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2. NaroNet: Discovery of tumor microenvironment elements from highly multiplexed images

Author

Jiménez-Sánchez, Daniel, Ariz, Mikel, Chang, Hang, Matias-Guiu, Xavier, de Andrea, Carlos E., and Ortiz-de-Solórzano, Carlos

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning, Quantitative Biology - Quantitative Methods, I.4.9
Abstract

Many efforts have been made to discover tumor-specific microenvironment elements (TMEs) from immunostained tissue sections. However, the identification of yet unknown but relevant TMEs from multiplex immunostained tissues remains a challenge, due to the number of markers involved (tens) and the complexity of their spatial interactions. We present NaroNet, which uses machine learning to identify and annotate known as well as novel TMEs from self-supervised embeddings of cells, organized at different levels (local cell phenotypes and cellular neighborhoods). Then it uses the abundance of TMEs to classify patients based on biological or clinical features. We validate NaroNet using synthetic patient cohorts with adjustable incidence of different TMEs and two cancer patient datasets. In both synthetic and real datasets, NaroNet unsupervisedly identifies novel TMEs, relevant for the user-defined classification task. As NaroNet requires only patient-level information, it renders state-of-the-art computational methods accessible to a broad audience, accelerating the discovery of biomarker signatures., Comment: 37 pages, 4 figures

Published
2021

3. Oncolytic DNX-2401 virotherapy plus pembrolizumab in recurrent glioblastoma: a phase 1/2 trial

Author

Nassiri, Farshad, Patil, Vikas, Yefet, Leeor S., Singh, Olivia, Liu, Jeff, Dang, Rachel M. A., Yamaguchi, Takafumi N., Daras, Mariza, Cloughesy, Timothy F., Colman, Howard, Kumthekar, Priya U., Chen, Clark C., Aiken, Robert, Groves, Morris D., Ong, Shirley S., Ramakrishna, Rohan, Vogelbaum, Michael A., Khagi, Simon, Kaley, Thomas, Melear, Jason M., Peereboom, David M., Rodriguez, Analiz, Yankelevich, Maxim, Nair, Suresh G., Puduvalli, Vinay K., Aldape, Kenneth, Gao, Andrew, López-Janeiro, Álvaro, de Andrea, Carlos E., Alonso, Marta M., Boutros, Paul, Robbins, Joan, Mason, Warren P., Sonabend, Adam M., Stupp, Roger, Fueyo, Juan, Gomez-Manzano, Candelaria, Lang, Frederick F., and Zadeh, Gelareh

Published
2023
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7. Neutrophil Extracellular Traps, Local IL-8 Expression, and Cytotoxic T-Lymphocyte Response in the Lungs of Patients With Fatal COVID-19

Author

Melero, Ignacio, Villalba-Esparza, María, Recalde-Zamacona, Borja, Jiménez-Sánchez, Daniel, Teijeira, Álvaro, Argueta, Alan, García-Tobar, Laura, Álvarez-Gigli, Laura, Sainz, Cristina, Garcia-Ros, David, Toledo, Estefanía, Abengozar-Muela, Marta, Fernández-Alonso, Mirian, Rodríguez-Mateos, Mariano, Reina, Gabriel, Carmona-Torre, Francisco, Quiroga, Jorge Augusto, Del Pozo, Jose L., Cross, Amy, López-Janeiro, Álvaro, Hardisson, David, Echeveste, José I., Lozano, Maria D., Ho, Ling-Pei, Klenerman, Paul, Issa, Fadi, Landecho, Manuel F., and de Andrea, Carlos E.

Published
2022
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9. Low-dose ionizing γ-radiation elicits the extrusion of neutrophil extracellular traps

Author

Teijeira, Alvaro, primary, Garasa, Saray, additional, Ochoa, Maria C., additional, Sanchez-Gregorio, Sandra, additional, Gomis, Gabriel, additional, Luri-Rey, Carlos, additional, Martinez-Monge, Rafael, additional, Pinci, Beatrice, additional, Valencia, Karmele, additional, Palencia, Belen, additional, Barbes, Benigno, additional, Bolanos, Elixabet, additional, Azpilikueta, Arantza, additional, Garcia-Cardosa, Marina, additional, Burguete, Javier, additional, Eguren-Santamaria, Iñaki, additional, Garate-Soraluze, Eneko, additional, Berraondo, Pedro, additional, Perez-Gracia, Jose L., additional, de Andrea, Carlos E., additional, Rodriguez-Ruiz, Maria E., additional, and Melero, Ignacio, additional

Published
2024
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13. Figure S3 from Analysis of Tumor Microenvironment Changes after Neoadjuvant Chemotherapy with or without Bevacizumab in Advanced Ovarian Cancer (GEICO-89T/MINOVA Study)

