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Whole-genome landscape of pancreatic neuroendocrine tumours
Abstract
The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2. Together with mutations in MEN1 and VHL, these mutations occur in 17% of patients. Somatic mutations, including point mutations and gene fusions, were commonly found in genes involved in four main pathways: chromatin remodelling, DNA damage repair, activation of mTOR signalling (including previously undescribed EWSR1 gene fusions), and telomere maintenance. In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling.
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“substitution signatures were dominated by C>A transversions in NpCpA or NpCpT contexts (Figures 2 and 3) previously associated with inactivation of the BER gene MUTYH [11].”
From Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers (2019) · cites this paper as [11]
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Clinically actionable genomic and transcriptomic landscape of advanced neuroendocrine neoplasms
Kreutzfeldt, S., Apostolidis, L., Oleś, M., Krieghoff‐Henning, E., Heilig, C. E., Heining, C., Möck, A., Teleanu, M., Hutter, B., Gieldon, L., et al. (2026) · Med · doi:10.1016/j.medj.2026.101130 · Cited by 1
Guan, J., Lu, Y., Zhang, H., & Huang, W. Y. (2026) · Frontiers in Oncology · doi:10.3389/fonc.2026.1796302 · Cited by 1
“Kosmahl ’ s embryonic-genital-ridge model (9) explains the classic SPN pro fi le (nuclear b -catenin, PR(+), CgA ( – )), whereas PanNETs arise from committed endocrine progenitors that retain membranous b -catenin and may harbor MEN1, DAXX or ATRX mutations (10, 11).”
Sciarra, A., Libera, L., Destro, A., Maragliano, R., Furlan, D., Guastafierro, V., Marchiori, D., Vanoli, A., González, R. S., Letovanec, I., et al. (2026) · Endocrine Pathology · doi:10.1007/s12022-026-09918-y · Cited by 1
Mulita, F., Kouroupi, M., Verras, G., Mitropoulou, A.-M., Bolanaki, H., Tzimagiorgis, I., Giatromanolaki, A. N., & Karayiannakis, A. J. (2026) · Diagnostics · doi:10.3390/diagnostics16121778 · Cited by 1
“Improved understanding of their pathogenesis may also help clarify the relationship between neurogenic and neuroendocrine components, particularly in cases presenting with synchronous lesions [34,35].”
Blázquez‐Encinas, R., García‐Vioque, V., Mafficini, A., Landoni, L., Ruiz-Palacios, D., Gutiérrez-Camacho, L., Moreno-Montilla, M. T., Alcala, N., Ventura, S., Eyras, E., et al. (2026) · Endocrine Pathology · doi:10.1007/s12022-026-09923-1 · Cited by 1
“How - ever, despite these advances, the molecular mechanisms underlying PanNETs behavior remain poorly understood and translation of this molecular information to the clinical practice is very limited [ 16, 27 , 28 ].”
Self-citationWhole genome and exome sequencing of pancreatic neuroendocrine tumours to investigate PRRT response
Boehm, E., Flynn, A., Caneborg, A., Hatzimihalis, A., Hogg, A., Waldeck, K., Jackett, L., Prall, O. W. J., Mitchell, C., Kong, G., et al. (2026) · Endocrine Related Cancer · doi:10.1530/erc-26-0207 · Cited by 1
“A subset of pancreatic NETs have inactivating variants of BRCA2 and CHEK2 , involved in the homologous recombination (HR) DNA repair pathway (14); however, BRCA alteration and HR deficiency have not correlated with better response to 177 Lutetium-based radionuclide therapy in prostate…”
Self-citationExpanded GEP-NET organoid culture for personalized therapy evaluation
Forsythe, S. D., Yellapragada, S. V., Pu, T., Nousome, D., Mathur, S., Akbulut, D., Sb, A., Kenny, K. A., Quezado, M., Cam, M., et al. (2026) · Science Advances · doi:10.1126/sciadv.aea4296 · Cited by 1
Bakr, H., Al-Awar, A., Spetz, J. K. E., & Forssell-Aronsson, E. B. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27198709 · Cited by 1
Spetz, J. K. E., Montelius, M., Berger, E., Johansson, J. A. M., Rassol, N., Ljungberg, M., & Forssell-Aronsson, E. B. (2026) · BMC Cancer · doi:10.1186/s12885-026-16975-3 · Cited by 1
“Consistent with this, p53 was predicted to be inhibited during tumor regrowth at 13 d. p53 is rarely mutated in NETs, but epigenetic and regulatory aberrations interfering with the p53 network activity have been described, which might inhibit p53 function [71–73].”
