erika M., Singleton, Kyle W., Dondlinger, Timothy, Anil, Aliya, Semmineh, Natenael B., Noviello, Teresa, Patel, Reyna A., Wang, Panwen, Wang, Junwen, Eschbacher, Jennifer M., Hawkins-Daarud, Andrea, Jackson, Pamela R., Grunfeld, Itamar S., Elrod, Christian, Mazza, Gina L., McGee, Sam C., Paulson, Lisa, Clark-Swanson, Kamala, Lassiter-Morris, Yvette, Smith, Kris A., Nakaji, Peter, Bendok, Bernard R., Zimmerman, Richard S., Krishna, Chandan, Patra, Devi P., Patel, Naresh P., Lyons, Mark, Neal, Matthew, Donev, Kliment, Mrugala, Maciej M., Porter, Alyx B., Beeman, Scott C., Jensen, Todd R., Schmainda, Kathleen M., Zhou, Yuxiang, Baxter, Leslie C., Plaisier, Christopher L., Li, Jing, Li, Hu, Lasorella, Anna, Quarles, C. Chad, Swanson, Kristin R., Ceccarelli, Michele, Iavarone, Antonio, and Tran, Nhan L.

Published
2023
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5. Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial

Author

Noviello, Teresa Maria Rosaria, Di Giacomo, Anna Maria, Caruso, Francesca Pia, Covre, Alessia, Mortarini, Roberta, Scala, Giovanni, Costa, Maria Claudia, Coral, Sandra, Fridman, Wolf H., Sautès-Fridman, Catherine, Brich, Silvia, Pruneri, Giancarlo, Simonetti, Elena, Lofiego, Maria Fortunata, Tufano, Rossella, Bedognetti, Davide, Anichini, Andrea, Maio, Michele, and Ceccarelli, Michele

Published
2023
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7. Temporospatial genomic profiling in glioblastoma identifies commonly altered core pathways underlying tumor progression

Author

Blomquist, Mylan R, Ensign, Shannon Fortin, D’Angelo, Fulvio, Phillips, Joanna J, Ceccarelli, Michele, Peng, Sen, Halperin, Rebecca F, Caruso, Francesca P, Garofano, Luciano, Byron, Sara A, Liang, Winnie S, Craig, David W, Carpten, John D, Prados, Michael D, Trent, Jeffrey M, Berens, Michael E, Iavarone, Antonio, Dhruv, Harshil, and Tran, Nhan L

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Clinical Research, Brain Cancer, Rare Diseases, Genetics, Human Genome, Cancer, Neurosciences, Brain Disorders, Aetiology, 2.1 Biological and endogenous factors, clonal evolution, contrast enhancement, glioblastoma, PI3K signaling, temporospatial heterogeneity
Abstract

BackgroundTumor heterogeneity underlies resistance and disease progression in glioblastoma (GBM), and tumors most commonly recur adjacent to the surgical resection margins in contrast non-enhancing (NE) regions. To date, no targeted therapies have meaningfully altered overall patient survival in the up-front setting. The aim of this study was to characterize intratumoral heterogeneity in recurrent GBM using bulk samples from primary resection and recurrent samples taken from contrast-enhancing (EN) and contrast NE regions.MethodsWhole exome and RNA sequencing were performed on matched bulk primary and multiple recurrent EN and NE tumor samples from 16 GBM patients who received standard of care treatment alone or in combination with investigational clinical trial regimens.ResultsPrivate mutations emerge across multi-region sampling in recurrent tumors. Genomic clonal analysis revealed increased enrichment in gene alterations regulating the G2M checkpoint, Kras signaling, Wnt signaling, and DNA repair in recurrent disease. Subsequent functional studies identified augmented PI3K/AKT transcriptional and protein activity throughout progression, validated by phospho-protein levels. Moreover, a mesenchymal transcriptional signature was observed in recurrent EN regions, which differed from the proneural signature in recurrent NE regions.ConclusionsSubclonal populations observed within bulk resected primary GBMs transcriptionally evolve across tumor recurrence (EN and NE regions) and exhibit aberrant gene expression of common signaling pathways that persist despite standard or targeted therapy. Our findings provide evidence that there are both adaptive and clonally mediated dependencies of GBM on key pathways, such as the PI3K/AKT axis, for survival across recurrences.