Author

Tavira, Beatriz, primary, Iscar, Teresa, primary, Manso, Luis, primary, Santaballa, Ana, primary, Gil-Martin, Marta, primary, García García, Yolanda, primary, Romeo, Margarita, primary, Iglesias, Maria, primary, de Juan Ferré, Ana, primary, Barretina-Ginesta, María Pilar, primary, Manzano, Aranzazu, primary, Gaba, Lydia, primary, Rubio, María Jesús, primary, de Andrea, Carlos E., primary, and González-Martín, Antonio, primary

Published
2024
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14. Supplementary Methods 1 from Analysis of Tumor Microenvironment Changes after Neoadjuvant Chemotherapy with or without Bevacizumab in Advanced Ovarian Cancer (GEICO-89T/MINOVA Study)

Author

Tavira, Beatriz, primary, Iscar, Teresa, primary, Manso, Luis, primary, Santaballa, Ana, primary, Gil-Martin, Marta, primary, García García, Yolanda, primary, Romeo, Margarita, primary, Iglesias, Maria, primary, de Juan Ferré, Ana, primary, Barretina-Ginesta, María Pilar, primary, Manzano, Aranzazu, primary, Gaba, Lydia, primary, Rubio, María Jesús, primary, de Andrea, Carlos E., primary, and González-Martín, Antonio, primary

Published
2024
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15. Data from Analysis of Tumor Microenvironment Changes after Neoadjuvant Chemotherapy with or without Bevacizumab in Advanced Ovarian Cancer (GEICO-89T/MINOVA Study)

Author

Tavira, Beatriz, primary, Iscar, Teresa, primary, Manso, Luis, primary, Santaballa, Ana, primary, Gil-Martin, Marta, primary, García García, Yolanda, primary, Romeo, Margarita, primary, Iglesias, Maria, primary, de Juan Ferré, Ana, primary, Barretina-Ginesta, María Pilar, primary, Manzano, Aranzazu, primary, Gaba, Lydia, primary, Rubio, María Jesús, primary, de Andrea, Carlos E., primary, and González-Martín, Antonio, primary

Published
2024
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16. Table S1 from Analysis of Tumor Microenvironment Changes after Neoadjuvant Chemotherapy with or without Bevacizumab in Advanced Ovarian Cancer (GEICO-89T/MINOVA Study)

Author

Tavira, Beatriz, primary, Iscar, Teresa, primary, Manso, Luis, primary, Santaballa, Ana, primary, Gil-Martin, Marta, primary, García García, Yolanda, primary, Romeo, Margarita, primary, Iglesias, Maria, primary, de Juan Ferré, Ana, primary, Barretina-Ginesta, María Pilar, primary, Manzano, Aranzazu, primary, Gaba, Lydia, primary, Rubio, María Jesús, primary, de Andrea, Carlos E., primary, and González-Martín, Antonio, primary

Published
2024
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17. The mutational load and a T-cell inflamed tumour phenotype identify ovarian cancer patients rendering tumour-reactive T cells from PD-1+ tumour-infiltrating lymphocytes

Author

Salas-Benito, Diego, Conde, Enrique, Tamayo-Uria, Ibon, Mancheño, Uxua, Elizalde, Edurne, Garcia-Ros, David, Aramendia, Jose M., Muruzabal, Juan C., Alcaide, Julia, Guillen-Grima, Francisco, Minguez, Jose A., Amores-Tirado, Jose, Gonzalez-Martin, Antonio, Sarobe, Pablo, Lasarte, Juan J., Ponz-Sarvise, Mariano, De Andrea, Carlos E., and Hervas-Stubbs, Sandra

Published
2021
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19. Analysis of Tumor Microenvironment Changes after Neoadjuvant Chemotherapy with or without Bevacizumab in Advanced Ovarian Cancer (GEICO-89T/MINOVA Study)

Author

Tavira, Beatriz, primary, Iscar, Teresa, additional, Manso, Luis, additional, Santaballa, Ana, additional, Gil-Martin, Marta, additional, García García, Yolanda, additional, Romeo, Margarita, additional, Iglesias, Maria, additional, de Juan Ferré, Ana, additional, Barretina-Ginesta, María Pilar, additional, Manzano, Aranzazu, additional, Gaba, Lydia, additional, Rubio, María Jesús, additional, de Andrea, Carlos E., additional, and González-Martín, Antonio, additional

Published
2023
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21. Cytology Smears in the Era of Molecular Biomarkers in Non-Small Cell Lung Cancer: Doing More With Less

Author

Lozano, Maria D., Echeveste, Jose I., Abengozar, Marta, Mejias, Luis D., Idoate, Miguel A., Calvo, Alfonso, and de Andrea, Carlos E.