Amair-Pinedo, F., Matos, I., Saurí, T., Hernando, J., & Capdevila, J. (2017) · Targeted oncology · doi:10.1007/s11523-017-0532-3 · Cited by 1
“, has enlarged the list of potential players in the mTOR pathway activation in panNETs, with namely DEPDC5, ESWR1 and the RET receptor ligand PSPN [27].”
BackgroundInfluentialWang, Z., Liu, L., Luo, J., Guo, J., Zhai, M., Zhang, W., & Yang, Z. (2018) · Oncology Letters · doi:10.3892/ol.2018.8184 · Cited by 1
“No mutations in frequently mutated genes identified in sporadic insulinoma or non‑func-tional PNET were present, for example YY1 , DAXX , ATRX , MUTYH or genes in the mammalian target of rapamycin pathway (9,10,16-18).”
Neuroendokrine Tumoren des Pankreas
Rinke, A., & Gress, T. M. (2019) · Der Internist · doi:10.1007/s00108-018-0545-8 · Cited by 1
Systemic Therapy for Neuroendocrine Neoplasms
Chan, D. L. H., & Singh, S. (2019) · Digestive Disease Interventions · doi:10.1055/s-0038-1675757 · Cited by 1
Gao, H.-L., Wang, W., Xu, H., Wu, C., Li, H., Ni, Q., Yu, X., & Liu, L. (2020) · World Journal of Clinical Cases · doi:10.12998/wjcc.v8.i17.3751 · Cited by 1
Pancreatic Neuroendocrine Neoplasms
Asa, S. L., & Klimstra, D. S. (2020) · Springer eBooks · doi:10.1007/978-3-030-54391-4_11 · Cited by 1
Genomic profiling of multiple tissues in two patients with multiple endocrine neoplasia type 1
Naruoka, A., Ohnami, S., Nagashima, T., Serizawa, M., Hatakeyama, K., Ohshima, K., Ohnami, S., Urakami, K., Horiuchi, Y., Kiyozumi, Y., et al. (2021) · Biomedical Research · doi:10.2220/biomedres.42.89 · Cited by 1
“A previous study showed that pancreatic neuroendocrine tumors (PanNETs) (Scarpa et al., 2017) had recurrent catastrophic rearrangements on chromosome 11q, all involving 11q13, some of which led to loss of MEN1.”
BackgroundMethodConvergence between germline and somatic mutations in pancreatic neuroendocrine tumors
Ling, C., Hong, X., Xu, M., Wang, Y., Ma, X., Cui, Y., Jiang, R., Cao, D., Wu, H., Tong, A., et al. (2022) · European Journal of Endocrinology · doi:10.1530/eje-21-0893 · Cited by 2
Kurzyńska, A., Pach, D., Skalniak, A., Stefańska, A., Opalińska, M., Przybylik‐Mazurek, E., & Hubalewska–Dydejczyk, A. (2022) · Journal of Clinical Medicine · doi:10.3390/jcm11195536 · Cited by 1
“Although a hereditary background should be considered in many types of NETs, especially in pancreatic ones [1,2], only about 10% are associated with inherited genetic syndromes [3].”
BackgroundEpidemiology, Pathogenesis, and Prognosis of Pancreatic Neuroendocrine Tumors
Keihanian, T., & Othman, M. O. (2022) · Springer eBooks · doi:10.1007/978-3-030-41683-6_36 · Cited by 1
Inositols as adjuvant treatments in oncology
Bizzarri, M., Vučenik, I., & Appetecchia, M. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-91673-8.00007-8 · Cited by 1
Skalniak, A., Trofimiuk–Müldner, M., Jabrocka‐Hybel, A., Totoń‐Żurańska, J., Wołkow, P. P., & Hubalewska–Dydejczyk, A. (2023) · Endokrynologia Polska · doi:10.5603/ep.a2023.0009 · Cited by 1
Haidar, M., Mahmasani, L. A., Chehade, L., Elias, C., Jebai, M. E., Temraz, S. N., Charafeddine, M., Darazi, M. H. A., & Shamseddine, A. I. (2023) · Nuclear Medicine Communications · doi:10.1097/mnm.0000000000001683 · Cited by 1
Radiosensitivity and early onset cancer
Chadwick, K. H. (2023) · Journal of Radiological Protection · doi:10.1088/1361-6498/acd857 · Cited by 1
“If the accumulation of somatic mutations leads to cancer [2–5] then it seems probable that DNA damage, possibly in the form of double strand breaks or double strand lesions, is involved.”