Published
2020

8. Landscape of immune-related signatures induced by targeting of different epigenetic regulators in melanoma: implications for immunotherapy

Author

Anichini, Andrea, Molla, Alessandra, Nicolini, Gabriella, Perotti, Valentina Eleonora, Sgambelluri, Francesco, Covre, Alessia, Fazio, Carolina, Lofiego, Maria Fortunata, Di Giacomo, Anna Maria, Coral, Sandra, Manca, Antonella, Sini, Maria Cristina, Pisano, Marina, Noviello, Teresa, Caruso, Francesca, Brich, Silvia, Pruneri, Giancarlo, Maurichi, Andrea, Santinami, Mario, Ceccarelli, Michele, Palmieri, Giuseppe, Maio, Michele, and Mortarini, Roberta

Published
2022
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10. A novel microRNA signature for the detection of melanoma by liquid biopsy

Author

Sabato, Claudia, Noviello, Teresa Maria Rosaria, Covre, Alessia, Coral, Sandra, Caruso, Francesca Pia, Besharat, Zein Mersini, Splendiani, Elena, Masuelli, Laura, Battistelli, Cecilia, Vacca, Alessandra, Catanzaro, Giuseppina, Po, Agnese, Anichini, Andrea, Maio, Michele, Ceccarelli, Michele, Di Giacomo, Anna Maria, and Ferretti, Elisabetta

Published
2022
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12. Pathway-based classification of glioblastoma uncovers a mitochondrial subtype with therapeutic vulnerabilities

Author

Garofano, Luciano, Migliozzi, Simona, Oh, Young Taek, D’Angelo, Fulvio, Najac, Ryan D., Ko, Aram, Frangaj, Brulinda, Caruso, Francesca Pia, Yu, Kai, Yuan, Jinzhou, Zhao, Wenting, Di Stefano, Anna Luisa, Bielle, Franck, Jiang, Tao, Sims, Peter, Suvà, Mario L., Tang, Fuchou, Su, Xiao-Dong, Ceccarelli, Michele, Sanson, Marc, Lasorella, Anna, and Iavarone, Antonio

Published
2021
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13. The molecular landscape of glioma in patients with Neurofibromatosis 1

Author

D’Angelo, Fulvio, Ceccarelli, Michele, Tala, Garofano, Luciano, Zhang, Jing, Frattini, Véronique, Caruso, Francesca P., Lewis, Genevieve, Alfaro, Kristin D., Bauchet, Luc, Berzero, Giulia, Cachia, David, Cangiano, Mario, Capelle, Laurent, de Groot, John, DiMeco, Francesco, Ducray, François, Farah, Walid, Finocchiaro, Gaetano, Goutagny, Stéphane, Kamiya-Matsuoka, Carlos, Lavarino, Cinzia, Loiseau, Hugues, Lorgis, Véronique, Marras, Carlo E., McCutcheon, Ian, Nam, Do-Hyun, Ronchi, Susanna, Saletti, Veronica, Seizeur, Romuald, Slopis, John, Suñol, Mariona, Vandenbos, Fanny, Varlet, Pascale, Vidaud, Dominique, Watts, Colin, Tabar, Viviane, Reuss, David E., Kim, Seung-Ki, Meyronet, David, Mokhtari, Karima, Salvador, Hector, Bhat, Krishna P., Eoli, Marica, Sanson, Marc, Lasorella, Anna, and Iavarone, Antonio

Published
2019
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14. Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma

Author

Sa, Jason K., Chang, Nakho, Lee, Hye Won, Cho, Hee Jin, Ceccarelli, Michele, Cerulo, Luigi, Yin, Jinlong, Kim, Sung Soo, Caruso, Francesca P., Lee, Mijeong, Kim, Donggeon, Oh, Young Taek, Lee, Yeri, Her, Nam-Gu, Min, Byeongkwi, Kim, Hye-Jin, Jeong, Da Eun, Kim, Hye-Mi, Kim, Hyunho, Chung, Seok, Woo, Hyun Goo, Lee, Jeongwu, Kong, Doo-Sik, Seol, Ho Jun, Lee, Jung-Il, Kim, Jinho, Park, Woong-Yang, Wang, Qianghu, Sulman, Erik P., Heimberger, Amy B., Lim, Michael, Park, Jong Bae, Iavarone, Antonio, Verhaak, Roel G. W., and Nam, Do-Hyun

