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Bolduan F, Müller-Bötticher N, Debnath O, Eichhorn I, Giesecke Y, Wetzel A, Sahay S, Zemojtel T, Jaeger M, Ungethuem U, Roderburg C, Kunze CA, Lehmann A, Horst D, Tacke F, Eils R, Wiedenmann B, Sigal M, Ishaque N. Small intestinal neuroendocrine tumors lack early genomic drivers, acquire DNA repair defects and harbor hallmarks of low REST expression. Sci Rep 2025; 15:17969. [PMID: 40410286 PMCID: PMC12102166 DOI: 10.1038/s41598-025-01912-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2024] [Accepted: 05/09/2025] [Indexed: 05/25/2025] Open
Abstract
The tumorigenesis of small intestinal neuroendocrine tumors (siNETs) is not understood and comprehensive genomic and transcriptomic data sets are limited. Therefore, we performed whole genome and transcriptome analysis of 39 well differentiated siNET samples. Our genomic data revealed a lack of recurrent driver mutations and demonstrated that multifocal siNETs from individual patients can arise genetically independently. We detected germline mutations in Fanconi anemia DNA repair pathway (FANC) genes, involved in homologous recombination (HR) DNA repair, in 9% of patients and found mutational signatures of defective HR DNA repair in late-stage tumor evolution. Furthermore, transcriptomic analysis revealed low expression of the transcriptional repressor REST. Summarizing, we identify a novel common transcriptomic signature of siNETs and demonstrate that genomic alterations alone do not explain initial tumor formation, while impaired DNA repair likely contributes to tumor evolution and represents a potential pharmaceutical target in a subset of patients.
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Affiliation(s)
- Felix Bolduan
- Department of Hepatology & Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353, Berlin, Germany
- BIH Charité Junior Digital Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, Charitéplatz 1, 10117, Berlin, Germany
| | - Niklas Müller-Bötticher
- Center of Digital Health, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Olivia Debnath
- Center of Digital Health, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Ines Eichhorn
- Department of Hepatology & Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353, Berlin, Germany
| | - Yvonne Giesecke
- Department of Hepatology & Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353, Berlin, Germany
| | - Alexandra Wetzel
- Department of Hepatology & Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353, Berlin, Germany
| | - Shashwat Sahay
- Center of Digital Health, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Tomasz Zemojtel
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Marten Jaeger
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Ute Ungethuem
- Core Facility Genomics, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Christoph Roderburg
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Catarina Alisa Kunze
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - Annika Lehmann
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
| | - David Horst
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, CCCC (Campus Mitte), Berlin, Germany
| | - Frank Tacke
- Department of Hepatology & Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353, Berlin, Germany
| | - Roland Eils
- Center of Digital Health, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Bertram Wiedenmann
- Department of Hepatology & Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353, Berlin, Germany.
| | - Michael Sigal
- Department of Hepatology & Gastroenterology, Charité Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353, Berlin, Germany.
- Berlin Institute for Medical Systems Biology, Hannoversche Straße 28, 10115, Berlin, Germany.
| | - Naveed Ishaque
- Center of Digital Health, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany.
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Loree JM, Chan D, Lim J, Stuart H, Fidelman N, Koea J, Posavad J, Cummins M, Doucette S, Myrehaug S, Naraev B, Bailey DL, Bellizzi A, Laidley D, Boyle V, Goodwin R, Del Rivero J, Michael M, Pasieka J, Singh S. Biomarkers to Inform Prognosis and Treatment for Unresectable or Metastatic GEP-NENs. JAMA Oncol 2024; 10:1707-1720. [PMID: 39361298 DOI: 10.1001/jamaoncol.2024.4330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2024]
Abstract
Importance Evidence-based treatment decisions for advanced gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) require individualized patient-centered decision-making that accounts for patient and cancer characteristics. Objective To create an accessible guidance document to educate clinicians and patients on biomarkers informing prognosis and treatment in unresectable or metastatic GEP-NENs. Methods A multidisciplinary panel in-person workshop was convened to define methods. English language articles published from January 2016 to January 2023 in PubMed (MEDLINE) and relevant conference abstracts were reviewed to investigate prognostic and treatment-informing features in unresectable or metastatic GEP-NENs. Data from included studies were used to form evidence-based recommendations. Quality of evidence and strength of recommendations were determined using the Grading of Recommendations, Assessment, Development and Evaluations framework. Consensus was reached via electronic survey following a modified Delphi method. Findings A total of 131 publications were identified, including 8 systematic reviews and meta-analyses, 6 randomized clinical trials, 29 prospective studies, and 88 retrospective cohort studies. After 2 rounds of surveys, 24 recommendations and 5 good clinical practice statements were developed, with full consensus among panelists. Recommendations focused on tumor and functional imaging characteristics, blood-based biomarkers, and carcinoid heart disease. A single strong recommendation was made for symptomatic carcinoid syndrome informing treatment in midgut neuroendocrine tumors. Conditional recommendations were made to use grade, morphology, primary site, and urinary 5-hydroxyindoleacetic levels to inform treatment. The guidance document was endorsed by the Commonwealth Neuroendocrine Tumour Collaboration and the North American Neuroendocrine Tumor Society. Conclusions and Relevance The study results suggest that select factors have sufficient evidence to inform care in GEP-NENs, but the evidence for most biomarkers is weak. This article may help guide management and identify gaps for future research to advance personalized medicine and improve outcomes for patients with GEP-NENs.
