Deep molecular profiling of lung neuroendocrine tumours and supra-carcinoids. Sexton-Oates A, Mathian É, Candeli N, Lim Y, Voegele C, Di Genova A, … , Dayton T, Alcala N, Foll M, Fernandez-Cuesta L. Mol Cancer, 2026. PMID: 42649496.

Assessment of the current and emerging criteria for the histopathological classification of lung neuroendocrine tumours in the lungNENomics project. Mathian E, Drouet Y, Sexton-Oates A, Papotti MG, Pelosi G, Vignaud J-M, … , Alcala N, Fernandez-Cuesta L, Lantuejoul S, Foll M. ESMO Open. 2024 PMID: 38878324

Druggable Growth Dependencies and Tumor Evolution Analysis in Patient-Derived Organoids of Neuroendocrine Neoplasms from Multiple body sites. Dayton TL, Alcala N, Moonen L, den Hartigh L, Geurts V, Mangiante L, … , Speel EJ, Foll M, Fernández-Cuesta L, Clevers H. Cancer Cell, 2023. PMID: 38086335. Check the associated Editorial and IARC Press Release.

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity. Mangiante L, Alcala N, Sexton-Oates A, Di Genova A, Gonzalez-Perez A, Khandekar A, … , Alexandrov LB, Galateau-Salle F, Foll M, Fernandez-Cuesta L. Nat Genet 2023 PMID: 36928603 – IARC Press Release 

Deep molecular profiling of lung neuroendocrine tumours and supra-carcinoids. Sexton-Oates A, Mathian É, Candeli N, Lim Y, Voegele C, Di Genova A, … , Dayton T, Alcala N, Foll M, Fernandez-Cuesta L. Mol Cancer, 2026. PMID: 42649496.

IASLC Update on Classification of Pulmonary Neuroendocrine Neoplasms. Beasley MB, Yatabe Y, Papotti M, Cooper WA, Derks JL, Fernandez-Cuesta L, … , Rekhtman N, Roden AC, Speel EJM, Travis WD. J Thorac Oncol, 2026. PMID: 42251892

LUNG CARCINOIDS (Lung Neuroendocrine Tumors). Koumarianou A, Derks J, Tsoli M, Volante M, Fernandez-Cuesta L, Prasad V, Filosso PL, Gibert B, Walter T, Durand A. Endocr Rev. 2026 PMID: 41526992

Basic science and translational implications of current knowledge on neuroendocrine tumors. Fernandez-Cuesta L, Alcala N, Mathian E, Derks J, Thirlwell C, Dayton T, Marinoni I, Perren A, Walter T, Foll M. J Clin Invest. 2025. PMID: 40026252

Identification of Defined Molecular Subgroups on the Basis of Immunohistochemical Analyses and Potential Therapeutic Vulnerabilities of Pulmonary Carcinoids. D.J.G. Leunissen, L. Moonen, J.H. von der Thüsen, M. A. den Bakker, L.M. Hillen, T.J.J van Weert, … , A. Sexton-Oates, A-M.C. Dingemans, E.J.M. Speel, J.L. Derks. Journal of Thoracic Oncology 2024. PMID: 39581377

Assessment of the current and emerging criteria for the histopathological classification of lung neuroendocrine tumours in the lungNENomics project. Mathian E, Drouet Y, Sexton-Oates A, Papotti MG, Pelosi G, Vignaud J-M, … , Alcala N, Fernandez-Cuesta L, Lantuejoul S, Foll M. ESMO Open 2024. PMID: 38878324

Clinical management of typical and atypical carcinoids/neuroendocrine tumors in ENETS centres of excellence (CoE): Survey from the ENETS lung NET task force. Koumarianou A, Filosso PL, Bodei L, Castano JP, Fernandez-Cuesta L, Deroose CM ,… , Singh S, Thirlwell C, Volante M, Walter T. J. Neuroendocrinol. 2024. PMID: 38754956