Subjects
Biological markers -- Research, Cytology -- Research, Gene expression -- Research, Non-small cell lung cancer -- Diagnosis -- Genetic aspects -- Research, Health
Abstract

* Context.--The rapid advances in targeted therapies in non-small cell lung cancer (NSCLC) make the optimization and implementation of cytology specimens for molecular testing a priority. Up to 70% of patients with NSCLC are diagnosed at advanced stages and tissue biopsies often cannot be taken. Although cytology samples provide high-quality material for molecular testing, molecular cytopathology is not yet well known or widely used.Objective.--To report the many advances in molecular cytopathology and the suitability and utility of cytology samples in molecular and genetic testing of NSCLC.Data Sources.--Data sources comprised published peer-reviewed literature and personal experience of the authors.Conclusions.--Molecular testing can be performed on cytologic specimens, especially on direct smears. Rapid onsite evaluation by cytopathologists has improved the adequacy and the management of cytology samples for molecular testing. Mutational profiling of NSCLC using next-generation sequencing can be performed on cytology samples from very small amounts of DNA. Fluorescence in situ hybridization assays on cytology specimens, including stained direct smear, offer some distinct advantages over their histologic counterpart, and are used to detect ALK and ROS1 rearrangements in NSCLC. Cytology specimens allow assessment of the entire tumor cell nucleus, avoiding signal loss from truncation artifacts. The use of cytology samples for assessing programmed death ligand-1 protein expression is currently being developed. Protocols for bisulfite conversion and DNA droplet digital polymerase chain reaction assays have been optimized for cytology smear to investigate aberrant DNA methylation of several NSCLC-related genes.(Arch Pathol Lab Med. 2018;142:291-298; doi: 10.5858/arpa.2017-0208-RA), Lung cancer is one of the most prevalent cancers and results in the largest number of cancer-related deaths in the world. (1) More than 85% of those cases are currently [...]

Published
2018
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22. Supplementary Data from Intratumoral Gene Transfer of mRNAs Encoding IL12 in Combination with Decoy-Resistant IL18 Improves Local and Systemic Antitumor Immunity

Author

Cirella, Assunta, primary, Bolaños, Elixabet, primary, Di Trani, Claudia Augusta, primary, de Andrea, Carlos E., primary, Sánchez-Gregorio, Sandra, primary, Etxeberria, Iñaki, primary, Gonzalez-Gomariz, Jose, primary, Olivera, Irene, primary, Brocco, Davide, primary, Glez-Vaz, Javier, primary, Luri-Rey, Carlos, primary, Azpilikueta, Arantza, primary, Rodríguez, Inmaculada, primary, Fernandez-Sendín, Myriam, primary, Egea, Josune, primary, Eguren, Iñaki, primary, Sanmamed, Miguel F., primary, Palencia, Belen, primary, Teijeira, Alvaro, primary, Berraondo, Pedro, primary, and Melero, Ignacio, primary

Published
2023
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23. Supplementary Figure from A Therapeutically Actionable Protumoral Axis of Cytokines Involving IL-8, TNFα, and IL-1β

Author

Olivera, Irene, primary, Sanz-Pamplona, Rebeca, primary, Bolaños, Elixabet, primary, Rodriguez, Inmaculada, primary, Etxeberria, Iñaki, primary, Cirella, Assunta, primary, Egea, Josune, primary, Garasa, Saray, primary, Migueliz, Itziar, primary, Eguren-Santamaria, Iñaki, primary, Sanmamed, Miguel F., primary, Glez-Vaz, Javier, primary, Azpilikueta, Arantza, primary, Alvarez, Maite, primary, Ochoa, María C., primary, Malacrida, Beatrice, primary, Propper, David, primary, de Andrea, Carlos E., primary, Berraondo, Pedro, primary, Balkwill, Frances R., primary, Teijeira, Álvaro, primary, and Melero, Ignacio, primary

Published
2023
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25. Data from Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer

Author

Ruiz-Fernández de Córdoba, Borja, primary, Moreno, Haritz, primary, Valencia, Karmele, primary, Perurena, Naiara, primary, Ruedas, Pablo, primary, Walle, Thomas, primary, Pezonaga-Torres, Alberto, primary, Hinojosa, Juan, primary, Guruceaga, Elisabet, primary, Pineda-Lucena, Antonio, primary, Abengózar-Muela, Marta, primary, Cochonneau, Denis, primary, Zandueta, Carolina, primary, Martínez-Canarias, Susana, primary, Teijeira, Álvaro, primary, Ajona, Daniel, primary, Ortiz-Espinosa, Sergio, primary, Morales, Xabier, primary, Ortiz de Solórzano, Carlos, primary, Santisteban, Marta, primary, Ramos-García, Luis I., primary, Guembe, Laura, primary, Strnad, Vratislav, primary, Heymann, Dominique, primary, Hervás-Stubbs, Sandra, primary, Pío, Rubén, primary, Rodríguez-Ruiz, María E., primary, de Andrea, Carlos E., primary, Vicent, Silvestre, primary, Melero, Ignacio, primary, Lecanda, Fernando, primary, and Martínez-Monge, Rafael, primary

