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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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“Loss of RB expression and KRAS mutations in P-NECs have been related to better response to platinum-based chemotherapy and can help to differentiate between P-NETs and P-NECs (Hijioka et al. 2017).”
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“The past decade has witnessed a remarkable advancement in the understanding of PNETs ’ physiology, the performance of their heterogeneity, and the modalities used for their treatment [1, 25, 29].”
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“Finally, fusion transcripts involving EWSR1 were reported in four tumours [8].”
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“…were higher than those reported in primary pNETs analyzed using whole-genome sequencing (median: 0.82 mutations/Mb, range: 0.04-4.56 mutations/Mb)[9], but were within the broader range reported in a cohort comprising primary and metastatic pNETs using a targeted cancer-gene sequencing panel…”
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“Radiation-induced DNA damage largely determines radiosensitivity, and PanNETs exhibit heterogeneous DNA repair capacities [ 40 ].”
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“…the molecular landscape of pancreatic neuroendocrine tumors (PNETs), highlighting recurrent alterations involving DNA damage repair (MUTYH, CHEK2, BRCA2), chromatin remodeling (MEN1, SETD2, ARID1A, MLL3), telomere maintenance (TERT), and mTOR pathway dysregulation (PTEN, TSC2, TSC1, DEPDC5) [34].”
InfluentialBrown, L. M., Hagenson, R. A., Sheltzer, J. M., & Kunstman, J. W. (2026) · Frontiers in Oncology · doi:10.3389/fonc.2026.1757796
“As a result, the published frequencies of reported mutations can be highly variable; for instance, MEN1 has been found mutated in 25-56% of PNETs (10, 11, 13, 30).”
InfluentialCiobanu, O. A., Martin, C. S., Fica, S. V., Herlea, V., Tudose, I., Vasilescu, F., Sandra, I., & Barbu, C. G. (2026) · Frontiers in Endocrinology · doi:10.3389/fendo.2026.1820433
“These fi ndings suggest that ATRX/DAXX loss may be associated with more aggressive disease and is linked to later-stage tumors (12, 22, 23, 61, 62), warranting a repeat biopsy in cases of tumor progression.”
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Evan, T., Srirajaskanthan, R., & Sarker, D. (2026) · Current clinical pathology · doi:10.1007/978-3-032-18790-1_17
Sexual dimorphism and estrogens in neuroendocrine neoplasms
Strachowska, M., & Jacenik, D. (2026) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2026.189613
Integrated genomics and transcriptomics reveal key events in pancreatic neuroendocrine neoplasm
Guo, S., Shi, X., Yin, X., Gao, S., Li, B., Wang, H., Li, Y., Wang, B., Xu, X., Zheng, K., et al. (2026) · BMC Biology · doi:10.1186/s12915-026-02637-0
“Over the last decade, several studies have begun to accumulate information that uncovers the characteristics of PanNENs [10, 15, 16, 29].”
InfluentialChowdhury, D., Mishra, A., Rao, M. M., Sahu, R., & Bodakhe, S. H. (2026) · Journal of Chemotherapy · doi:10.1080/1120009x.2026.2676345
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Erbliche neuroendokrine Neoplasien
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Neuroendocrine tumours through an epigenetic lens: Emerging insights for diagnosis and treatment
Jacquot, V., Chevalier, B., Walter, T., Gibert, B., & Ouzounova, M. (2026) · Journal of Neuroendocrinology · doi:10.1111/jne.70211
“5,10 In contrast, NECs are characterized by poor epithelial differentiation, marked cellular atypia, and frequent molecular or genetic abnormalities, while retaining expression of neuroendocrine markers.”
Genomic Catastrophe Defines the Evolutionary Trajectory of Adrenocortical Carcinoma
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A systematic scoping review of the molecular pathogenesis of digestive system cancers (2013–2025)
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“These include intrinsically low tumor antigenicity coupled with relatively insufficient antigen-presenting capacity [17, 43], limited infiltration by effector T cells [44–46], and, in a subset of cases, a suppressive tumor microenvironment enriched for tumor-associated macrophages [47].”
InfluentialJafari, P., Husain, A. N., & Setia, N. (2026) · Clinics in Laboratory Medicine · doi:10.1016/j.cll.2026.06.011
Tumor-specific Kinase Motif Enrichment Analysis Identifies Personalized Therapeutic Cancer TargetsPreprint
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“In PNETs, more than half the tumors showed evidence of somatic MEN1 mutations, while other common mutations included DAXX, SETD2 , and TP53 , consistent with previous reports [52-54].”
Shekhda, K. M., Howat, J., Gao, Y., Bel-Ange, A., Grozinsky‐Glasberg, S., Kaltsas, G., Ho, K. M. A., Hayes, A. R., Mandair, D., Toumpanakis, C., et al. (2026) · Journal of the Endocrine Society · doi:10.1210/jendso/bvag178
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Pancreatic Cyst Fluid Analysis
Thyen, A. J., Roch, A. M., & Ceppa, E. P. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-28605-6.00005-4
Second primary malignancies in neuroendocrine tumors: a single-center cohort study
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“16,19,34 Multiple lesions of PanNETs could be interpreted as intra-pancreatic metastasis or respectively, synchronously development.”
Self-citationHeteroGeNETics: Neuroendocrine tumor genetics reflect their heterogeneous complex diversity
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The metastatic spectrum in functional and non-functional NENs: mechanistic insights from multi-omics
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“As summarized in Figure 1, MEN1, DAXX, ATRX, and mTOR-pathway alterations are recurrent in well-differentiated pancreatic NETs across functional categories and connect chromatin regulation, telomere maintenance, and growth signaling (10, 31 – 33).”
PSIP1::TBL1X : a recurrent gene fusion in pancreatic neuroendocrine tumors
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The Role of the Surgical Pathologist in the Recognition of Hereditary Neuroendocrine Tumors
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Comprehensive somatic profiling of gastroenteropancreatic neuroendocrine neoplasms
Mohindroo, C., Agarwal, P., Lee, V., He, J., Anders, R. A., Bever, K., Laheru, D. A., & Jesus‐Acosta, A. D. (2026) · Endocrine Oncology · doi:10.1530/eo-26-0044
“Consistent with previous reports, mutations in TP53, MEN1, KRAS , and DAXX/ATRX were among the most prevalent alterations detected in our cohort and demonstrated significant associations with clinical features (7, 17, 18, 19, 20).”
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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