Yang, K., Ying, H., Guan, M., Wang, L., Xu, J., & Cheng, Y. (2023) · Journal of Pancreatology · doi:10.1097/jp9.0000000000000143 · Cited by 1
Promising targetable biomarkers in pancreatic neuroendocrine tumours
Borghesani, M., Gervaso, L., Cella, C. A., Benini, L., Ciardiello, D., Algeri, L., Ferrero, A., Valenza, C., Guidi, L., Zampino, M. G., et al. (2023) · Expert Review of Endocrinology & Metabolism · doi:10.1080/17446651.2023.2248239 · Cited by 1
“Germline VHL mutations were reported in only 1% of clinically sporadic PanNETs, however up to 25% of PanNETs display somatic or epigenetic VHL alterations with reduction in its expression levels [7,16].”
Influential
Metadata
- Authors
- Initiative, A. P. C. G., Scarpa, A., Chang, D. K., Nones, K., Corbo, V., Patch, A.-M., Bailey, P., Lawlor, R. T., Johns, A. L., Miller, D. K., Mafficini, A., Rusev, B., Scardoni, M., Antonello, D., Barbi, S., Sikora, K. O., Cingarlini, S., Vicentini, C., McKay, S., Quinn, M. C. J., Bruxner, T. J. C., Christ, A. N., Harliwong, I., Idrisoglu, S., McLean, S., Nourse, C., Nourbakhsh, E., Wilson, P. J., Anderson, M. J., Fink, J. L., Newell, F., Waddell, N., Holmes, O., Kazakoff, S. H., Leonard, C., Wood, S., Xu, Q., Nagaraj, S. H., Amato, E., Dalai, I., Bersani, S., Cataldo, I., Dei Tos, A. P., Capelli, P., Davì, M. V., Landoni, L., Malpaga, A., Miotto, M., Whitehall, V. L. J., Leggett, B. A., Harris, J. L., Harris, J., Jones, M. D., Humphris, J., Chantrill, L. A., Chin, V., Nagrial, A. M., Pajic, M., Scarlett, C. J., Pinho, A., Rooman, I., Toon, C., Wu, J., Pinese, M., Cowley, M., Barbour, A., Mawson, A., Humphrey, E. S., Colvin, E. K., Chou, A., Lovell, J. A., Jamieson, N. B., Duthie, F., Gingras, M.-C., Fisher, W. E., Dagg, R. A., Lau, L. M. S., Lee, M., Pickett, H. A., Reddel, R. R., Samra, J. S., Kench, J. G., Merrett, N. D., Epari, K., Nguyen, N. Q., Zeps, N., Falconi, M., Simbolo, M., Butturini, G., Van Buren, G., Partelli, S., Fassan, M., Khanna, K. K., Gill, A. J., Wheeler, D. A., Gibbs, R. A., Musgrove, E. A., Bassi, C., Tortora, G., Pederzoli, P., Pearson, J. V., Waddell, N., Biankin, A. V., & Grimmond, S. M.
- Affiliations
- University of Verona (IT)
- Garvan Institute of Medical Research (AU)
- The University of Queensland (AU)
- Queensland University of Technology (AU)
- Glasgow Royal Infirmary (GB)
- Baylor College of Medicine (US)
- Children's Hospital at Westmead (AU)
- The University of Sydney (AU)
- Fremantle Hospital (AU)
- Royal Adelaide Hospital (AU)
- The University of Melbourne (AU)
- Corresponding author
- Scarpa, Aldo
- Biankin, Andrew V.
- Grimmond, Sean M.
- ORCID
- Scarpa, Aldo
- Chang, David K.
- Corbo, Vincenzo
- Patch, Ann-Marie
- Bailey, Peter
- Lawlor, Rita T.
- Johns, Amber L.
- Mafficini, Andrea
- Rusev, Borislav
- Antonello, Davide
- Barbi, Stefano
- Cingarlini, Sara
- Vicentini, Caterina
- Quinn, Michael C. J.