Published
2020
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15. Abstract 1507: Multiregional sampling of high grade glioma identifies regional biologic signatures

Author

Blomquist, Mylan R., primary, Hu, Leland S., additional, D'Angelo, Fulvio, additional, Weiskittel, Taylor M., additional, Caruso, Francesca P., additional, Ensign, Shannon P. Fortin, additional, Sereduk, Christopher, additional, De Leon, Gustavo, additional, Curtin, Lee, additional, Urcuyo, Javier, additional, Gonzalez, Ashlynn, additional, Nespodzany, Ashley, additional, Noviello, Teresa, additional, Eschbacher, Jennifer M., additional, Smith, Kris A., additional, Nakaji, Peter, additional, Bendok, Bernard R., additional, Zimmerman, Richard S., additional, Krishna, Chandan, additional, Patra, Devi, additional, Patel, Naresh, additional, Lyons, Mark, additional, Donev, Kliment, additional, Mrugala, Maciej, additional, Porter, Alyx, additional, Lasorella, Anna, additional, Swanson, Kristin R., additional, Ceccarelli, Michele, additional, Iavarone, Antonio, additional, and Tran, Nhan L., additional

Published
2023
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18. JAK/Stat5-mediated subtype-specific lymphocyte antigen 6 complex, locus G6D (LY6G6D) expression drives mismatch repair proficient colorectal cancer

Author

Giordano, Guido, Parcesepe, Pietro, D’Andrea, Mario Rosario, Coppola, Luigi, Di Raimo, Tania, Remo, Andrea, Manfrin, Erminia, Fiorini, Claudia, Scarpa, Aldo, Amoreo, Carla Azzurra, Conciatori, Fabiana, Milella, Michele, Caruso, Francesca Pia, Cerulo, Luigi, Porras, Almudena, and Pancione, Massimo

Published
2019
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19. Abstract 770: Multiregional imaging and genomic analysis in high-grade IDH-mutant astrocytoma identifies intratumor subclones with aggressive features

Author

Ensign, Shannon P. Fortin, primary, D'Angelo, Fulvio, additional, Caruso, Francesca P., additional, Sereduk, Christopher, additional, Singleton, Kyle, additional, Eschbacher, Jennifer, additional, Mazza, Gina, additional, Mrugala, Maciej, additional, Porter, Alyx, additional, Bendok, Bernard, additional, Zimmerman, Richard, additional, Smith, Kris, additional, Nakaji, Peter, additional, Swanson, Kamala, additional, Wang, Junwen, additional, Semmineh, Nathenael, additional, Quarles, Christopher, additional, Lasorella, Anna, additional, Swanson, Kristin, additional, Ceccarelli, Michele, additional, Iavarone, Antonio, additional, Hu, Leland, additional, and Tran, Nhan L., additional

Published
2022
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20. The molecular landscape of glioma in patients with Neurofibromatosis 1

Author

D'Angelo, Fulvio, Ceccarelli, Michele, Tala, Garofano, Luciano, Zhang, Jing, Frattini, Véronique, and Caruso, Francesca P.

Subjects
Neurofibromatosis -- Physiological aspects, Gliomas -- Genetic aspects -- Development and progression -- Care and treatment, Gene mutation -- Health aspects, Gene expression -- Health aspects, Biological sciences, Health
Abstract