Published
2023
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26. Data from Intratumoral Gene Transfer of mRNAs Encoding IL12 in Combination with Decoy-Resistant IL18 Improves Local and Systemic Antitumor Immunity

Author

Cirella, Assunta, primary, Bolaños, Elixabet, primary, Di Trani, Claudia Augusta, primary, de Andrea, Carlos E., primary, Sánchez-Gregorio, Sandra, primary, Etxeberria, Iñaki, primary, Gonzalez-Gomariz, Jose, primary, Olivera, Irene, primary, Brocco, Davide, primary, Glez-Vaz, Javier, primary, Luri-Rey, Carlos, primary, Azpilikueta, Arantza, primary, Rodríguez, Inmaculada, primary, Fernandez-Sendín, Myriam, primary, Egea, Josune, primary, Eguren, Iñaki, primary, Sanmamed, Miguel F., primary, Palencia, Belen, primary, Teijeira, Alvaro, primary, Berraondo, Pedro, primary, and Melero, Ignacio, primary

Published
2023
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27. Data from A Therapeutically Actionable Protumoral Axis of Cytokines Involving IL-8, TNFα, and IL-1β

Author

Olivera, Irene, primary, Sanz-Pamplona, Rebeca, primary, Bolaños, Elixabet, primary, Rodriguez, Inmaculada, primary, Etxeberria, Iñaki, primary, Cirella, Assunta, primary, Egea, Josune, primary, Garasa, Saray, primary, Migueliz, Itziar, primary, Eguren-Santamaria, Iñaki, primary, Sanmamed, Miguel F., primary, Glez-Vaz, Javier, primary, Azpilikueta, Arantza, primary, Alvarez, Maite, primary, Ochoa, María C., primary, Malacrida, Beatrice, primary, Propper, David, primary, de Andrea, Carlos E., primary, Berraondo, Pedro, primary, Balkwill, Frances R., primary, Teijeira, Álvaro, primary, and Melero, Ignacio, primary

Published
2023
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28. Supplementary Data from Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer

Author

Ruiz-Fernández de Córdoba, Borja, primary, Moreno, Haritz, primary, Valencia, Karmele, primary, Perurena, Naiara, primary, Ruedas, Pablo, primary, Walle, Thomas, primary, Pezonaga-Torres, Alberto, primary, Hinojosa, Juan, primary, Guruceaga, Elisabet, primary, Pineda-Lucena, Antonio, primary, Abengózar-Muela, Marta, primary, Cochonneau, Denis, primary, Zandueta, Carolina, primary, Martínez-Canarias, Susana, primary, Teijeira, Álvaro, primary, Ajona, Daniel, primary, Ortiz-Espinosa, Sergio, primary, Morales, Xabier, primary, Ortiz de Solórzano, Carlos, primary, Santisteban, Marta, primary, Ramos-García, Luis I., primary, Guembe, Laura, primary, Strnad, Vratislav, primary, Heymann, Dominique, primary, Hervás-Stubbs, Sandra, primary, Pío, Rubén, primary, Rodríguez-Ruiz, María E., primary, de Andrea, Carlos E., primary, Vicent, Silvestre, primary, Melero, Ignacio, primary, Lecanda, Fernando, primary, and Martínez-Monge, Rafael, primary

Published
2023
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29. Supplementary Figure from Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer

Author

Ruiz-Fernández de Córdoba, Borja, primary, Moreno, Haritz, primary, Valencia, Karmele, primary, Perurena, Naiara, primary, Ruedas, Pablo, primary, Walle, Thomas, primary, Pezonaga-Torres, Alberto, primary, Hinojosa, Juan, primary, Guruceaga, Elisabet, primary, Pineda-Lucena, Antonio, primary, Abengózar-Muela, Marta, primary, Cochonneau, Denis, primary, Zandueta, Carolina, primary, Martínez-Canarias, Susana, primary, Teijeira, Álvaro, primary, Ajona, Daniel, primary, Ortiz-Espinosa, Sergio, primary, Morales, Xabier, primary, Ortiz de Solórzano, Carlos, primary, Santisteban, Marta, primary, Ramos-García, Luis I., primary, Guembe, Laura, primary, Strnad, Vratislav, primary, Heymann, Dominique, primary, Hervás-Stubbs, Sandra, primary, Pío, Rubén, primary, Rodríguez-Ruiz, María E., primary, de Andrea, Carlos E., primary, Vicent, Silvestre, primary, Melero, Ignacio, primary, Lecanda, Fernando, primary, and Martínez-Monge, Rafael, primary