Multi-omic dataset of patient-derived tumor organoids of neuroendocrine neoplasms.  Alcala N, Voegele C, Mangiante L, Sexton-Oates A, Clevers H, Fernandez-Cuesta L, Dayton TL, Foll M. GigaScience, Volume 13, 2024. PMID: 38451475

Druggable growth dependencies and tumor evolution analysis in patient-derived organoids of neuroendocrine neoplasms from multiple body sites. Dayton L, Alcala N, Moonen L, den Hartigh L, Geurts V, Mangiante L, … , Speel EJ, Foll M, Fernandez-Cuesta L, Clevers H. Cancer Cell, 2023. PMID: 38086335. Check the associated Editorial and IARC Press Release.

Spotlight on Small-Cell Lung Cancer and Other Lung Neuroendocrine Neoplasms. Fernandez-Cuesta L, Sexton-Oates A, Bayat L, Foll M, Lau SCM, Leal T. ASCO Educational Book 2023. PMID: 37229617

Differential Orthopedia Homeobox expression in pulmonary carcinoids is associated with changes in DNA methylation. Moonen L, Mangiante L, Leunissen DJG, Lap LMV, Gabriel A, Hillen LM, … , Alcala N, Fernandez-Cuesta L, Derks JL, Speel EM. Int J Cancer 2022. PMID: 35076935

A molecular map of lung neuroendocrine neoplasms. Gabriel AAG, Mathian E, Mangiante L, Voegele C, Cahais V, Ghantous A, McKay JD, Alcala N, Fernandez-Cuesta L, Foll M. Gigascience 2020. PMID: 33124659.

Accessing and reviewing Controlled Access Data of Rare Cancers. Q&A with Matthieu Foll. Gigascience Blog 2020.

New molecular classification of large cell neuroendocrine carcinoma and small cell lung carcinoma with potential therapeutic impacts. Lantuejoul S, Fernandez-Cuesta L, Damiola F, Girard N, McLeer A. Transl Lung Cancer Res. 2020. PMID: 33209646.

Impact clinique des études moléculaires des tumeurs neuroendocrines pulmonaires. Foll M, Fernandez-Cuesta L. Correspondances en Onco-Thoracique. 2020.

Molecular studies of lung neuroendocrine neoplasms uncover new concepts and entities. Fernandez-Cuesta L, Foll M. Transl Lung Cancer Res. 2019 PMID: 32038931

Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids. Alcala N, Leblay N, Gabriel AAG, Mangiante L, Hervas D, Giffon T, … , Lantuejoul S, McKay JD, Foll M, Fernandez-Cuesta L. Nat Commun. 2019 PMID: 31431620 – IARC Press Release

A common classification framework for neuroendocrine neoplasms: an International Agency for Research on Cancer (IARC) and World Health Organization (WHO) expert consensus proposal. Rindi G, Klimstra DS, Abedi-Ardekani B, Asa SL, Bosman FT, Brambilla E, … , Tallini G, Trouillas J, van Krieken JH, Cree IA. Mod Pathol. 2018 PMID: 30140036

Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors. George J, Walter V, Peifer M, Alexandrov LB, Seidel D, Leenders F, … , Hayes DN, Brambilla E, Fernandez-Cuesta L, Thomas RK. Nat Commun. 2018 PMID: 29535388

New insights into the molecular characteristics of pulmonary carcinoids and large cell neuroendocrine carcinomas, and the impact on their clinical management. Derks JL, Leblay N, Lantuejoul S, Dingemans AC, Speel EM, Fernandez-Cuesta L. J Thorac Oncol. 2018 Review. Erratum in: J Thorac Oncol. 2018 Aug;13(8):1229. PMID: 29454048

Molecular subtypes of pulmonary large-cell neuroendocrine carcinoma predict chemotherapy treatment outcome. Derks JL, Leblay N, Thunnissen E, van Suylen RJ, den Bakker M, Groen HJM, … , Fernandez-Cuesta L, Speel EM, Dingemans AC; PALGA-Group. Clin Cancer Res. 2018 PMID: 29066508

Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids. Fernandez-Cuesta L, Peifer M, Lu X, Sun R, Ozretić L, Seidal D, … , Brambilla E, Haas SA, Buettner R, Thomas RK. Nat Commun. 2014 PMID: 24670920

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Peifer M, Fernández-Cuesta L, Sos ML, George J, Seidel D, Kasper LH, … , Heukamp LC, Brindle PK, Haas S, Thomas RK. Nat Genet. 2012 PMID: 22941188

Moving Beyond Morphology: Toward a Morpho-Molecular Classification of Pleural Mesothelioma. Drevet G, Kalson L, Mangé L, Galateau-Salle F, Scherpereel A, Chalabreysse L, … , Alcala A, Maury JM, Fernandez-Cuesta L, Foll M. J Thorac Oncol. 2026 PMID: 41718511

Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity. Mangiante L, Alcala N, Sexton-Oates A, Di Genova A, Gonzalez-Perez A, Khandekar A, … , Alexandrov LB, Galateau-Salle F, Foll M, Fernandez-Cuesta L. Nat Genet 2023 PMID: 36928603 – IARC Press Release

Lifting the curtain on molecular differences between malignant pleural mesotheliomas. Nat Genet. 2023 PMID: 36928604 Research Briefing

A molecular phenotypic map of Malignant Pleural Mesothelioma. Di Genova A,  Mangiante L,  Sexton-Oates A,  Voegele C,  Fernandez-Cuesta L,  Alcala N,  Foll M. GigaScience 2023 PMID: 36705549

Challenges in lung and thoracic pathology: molecular advances in the classification of pleural mesotheliomas. Fernandez-Cuesta L, Mangiante L, Alcala N, Foll M. Virchows Arch. 2021 PMID: 33411030 Review

Redefining malignant pleural mesothelioma types as a continuum uncovers immune-vascular interactions. Alcala N, Mangiante L, Le-Stang N, Gustafon CE, Boyault S, Damiola F, … , McKay JD, Foll M, Galateau-Salle F, Fernandez-Cuesta L. EBioMedicine 2019 PMID: 31648983 – EBioMedicine editorial – IARC Press Release

EURACAN/IASLC proposals for updating the histologic classification of pleural mesothelioma: towards a more multidisciplinary approach. Nicholson AG, Sauter JL, Nowak AK, Kindler HL, Gill RR, Remy-Jardin M, … , Cree I, Rusch VW, Girard N, Galateau-Salle F. J Thorac Oncol. 2019 PMID: 31546041

Highlights of the 14th international mesothelioma interest group meeting: Pathologic separation of benign from malignant mesothelial proliferations and histologic/molecular analysis of malignant mesothelioma subtypes. Churg A, Nabeshima K, Ali G, Bruno R, Fernandez-Cuesta L, Galateau-Salle F. Lung Cancer 2018 PMID: 30268487

BAP1 Is Altered by Copy Number Loss, Mutation, and/or Loss of Protein Expression in More Than 70% of Malignant Peritoneal Mesotheliomas. Leblay N, Leprêtre F, Le Stang N, Gautier-Stein A, Villeneuve L, Isaac S, … , Gilly FN, Foll M, Fernandez-Cuesta L, Brevet M. J Thorac Oncol. 2017 PMID: 28034829

Assessment of the current and emerging criteria for the histopathological classification of lung neuroendocrine tumours in the lungNENomics project. Mathian E, Drouet Y, Sexton-Oates, Papotti MG, Pelosi G, Vignaud J-M, … , Alcala N, Fernandez-Cuesta L, Sylvie Lantuejoul S, Foll M. ESMO Open. 2024 PMID: 38878324

HaloAE: A Local Transformer Auto-Encoder for Anomaly Detection and Localization Based on HaloNet. Mathian E, Liu H, Fernandez-Cuesta L, Samaras D, Foll M, Chen L. Proceedings of the 18th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications (VISIGRAPP 2023) – Volume 5: VISAPP; ISBN 978-989-758-634-7; ISSN 2184-4321, SciTePress, pages 325-337. DOI: 10.5220/0011865900003417

Druggable Growth Dependencies and Tumor Evolution Analysis in Patient-Derived Organoids of Neuroendocrine Neoplasms from Multiple body sites. Dayton TL, Alcala N, Moonen L, den Hartigh L, Geurts V, Mangiante L, … , Speel EJ, Foll M, Fernández-Cuesta L, Clevers H.  Cancer Cell, 2023. Check the associated Editorial and IARC Press Release.