Neurofibromatosis type 1 (NF1) is a common tumor predisposition syndrome in which glioma is one of the prevalent tumors. Gliomagenesis in NF1 results in a heterogeneous spectrum of low- to high-grade neoplasms occurring during the entire lifespan of patients. The pattern of genetic and epigenetic alterations of glioma that develops in NF1 patients and the similarities with sporadic glioma remain unknown. Here, we present the molecular landscape of low- and high-grade gliomas in patients affected by NF1 (NF1-glioma). We found that the predisposing germline mutation of the NF1 gene was frequently converted to homozygosity and the somatic mutational load of NF1-glioma was influenced by age and grade. High-grade tumors harbored genetic alterations of TP53 and CDKN2A, frequent mutations of ATRX associated with Alternative Lengthening of Telomere, and were enriched in genetic alterations of transcription/chromatin regulation and PI3 kinase pathways. Low-grade tumors exhibited fewer mutations that were over-represented in genes of the MAP kinase pathway. Approximately 50% of low-grade NF1-gliomas displayed an immune signature, T lymphocyte infiltrates, and increased neo-antigen load. DNA methylation assigned NF1-glioma to LGm6, a poorly defined Isocitrate Dehydrogenase 1 wild-type subgroup enriched with ATRX mutations. Thus, the profiling of NF1-glioma defined a distinct landscape that recapitulates a subset of sporadic tumors. An integrated analysis of glioma samples from patients with neurofibromatosis 1 annotates their mutational, epigenetic, transcriptional, and immunological features and uncovers similitudes with a subset of sporadic gliomas., Author(s): Fulvio D'Angelo [sup.1] [sup.2] , Michele Ceccarelli [sup.2] [sup.3] , Tala [sup.1] , Luciano Garofano [sup.1] [sup.2] , Jing Zhang [sup.1] , Véronique Frattini [sup.1] , Francesca P. Caruso [...]

Published
2019
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21. Additional file 2 of Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma

Author

Sa, Jason K., Nakho Chang, Lee, Hye Won, Cho, Hee Jin, Ceccarelli, Michele, Cerulo, Luigi, Jinlong Yin, Kim, Sung Soo, Caruso, Francesca P., Mijeong Lee, Donggeon Kim, Oh, Young Taek, Yeri Lee, Nam-Gu Her, Byeongkwi Min, Kim, Hye-Jin, Jeong, Da Eun, Kim, Hye-Mi, Hyunho Kim, Chung, Seok, Woo, Hyun Goo, Jeongwu Lee, Doo-Sik Kong, Seol, Ho Jun, Lee, Jung-Il, Jinho Kim, Woong-Yang Park, Qianghu Wang, Sulman, Erik P., Heimberger, Amy B., Lim, Michael, Park, Jong Bae, Iavarone, Antonio, Verhaak, Roel G. W., and Do-Hyun Nam

Abstract

Additional file 2. Review History.

Published
2020
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22. Additional file 1 of Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma

Author

Sa, Jason K., Nakho Chang, Lee, Hye Won, Cho, Hee Jin, Ceccarelli, Michele, Cerulo, Luigi, Jinlong Yin, Kim, Sung Soo, Caruso, Francesca P., Mijeong Lee, Donggeon Kim, Oh, Young Taek, Yeri Lee, Nam-Gu Her, Byeongkwi Min, Kim, Hye-Jin, Jeong, Da Eun, Kim, Hye-Mi, Hyunho Kim, Chung, Seok, Woo, Hyun Goo, Jeongwu Lee, Doo-Sik Kong, Seol, Ho Jun, Lee, Jung-Il, Jinho Kim, Woong-Yang Park, Qianghu Wang, Sulman, Erik P., Heimberger, Amy B., Lim, Michael, Park, Jong Bae, Iavarone, Antonio, Verhaak, Roel G. W., and Do-Hyun Nam

Subjects
stomatognathic system, skin and connective tissue diseases, hormones, hormone substitutes, and hormone antagonists
Abstract

Additional file 1: Figure S1. A schematic illustration on identification of MA-TAM signature and master regulators. Figure S2. MA-TAM target gene pathway enrichment. Figure S3. Global regulatory network of MA-TAM. Figure S4. Multi-color immunohistochemical images of MA-TAM encoding molecules. Figure S5. Effects of MARCO and CCL7 on mesenchymal markers. Figure S6. Effects of TAM-derived CM on GSC stemness in response to irradiation. Figure S7. Effects of anti-MARCO therapeutic antibodies. Figure S8. In vivo effects of MARCOhigh TAMs in PDX models. Figure S9. Clinical correlation of MA-TAM master regulators. Figure S10. Single cell analysis of MA-TAM signature. Figure S11. Transcriptome analysis of scTHI at single-cell resolution. Figure S12. Cytokine array-based characterization of MARCOhigh TAMs. Figure S13. Anatomical expression of MA-TAM signature.