Published
2023
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30. Synergistic effects of combined immunotherapy strategies in a model of multifocal hepatocellular carcinoma

Author

Ochoa, Maria Carmen, primary, Sanchez-Gregorio, Sandra, additional, de Andrea, Carlos E., additional, Garasa, Saray, additional, Alvarez, Maite, additional, Olivera, Irene, additional, Glez-Vaz, Javier, additional, Luri-Rey, Carlos, additional, Etxeberria, Iñaki, additional, Cirella, Assunta, additional, Azpilikueta, Arantza, additional, Berraondo, Pedro, additional, Argemi, Josepmaria, additional, Sangro, Bruno, additional, Teijeira, Alvaro, additional, and Melero, Ignacio, additional

Published
2023
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31. Reference standards for gene fusion molecular assays on cytological samples: an international validation study

Author

Malapelle, U, Pepe, F, Pisapia, P, Altimari, A, Bellevicine, C, Brunnström, H, Bruno, R, Büttner, R, Cirnes, L, De Andrea, C, de Biase, D, Dumur, C, Ericson Lindquist, K, Fontanini, G, Gautiero, E, Gentien, D, Hofman, P, Hofman, V, Iaccarino, A, Lozano, M, Mayo-de-Las-Casas, C, Merkelbach-Bruse, S, Pagni, F, Roman, R, Schmitt, F, Siemanowski, J, Roy-Chowdhuri, S, Tallini, G, Tresserra, F, Vander Borght, S, Vielh, P, Vigliar, E, Vita, G, Weynand, B, Rosell, R, Molina Vila, M, Troncone, G, Malapelle, Umberto, Pepe, Francesco, Pisapia, Pasquale, Altimari, Annalisa, Bellevicine, Claudio, Brunnström, Hans, Bruno, Rossella, Büttner, Reinhard, Cirnes, Luis, De Andrea, Carlos E, de Biase, Dario, Dumur, Catherine I, Ericson Lindquist, Kajsa, Fontanini, Gabriella, Gautiero, Eugenio, Gentien, David, Hofman, Paul, Hofman, Veronique, Iaccarino, Antonino, Lozano, Maria Dolores, Mayo-de-Las-Casas, Clara, Merkelbach-Bruse, Sabine, Pagni, Fabio, Roman, Ruth, Schmitt, Fernando C, Siemanowski, Janna, Roy-Chowdhuri, Sinchita, Tallini, Giovanni, Tresserra, Francesc, Vander Borght, Sara, Vielh, Philippe, Vigliar, Elena, Vita, Giulia Anna Carmen, Weynand, Birgit, Rosell, Rafael, Molina Vila, Miguel Angel, Troncone, Giancarlo, Malapelle, U, Pepe, F, Pisapia, P, Altimari, A, Bellevicine, C, Brunnström, H, Bruno, R, Büttner, R, Cirnes, L, De Andrea, C, de Biase, D, Dumur, C, Ericson Lindquist, K, Fontanini, G, Gautiero, E, Gentien, D, Hofman, P, Hofman, V, Iaccarino, A, Lozano, M, Mayo-de-Las-Casas, C, Merkelbach-Bruse, S, Pagni, F, Roman, R, Schmitt, F, Siemanowski, J, Roy-Chowdhuri, S, Tallini, G, Tresserra, F, Vander Borght, S, Vielh, P, Vigliar, E, Vita, G, Weynand, B, Rosell, R, Molina Vila, M, Troncone, G, Malapelle, Umberto, Pepe, Francesco, Pisapia, Pasquale, Altimari, Annalisa, Bellevicine, Claudio, Brunnström, Hans, Bruno, Rossella, Büttner, Reinhard, Cirnes, Luis, De Andrea, Carlos E, de Biase, Dario, Dumur, Catherine I, Ericson Lindquist, Kajsa, Fontanini, Gabriella, Gautiero, Eugenio, Gentien, David, Hofman, Paul, Hofman, Veronique, Iaccarino, Antonino, Lozano, Maria Dolores, Mayo-de-Las-Casas, Clara, Merkelbach-Bruse, Sabine, Pagni, Fabio, Roman, Ruth, Schmitt, Fernando C, Siemanowski, Janna, Roy-Chowdhuri, Sinchita, Tallini, Giovanni, Tresserra, Francesc, Vander Borght, Sara, Vielh, Philippe, Vigliar, Elena, Vita, Giulia Anna Carmen, Weynand, Birgit, Rosell, Rafael, Molina Vila, Miguel Angel, and Troncone, Giancarlo