Mathematical constraints on FST: multiallelic markers in arbitrarily many populations. Alcala N and Rosenberg NA. Philosophical Transactions of the Royal Society series B. 2022. PMID: 35430885

FSTruct: An FST‐based tool for measuring ancestry variation in inference of population structure. Morrison ML, Alcala N, and Rosenberg NA. Molecular Ecology Resources. 2022. PMID: 35596736 

• An Integrative RNA Spliceosomic Landscape of Pancreatic Neuroendocrine Tumors Identifies Clinically Relevant Molecular Subgroups. Blazquez-Encinas R, Garcia-Vioque V, Mafficini a, Landoni L, Ruiz-Palacios D, Gutierrez-Camacho L, … , Scarpa A, Ibañez-Costa A, Pedraza-Arevalo S, Castaño JP. Endocr Pathol. 2026 PMID: 42424015
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• Controversies in NEN: An ENETS position statement on the treatment of patients with Grade 3 well-differentiated neuroendocrine tumours of the gastro-enteropancreatic tract. McNamara MG, Sorbye H, Begum N, Christ E, Fazio N, Fernandez-Cuesta L, … , Kasajima A, Salazar R, Speel EJM, Kjaer A. J Neuroendocrinol. 2025 PMID: 40781987
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• The European Prospective Investigation into Cancer and Nutrition Cohort (EPIC): a gateway to rare cancer epidemiological research. Fernandez-Cuesta L*, Voegele C*, Hemon B, Alcala K, Aune D, Caini S, … , Gunter MJ, Trama A, Alcala N, Foll M. ESMO Rare Cancers. 2025. PMID: 40661340
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• ONECUT2 reprograms neuroendocrine fate and is an actionable therapeutic target in small cell lung cancer. Gutiérrez M, Zamora I, Iriarte R, Pajares MJ, Yang Q, Qian C, … , You S, Freeman MR, Encío I, Rotinen M. Mol Med. 2025. PMID: 40500731
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• TERT expression defines clinical outcome in pulmonary carcinoids. Werr L, Bartenhagen C, Rosswog C, Cartolano M, Voegele C, Sexton-Oates A, … , Foll M, Peifer M, Thomas RK, Fischer, M. JCO. 2024. PMID: 39348606
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• Altered splicing machinery in lung carcinoids unveils NOVA1, PRPF8 and SRSF10 as novel candidates to understand tumor biology and expand biomarker discovery. Blázquez-Encinas R, García-Vioque V, Caro-Cuenca T, Moreno-Montilla MT, Mangili F, Alors-Pérez E, … , Alcala N, Pedraza-Arevalo S, Ibáñez-Costa A, Castaño JP. J Transl Med. 2023. PMID: 38049848
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• Detection of acquired TERT amplification in addition to predisposing p53 and Rb pathways alterations in EGFR-mutant lung adenocarcinomas transformed into small-cell lung cancers. Mc Leer A, Foll M, Brevet M, Antoine M, Novello S, Mondet J, … , Letouzé E, Lantuéjoul S, Fernandez-Cuesta L, Moro-Sibilot D. Lung Cancer. 2022. PMID: 35183375
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• Comprehensive molecular and pathological evaluation of transitional mesothelioma assisted by deep learning approach: a multi-institutional study of the International Mesothelioma Panel from MESOPATH Référence Center. Galateau Salle F, Le Stang N, Tirode F, Courtiol P, Nicholson AG, Tsao MS, … , Fernandez-Cuesta L, Pairon JC, Rusch V, Girard N. 
J Thorac Oncol. 2020. PMID: 32165206