Published
2020
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24. Multimodalsingle‐cellanalysis reveals distinct radioresistant stem‐like and progenitor cell populations in murine glioma

Author

Alexander, Jes, primary, LaPlant, Quincey C., additional, Pattwell, Siobhan S., additional, Szulzewsky, Frank, additional, Cimino, Patrick J., additional, Caruso, Francesca P., additional, Pugliese, Pietro, additional, Chen, Zhihong, additional, Chardon, Florence, additional, Hill, Andrew J., additional, Spurrell, Cailyn, additional, Ahrendsen, Dakota, additional, Pietras, Alexander, additional, Starita, Lea M., additional, Hambardzumyan, Dolores, additional, Iavarone, Antonio, additional, Shendure, Jay, additional, and Holland, Eric C., additional

Published
2020
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26. A review of COVID-19 biomarkers and drug targets: resources and tools.

Author

Caruso, Francesca P, Scala, Giovanni, Cerulo, Luigi, and Ceccarelli, Michele

Subjects
*COVID-19, *BIOMARKERS, *VACCINE development, *MACHINE learning, *ARTIFICIAL intelligence
Abstract

The stratification of patients at risk of progression of COVID-19 and their molecular characterization is of extreme importance to optimize treatment and to identify therapeutic options. The bioinformatics community has responded to the outbreak emergency with a set of tools and resource to identify biomarkers and drug targets that we review here. Starting from a consolidated corpus of 27 570 papers, we adopt latent Dirichlet analysis to extract relevant topics and select those associated with computational methods for biomarker identification and drug repurposing. The selected topics span from machine learning and artificial intelligence for disease characterization to vaccine development and to therapeutic target identification. Although the way to go for the ultimate defeat of the pandemic is still long, the amount of knowledge, data and tools generated so far constitutes an unprecedented example of global cooperation to this threat. [ABSTRACT FROM AUTHOR]

Published
2021
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27. Multimodal single‐cell analysis reveals distinct radioresistant stem‐like and progenitor cell populations in murine glioma.

Author

Alexander, Jes, LaPlant, Quincey C., Pattwell, Siobhan S., Szulzewsky, Frank, Cimino, Patrick J., Caruso, Francesca P., Pugliese, Pietro, Chen, Zhihong, Chardon, Florence, Hill, Andrew J., Spurrell, Cailyn, Ahrendsen, Dakota, Pietras, Alexander, Starita, Lea M., Hambardzumyan, Dolores, Iavarone, Antonio, Shendure, Jay, and Holland, Eric C.

Published
2020
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28. Abstract A046: Identification and validation of HCC-specific gene transcriptional signature for tumor antigen discovery

Author

Petrizzo, Annacarmen, primary, Caruso, Francesca P., additional, Tagliamonte, Maria, additional, Tornesello, Maria Lina, additional, Ceccarelli, Michele, additional, Costa, Valerio, additional, Aprile, Marianna, additional, Esposito, Roberta, additional, Ciliberto, Gennaro, additional, Buonaguro, Franco M., additional, and Buonaguro, Luigi, additional

Published
2016
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29. A review of COVID-19 biomarkers and drug targets: resources and tools

Author

Giovanni Scala, Michele Ceccarelli, Luigi Cerulo, Francesca Pia Caruso, Caruso, Francesca P, Scala, Giovanni, Cerulo, Luigi, and Ceccarelli, Michele

Subjects
Biomarker identification, Drug, AcademicSubjects/SCI01060, Coronavirus disease 2019 (COVID-19), Computer science, media_common.quotation_subject, MEDLINE, Disease, Antiviral Agents, Machine Learning, 03 medical and health sciences, Drug Delivery Systems, 0302 clinical medicine, Resource (project management), Humans, Molecular Biology, 030304 developmental biology, media_common, 0303 health sciences, SARS-CoV-2, Drug Repositioning, COVID-19, Articles, Data science, COVID-19 Drug Treatment, Drug repositioning, 030220 oncology & carcinogenesis, Identification (biology), Biomarkers, Information Systems
Abstract