Abstract

AIMS: Gene fusions assays are key for personalised treatments of advanced human cancers. Their implementation on cytological material requires a preliminary validation that may make use of cell line slides mimicking cytological samples. In this international multi-institutional study, gene fusion reference standards were developed and validated. METHODS: Cell lines harbouring EML4(13)-ALK(20) and SLC34A2(4)-ROS1(32) gene fusions were adopted to prepare reference standards. Eight laboratories (five adopting amplicon-based and three hybridisation-based platforms) received, at different dilution points two sets of slides (slide A 50.0%, slide B 25.0%, slide C 12.5% and slide D wild type) stained by Papanicolaou (Pap) and May Grunwald Giemsa (MGG). Analysis was carried out on a total of 64 slides. RESULTS: Four (50.0%) out of eight laboratories reported results on all slides and dilution points. While 12 (37.5%) out of 32 MGG slides were inadequate, 27 (84.4%) out of 32 Pap slides produced libraries adequate for variant calling. The laboratories using hybridisation-based platforms showed the highest rate of inadequate results (13/24 slides, 54.2%). Conversely, only 10.0% (4/40 slides) of inadequate results were reported by laboratories adopting amplicon-based platforms. CONCLUSIONS: Reference standards in cytological format yield better results when Pap staining and processed by amplicon-based assays. Further investigation is required to optimise these standards for MGG stained cells and for hybridisation-based approaches.

Published
2023

36. Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury

Author

Cross, Amy R., primary, de Andrea, Carlos E., additional, Villalba-Esparza, María, additional, Landecho, Manuel F., additional, Cerundolo, Lucia, additional, Weeratunga, Praveen, additional, Etherington, Rachel E., additional, Denney, Laura, additional, Ogg, Graham, additional, Ho, Ling-Pei, additional, Roberts, Ian S.D., additional, Hester, Joanna, additional, Klenerman, Paul, additional, Melero, Ignacio, additional, Sansom, Stephen N., additional, and Issa, Fadi, additional

Published
2023
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37. Intratumoral Gene Transfer of mRNAs Encoding IL12 in Combination with Decoy-Resistant IL18 Improves Local and Systemic Antitumor Immunity

Author

Cirella, Assunta, primary, Bolaños, Elixabet, additional, Di Trani, Claudia Augusta, additional, de Andrea, Carlos E., additional, Sánchez-Gregorio, Sandra, additional, Etxeberria, Iñaki, additional, Gonzalez-Gomariz, Jose, additional, Olivera, Irene, additional, Brocco, Davide, additional, Glez-Vaz, Javier, additional, Luri-Rey, Carlos, additional, Azpilikueta, Arantza, additional, Rodríguez, Inmaculada, additional, Fernandez-Sendín, Myriam, additional, Egea, Josune, additional, Eguren, Iñaki, additional, Sanmamed, Miguel F., additional, Palencia, Belen, additional, Teijeira, Alvaro, additional, Berraondo, Pedro, additional, and Melero, Ignacio, additional

Published
2022
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38. Biomarkers of tumor-reactive CD4+and CD8+TILs associate with improved prognosis in endometrial cancer.

Author

Palomero, Jara, primary, Panisello, Carla, additional, Lozano-Rabella, Maria, additional, Tirtakasuma, Ricky, additional, Díaz-Gómez, Judit, additional, Grases, Daniela, additional, Pasamar, Helena, additional, Arregui, Laura, additional, Dorca Duch, Eduard, additional, Guerra Fernández, Esther, additional, Vivancos, Ana, additional, de Andrea, Carlos E, additional, Melero, Ignacio, additional, Ponce, Jordi, additional, Vidal, August, additional, Piulats, Josep Maria, additional, Matias-Guiu, Xavier, additional, and Gros, Alena, additional

Published
2022
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40. The association between the tumor immune microenvironments and clinical outcome in low‐grade, early‐stage endometrial cancer patients

Author

López‐Janeiro, Álvaro, primary, Villalba‐Esparza, María, additional, Brizzi, María Emilia, additional, Jiménez‐Sánchez, Daniel, additional, Ruz‐Caracuel, Ignacio, additional, Kadioglu, Ece, additional, Masetto, Ivan, additional, Goubert, Virginie, additional, Garcia‐Ros, David, additional, Melero, Ignacio, additional, Peláez‐García, Alberto, additional, Hardisson, David, additional, and de Andrea, Carlos E, additional

Published
2022
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42. Proteomic analysis of low-grade, early-stage endometrialcarcinoma reveals new dysregulated pathways associated with cell death and cell signaling