- Bruxner, Timothy J. C.
- Christ, Angelika N.
- Harliwong, Ivon
- Nourbakhsh, Ehsan
- Wilson, Peter J.
- Anderson, Matthew J.
- Fink, J. Lynn
- Newell, Felicity
- Holmes, Oliver
- Kazakoff, Stephen H.
- Leonard, Conrad
- Wood, Scott
- Nagaraj, Shivashankar Hiriyur
- Bersani, Samantha
- Cataldo, Ivana
- Davì, Maria Vittoria
- Landoni, Luca
- Malpaga, Anna
- Miotto, Marco
- Whitehall, Vicki L. J.
- Leggett, Barbara A.
- Harris, Jonathan
- Jones, Marc D.
- Chantrill, Lorraine A.
- Chin, Venessa
- Nagrial, Adnan M.
- Pajic, Marina
- Scarlett, Christopher J.
- Pinho, Andreia
- Rooman, Ilse
- Toon, Christopher
- Wu, Jianmin
- Pinese, Mark
- Cowley, Mark
- Barbour, Andrew
- Mawson, Amanda
- Colvin, Emily K.
- Chou, Angela
- Jamieson, Nigel B.
- Gingras, Marie-Claude
- Dagg, Rebecca A.
- Lau, Loretta M. S.
- Lee, Michael
- Pickett, Hilda A.
- Reddel, Roger R.
- Samra, Jaswinder S.
- Kench, James G.
- Merrett, Neil D.
- Nguyen, Nam Q.
- Zeps, Nikolajs
- Falconi, Massimo
- Simbolo, Michele
- Partelli, Stefano
- Fassan, Matteo
- Khanna, Kum Kum
- Gill, Anthony J.
- Wheeler, David A.
- Gibbs, Richard A.
- Bassi, Claudio
- Tortora, Giampaolo
- Pearson, John V.
- Waddell, Nicola
- Biankin, Andrew V.
- Grimmond, Sean M.
- Venue
- Nature
- Published
- 2017-02-15
- Volume
- 543
- Issue
- 7643
- Pages
- 65-71
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2589112207
- Cited by
- 999
- References
- 62
- Citations by year
- 2026: 65 · 2025: 101 · 2024: 103 · 2023: 110 · 2022: 126 · 2021: 108 · 2020: 131 · 2019: 89 · 2018: 103 · 2017: 52
- FWCI
- 81.15
- Type
- journal article
- Language
- en
- Update notices
- erratum (2017-09-27)
- Open access
- closed
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (acceptedVersion)
- QUT ePrints (Queensland University of Technology) (submittedVersion)
- UWA Profiles and Research Repository (UWA) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- Archivio Istituzionale della Ricerca - Università Vita-Salute San Raffaele (submittedVersion)
- NOVA (University of Newcastle Australia) (submittedVersion)
- VUBIR (Vrije Universiteit Brussel) (submittedVersion)
- Padua Research Archive (University of Padova) (submittedVersion)
- Funders
- Pancreatic Cancer UK (RIF2015_A06_Jamieson, FLF2015_04_GLASGOW)
- Wellcome Trust (103721/Z/14/Z)
- Cancer Research UK (23526, 17263, 22533)
- Academy of Medical Sciences (AMS-SGCL9-Jamieson)
- Medical Research Council (MR/N005813/1)
- Topics
- Health Sciences › Medicine › Oncology › Neuroendocrine Tumor Research Advances
- Health Sciences › Medicine › Oncology › Pancreatic and Hepatic Oncology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- pancreatic neuroendocrine tumors, mutational signatures, MUTYH, germline mutations, CHEK2, BRCA2, MEN1, VHL, chromatin remodeling, DNA repair, mTOR signaling, telomere maintenance, hypoxia, carcinogenesis
- MeSH terms
- Base Sequence, Calmodulin-Binding Proteins, Chromosome Aberrations, DNA Mutational Analysis, DNA Repair, Female, Humans, Male, Pancreatic Neoplasms, Genome, Human, RNA-Binding Proteins, Telomere, Germ-Line Mutation, Carcinoma, Neuroendocrine, Genomics, RNA-Binding Protein EWS, Chromatin Assembly and Disassembly, DNA Glycosylases, DNA Copy Number Variations, TOR Serine-Threonine Kinases
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