The stratification of patients at risk of progression of COVID-19 and their molecular characterization is of extreme importance to optimize treatment and to identify therapeutic options. The bioinformatics community has responded to the outbreak emergency with a set of tools and resource to identify biomarkers and drug targets that we review here. Starting from a consolidated corpus of 27 570 papers, we adopt latent Dirichlet analysis to extract relevant topics and select those associated with computational methods for biomarker identification and drug repurposing. The selected topics span from machine learning and artificial intelligence for disease characterization to vaccine development and to therapeutic target identification. Although the way to go for the ultimate defeat of the pandemic is still long, the amount of knowledge, data and tools generated so far constitutes an unprecedented example of global cooperation to this threat.

Published
2020

30. The molecular landscape of glioma in patients with Neurofibromatosis 1

Author

Dominique Vidaud, Mariona Suñol, Tala, Francesco DiMeco, John de Groot, Gaetano Finocchiaro, Fulvio D'Angelo, Luc Bauchet, Marica Eoli, Véronique Lorgis, David Meyronet, Kristin Alfaro, Luciano Garofano, John M. Slopis, Laurent Capelle, Pascale Varlet, Giulia Berzero, Mario Cangiano, Veronica Saletti, Romuald Seizeur, Jing Zhang, Carlo Efisio Marras, Veronique Frattini, Walid Farah, Cinzia Lavarino, David Cachia, Genevieve Lewis, Michele Ceccarelli, Seung-Ki Kim, David E. Reuss, Hugues Loiseau, Carlos Kamiya-Matsuoka, Do-Hyun Nam, Krishna P. Bhat, Stéphane Goutagny, Karima Mokhtari, François Ducray, Anna Lasorella, Colin Watts, Francesca Pia Caruso, Hector Salvador, Antonio Iavarone, F. Vandenbos, Ian E. McCutcheon, Susanna Ronchi, Viviane Tabar, Marc Sanson, D'Angelo, Fulvio, Ceccarelli, Michele, Tala, Garofano, Luciano, Zhang, Jing, Frattini, Veronique, Caruso, Francesca P., Lewis, Genevieve, Alfaro, Kristin D., Bauchet, Luc, Berzero, Giulia, Cachia, David, Cangiano, Mario, Capelle, Laurent, de Groot, John, Dimeco, Francesco, Ducray, Francoi, Farah, Walid, Finocchiaro, Gaetano, Goutagny, Stephane, Kamiya-Matsuoka, Carlo, Lavarino, Cinzia, Loiseau, Hugue, Lorgis, Veronique, Marras, Carlo E., Mccutcheon, Ian, Nam, Do-Hyun, Ronchi, Susanna, Saletti, Veronica, Seizeur, Romuald, Slopis, John, Sunol, Mariona, Vandenbos, Fanny, Varlet, Pascale, Vidaud, Dominique, Watts, Colin, Tabar, Viviane, Reuss, David E., Kim, Seung-Ki, Meyronet, David, Mokhtari, Karima, Salvador, Hector, Bhat, Krishna P., Eoli, Marica, Sanson, Marc, Lasorella, Anna, Iavarone, Antonio, D'Angelo, F., Ceccarelli, M., Garofano, L., Zhang, J., Frattini, V., Caruso, F. P., Lewis, G., Alfaro, K. D., Bauchet, L., Berzero, G., Cachia, D., Cangiano, M., Capelle, L., de Groot, J., Dimeco, F., Ducray, F., Farah, W., Finocchiaro, G., Goutagny, S., Kamiya-Matsuoka, C., Lavarino, C., Loiseau, H., Lorgis, V., Marras, C. E., Mccutcheon, I., Nam, D. -H., Ronchi, S., Saletti, V., Seizeur, R., Slopis, J., Sunol, M., Vandenbos, F., Varlet, P., Vidaud, D., Watts, C., Tabar, V., Reuss, D. E., Kim, S. -K., Meyronet, D., Mokhtari, K., Salvador, H., Bhat, K. P., Eoli, M., Sanson, M., Lasorella, A., Iavarone, A., Columbia University Medical Center (CUMC), Columbia University [New York], University of Sannio [Benevento], The University of Texas M.D. Anderson Cancer Center [Houston], CHU Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Hôpital Gui de Chauliac, Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Institut du Cerveau et de la Moëlle Epinière = Brain and Spine Institute (ICM), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université - Faculté de Médecine (SU FM), Sorbonne Université (SU), Medical University of South Carolina [Charleston] (MUSC), Service de Neurochirurgie [CHU Pitié-Salpêtrière], CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Fondazione IRCCS Istituto Neurologico 'Carlo Besta', University of Milan, Hospices Civils de Lyon (HCL), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service de neurochirurgie [CHU de Dijon], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Hôpital Beaujon [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), CHU Bordeaux [Bordeaux], Département d'oncologie médicale [Centre Georges-François Leclerc], Centre Régional de Lutte contre le cancer Georges-François Leclerc [Dijon] (UNICANCER/CRLCC-CGFL), UNICANCER-UNICANCER, Sungkyunkwan University [Suwon] (SKKU), Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Hôpital Pasteur [Nice] (CHU), Institut de psychiatrie et neurosciences (U894 / UMS 1266), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Sainte Anne [Paris], Génétique, physiopathologie et approches thérapeutiques des maladies héréditaires du système nerveux (EA 7331), Université Paris Descartes - Paris 5 (UPD5), Hôpital Cochin [AP-HP], University of Birmingham [Birmingham], Memorial Sloane Kettering Cancer Center [New York], German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg] (DKFZ), Heidelberg University, Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [APHP]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Pitié-Salpêtrière [APHP], Centre de Recherche en Cancérologie de Lyon (CRCL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Beaujon, Centre Régional de Lutte contre le cancer - Centre Georges-François Leclerc (CRLCC - CGFL), and CHU Cochin [AP-HP]