Author

Instituto de Salud Carlos III, European Commission, López-Janeiro, Álvaro [0000-0002-5744-3115], Ruz-Caracuel, Ignacio [0000-0002-2298-4683], Ramón-Patino, Jorge L. [0000-0002-7308-823X], Ríos, Vivian de los [0000-0001-5582-6879], Villalba Esparza, María [0000-0002-9183-0610], Berjón, Alberto [0000-0002-3467-106X], Kadioglu, Ece [0000-0001-8679-8030], Heredia-Soto, Victoria [0000-0002-0704-7958], Barderas, Rodrigo [0000-0003-3539-7469], Casal, J. Ignacio [0000-0003-1085-2840], De Andrea, Carlos E. [0000-0002-7628-8050], Mendiola, Marta [0000-0002-2463-1304], Peláez-García, Alberto [0000-0002-5401-3216], Hardisson, David [0000-0002-2183-3699], López-Janeiro, Álvaro, Ruz-Caracuel, Ignacio, Ramón-Patino, Jorge L., Ríos, Vivian de los, Villalba Esparza, María, Berjón, Alberto, Yébenes, Laura, Hernández, Alicia, Masetto, Ivan, Kadioglu, Ece, Goubert, Virginie, Heredia-Soto, Victoria, Barderas, Rodrigo, Casal, J. Ignacio, De Andrea, Carlos E., Redondo, Andrés, Mendiola, Marta, Peláez-García, Alberto, Hardisson, David, Instituto de Salud Carlos III, European Commission, López-Janeiro, Álvaro [0000-0002-5744-3115], Ruz-Caracuel, Ignacio [0000-0002-2298-4683], Ramón-Patino, Jorge L. [0000-0002-7308-823X], Ríos, Vivian de los [0000-0001-5582-6879], Villalba Esparza, María [0000-0002-9183-0610], Berjón, Alberto [0000-0002-3467-106X], Kadioglu, Ece [0000-0001-8679-8030], Heredia-Soto, Victoria [0000-0002-0704-7958], Barderas, Rodrigo [0000-0003-3539-7469], Casal, J. Ignacio [0000-0003-1085-2840], De Andrea, Carlos E. [0000-0002-7628-8050], Mendiola, Marta [0000-0002-2463-1304], Peláez-García, Alberto [0000-0002-5401-3216], Hardisson, David [0000-0002-2183-3699], López-Janeiro, Álvaro, Ruz-Caracuel, Ignacio, Ramón-Patino, Jorge L., Ríos, Vivian de los, Villalba Esparza, María, Berjón, Alberto, Yébenes, Laura, Hernández, Alicia, Masetto, Ivan, Kadioglu, Ece, Goubert, Virginie, Heredia-Soto, Victoria, Barderas, Rodrigo, Casal, J. Ignacio, De Andrea, Carlos E., Redondo, Andrés, Mendiola, Marta, Peláez-García, Alberto, and Hardisson, David

Abstract

Low-grade, early-stage endometrial carcinoma (EC) is the most frequent malignant tumor of the uterine corpus. However, the molecular alterations that underlie these tumors are far from being fully understood. The purpose of this study is to describe dysregulated molecular pathways from EC patients. Sixteen samples of tumor tissue and paired healthy controls were collected and both were subjected to mass spectrometry (MS)/MS proteomic analysis. Gene ontology and pathway analysis was performed to discover dysregulated pathways and/or proteins using different databases and bioinformatic tools. Dysregulated pathways were cross-validated in an independent external cohort. Cell signaling, immune response, and cell death-associated pathways were robustly identified. The SLIT/ROBO signaling pathway demonstrated dysregulation at the proteomic and transcriptomic level. Necroptosis and ferroptosis were cell death-associated processes aberrantly regulated, in addition to apoptosis. Immune response-associated pathways showed a dominance of innate immune responses. Tumor immune infiltrates measured by immunofluorescence demonstrated diverse lymphoid and myeloid populations. Our results suggest a role of SLIT/ROBO, necroptosis, and ferroptosis, as well as a prominent role of innate immune response in low-grade, early-stage EC. These results could guide future research in this group of tumors

Published
2021

43. Synplex: In silico modelling of the tumor microenvironment from multiplex immunofluorescence images

Author

Jimenez-Sanchez, Daniel, Ariz, Mikel, De Andrea, Carlos E., and Ortiz-De-Solorzano

Subjects
Multiplex imaging, In silico, tumor microenvironment
Abstract

Set of images generated by Synplex, which were used for its validation. For further description of the method check the paper "Synplex: In silico modelling of the tumor microenvironment from multiplex immunofluorescence images". For further description of the code implementation check (https://github.com/djimenezsanchez/Synplex). The files stored in this repository represents to specific experiments: First validation experiment: Simulation of tissue samples from user-defined parameters Multiplex_Synthetic_Images.zip: 45 multiplex images simulated from user-defined parameters Multiplex_Synthetic_Masks.zip: 45 mask images generated during the simulation process, containing neighborhoods, phenotypes, and graphs on the optimization process First proof-of-principle experiment: Use of tumor simulations for augmenting training datasets in AI-based patient prediction systems POLE_mutation_Synthetic_Images.zip: 74 multiplex images simulated from real endometrial quantifications. Some patients show the POLE mutation and others the WT version of it. &nbsp

Published
2022
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44. Targeting the extra domain A of fibronectin for cancer therapy with CAR-T cells

Author

Martín-Otal, Celia, primary, Lasarte-Cia, Aritz, additional, Serrano, Diego, additional, Casares, Noelia, additional, Conde, Enrique, additional, Navarro, Flor, additional, Sánchez-Moreno, Inés, additional, Gorraiz, Marta, additional, Sarrión, Patricia, additional, Calvo, Alfonso, additional, De Andrea, Carlos E, additional, Echeveste, José, additional, Vilas, Amaia, additional, Rodriguez-Madoz, Juan Roberto, additional, San Miguel, Jesús, additional, Prosper, Felipe, additional, Hervas-Stubbs, Sandra, additional, Lasarte, Juan Jose, additional, and Lozano, Teresa, additional

Published
2022
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47. A Therapeutically Actionable Protumoral Axis of Cytokines Involving IL-8, TNFα, and IL-1β

Author

Olivera, Irene, primary, Sanz-Pamplona, Rebeca, additional, Bolaños, Elixabet, additional, Rodriguez, Inmaculada, additional, Etxeberria, Iñaki, additional, Cirella, Assunta, additional, Egea, Josune, additional, Garasa, Saray, additional, Migueliz, Itziar, additional, Eguren-Santamaria, Iñaki, additional, Sanmamed, Miguel F., additional, Glez-Vaz, Javier, additional, Azpilikueta, Arantza, additional, Alvarez, Maite, additional, Ochoa, María C., additional, Malacrida, Beatrice, additional, Propper, David, additional, de Andrea, Carlos E., additional, Berraondo, Pedro, additional, Balkwill, Frances R., additional, Teijeira, Álvaro, additional, and Melero, Ignacio, additional

Published
2022
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48. Abstract 3826: A therapeutically actionable pro-tumoral axis of cytokines involving interleukin-8, TNFα and IL-1β

Author

Olivera, Irene, primary, Sanz-Pamplona, Rebeca, additional, Bolaños, Elixabet, additional, Rodriguez, Inmaculada, additional, Etxeberria, Iñaki, additional, Cirella, Assunta, additional, Garasa, Saray, additional, Migueliz, Itziar, additional, Eguren, Iñaki, additional, Sanmamed, Miguel F., additional, Glez-Vaz, Javier, additional, Azpilikueta, Arantza, additional, Alvarez, Maite, additional, Ochoa, Maria C., additional, De Andrea, Carlos E., additional, Berraondo, Pedro, additional, Teijeira, Álvaro, additional, and Melero, Ignacio, additional

Published
2022
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49. Identifying mechanisms of acquired immune escape from sequential, paired biopsies.

Author

Hodi, F. Stephen, primary, Spigel, David R., additional, De Andrea, Carlos E., additional, Sanmamed, Miguel F., additional, Garralda, Elena, additional, Tabernero, Josep, additional, Gomez-Roca, Carlos A., additional, Szabados, Bernadett, additional, Powles, Thomas, additional, Pachynski, Russell Kent, additional, Fong, Lawrence, additional, Rizvi, Naiyer, additional, Yoon, Shinkyo, additional, Kim, Tae Won, additional, Oh, Do-Youn, additional, Nicholas, Alan, additional, Tea, Joy S., additional, Abbas, Alexander R., additional, and Price, Richard, additional

Published
2022
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50. Exploiting 4-1BB immune checkpoint to enhance the efficacy of oncolytic virotherapy for diffuse intrinsic pontine gliomas

Author

Laspidea, Virginia, primary, Puigdelloses, Montserrat, additional, Labiano, Sara, additional, Marrodán, Lucía, additional, Garcia-Moure, Marc, additional, Zalacain, Marta, additional, Gonzalez-Huarriz, Marisol, additional, Martínez-Vélez, Naiara, additional, Ausejo-Mauleon, Iker, additional, de la Nava, Daniel, additional, Herrador-Cañete, Guillermo, additional, Marco-Sanz, Javier, additional, Guruceaga, Elisabeth, additional, de Andrea, Carlos E., additional, Villalba, María, additional, Becher, Oren, additional, Squatrito, Massimo, additional, Matía, Verónica, additional, Gállego Pérez-Larraya, Jaime, additional, Patiño-García, Ana, additional, Gupta, Sumit, additional, Gomez-Manzano, Candelaria, additional, Fueyo, Juan, additional, and Alonso, Marta M., additional

Published
2022
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