Subjects
0301 basic medicine, Adult, Male, congenital, hereditary, and neonatal diseases and abnormalities, X-linked Nuclear Protein, Neurofibromatosis 1, Adolescent, [SDV]Life Sciences [q-bio], T-Lymphocytes, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Cohort Studies, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Germline mutation, CDKN2A, Antigens, Neoplasm, Glioma, medicine, Humans, Epigenetics, Neurofibromatosis, 10. No inequality, Child, Gene, neoplasms, ATRX, Germ-Line Mutation, Cancer, Neurofibromin 1, Brain Neoplasms, Reproducibility of Results, General Medicine, DNA Methylation, Middle Aged, medicine.disease, 3. Good health, nervous system diseases, 030104 developmental biology, 030220 oncology & carcinogenesis, Child, Preschool, DNA methylation, Cancer research, Genomics, Bioinformatic, Female, Transcriptome
Abstract

Neurofibromatosis type 1 (NF1) is a common tumor predisposition syndrome in which glioma is one of the prevalent tumors. Gliomagenesis in NF1 results in a heterogeneous spectrum of low- to high-grade neoplasms occurring during the entire lifespan of patients. The pattern of genetic and epigenetic alterations of glioma that develops in NF1 patients and the similarities with sporadic glioma remain unknown. Here, we present the molecular landscape of low- and high-grade gliomas in patients affected by NF1 (NF1-glioma). We found that the predisposing germline mutation of the NF1 gene was frequently converted to homozygosity and the somatic mutational load of NF1-glioma was influenced by age and grade. High-grade tumors harbored genetic alterations of TP53 and CDKN2A, frequent mutations of ATRX associated with Alternative Lengthening of Telomere, and were enriched in genetic alterations of transcription/chromatin regulation and PI3 kinase pathways. Low-grade tumors exhibited fewer mutations that were over-represented in genes of the MAP kinase pathway. Approximately 50% of low-grade NF1-gliomas displayed an immune signature, T lymphocyte infiltrates, and increased neo-antigen load. DNA methylation assigned NF1-glioma to LGm6, a poorly defined Isocitrate Dehydrogenase 1 wild-type subgroup enriched with ATRX mutations. Thus, the profiling of NF1-glioma defined a distinct landscape that recapitulates a subset of sporadic tumors. An integrated analysis of glioma samples from patients with neurofibromatosis 1 annotates their mutational, epigenetic, transcriptional, and immunological features and uncovers similitudes with a subset of sporadic gliomas.

Published
2018

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