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Affiliation(s)
- Jonathan M Loree
- BC Cancer, Vancouver Centre, Vancouver, British Columbia, Canada
| | - David Chan
- Northern Clinical School, University of Sydney, Sydney, Australia
- ENETS Centre of Excellence, Department of Medical Oncology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Jennifer Lim
- St George Hospital, Sydney, New South Wales, Australia
- University of New South Wales, Sydney, New South Wales, Australia
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Heather Stuart
- University of British Columbia and BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Jonathan Koea
- Te Whatu Ora Waitemata and the University of Auckland, Auckland, New Zealand
| | - Jason Posavad
- Canadian Neuroendocrine Tumours Society, Cornwall, Ontario, Canada
| | | | | | - Sten Myrehaug
- Odette Cancer Centre, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Boris Naraev
- Tampa General Hospital Cancer Institute, Tampa, Florida
| | - Dale L Bailey
- Department of Nuclear Medicine, Royal North Shore Hospital, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | | | - David Laidley
- Western University, London, Ontario, Canada
- Lawson Health Research Institute, London, Ontario, Canada
| | - Veronica Boyle
- School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Department of Oncology, Auckland City Hospital, Te Whatu Ora Tamaki Makaurau, Auckland, New Zealand
| | - Rachel Goodwin
- Ottawa Hospital Cancer Centre, University of Ottawa, Ottawa, Ontario, Canada
| | - Jaydi Del Rivero
- Developmental Therapeutics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael Michael
- NET Unit and ENETS Centre of Excellence, Peter MacCallum Cancer Centre, Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Janice Pasieka
- Section of General Surgery, Division of Endocrine Surgery and Surgical Oncology, Department of Surgery and Oncology, University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
| | - Simron Singh
- University of Toronto, Toronto, Ontario, Canada
- Sunnybrook Odette Cancer Center, Sunnybrook Health Sciences Center, Toronto, Ontario, Canada
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3
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Tan B, Zhang B, Chen H. Gastroenteropancreatic neuroendocrine neoplasms: epidemiology, genetics, and treatment. Front Endocrinol (Lausanne) 2024; 15:1424839. [PMID: 39411312 PMCID: PMC11474919 DOI: 10.3389/fendo.2024.1424839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 09/10/2024] [Indexed: 10/19/2024] Open
Abstract
The incidence of gastroenteropancreatic neuroendocrine neoplasms (GEP NEN) is increasing at a rapid pace and is becoming an increasingly important consideration in clinical care. Epidemiological data from multiple countries indicate that the incidence of gastroenteropancreatic neuroendocrine neoplasms (GEP NEN) exhibits regional, site-specific, and gender-based variations. While the genetics and pathogenesis of some GEP NEN, particularly pancreatic NENs, have been investigated, there are still many mechanisms that require further investigation. The management of GEP NEN is diverse, but surgery remains the primary option for most cases. Peptide receptor radionuclide therapy (PRRT) is an effective treatment, and several clinical trials are exploring the potential of immunotherapy and targeted therapy, as well as combination therapy.
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Affiliation(s)
- Baizhou Tan
- Department of Histology and Embryology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Beiyu Zhang
- Department of Histology and Embryology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
- Queen Mary School, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Hongping Chen
- Department of Histology and Embryology, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
- Jiangxi Key Laboratory of Experimental Animals, Nanchang University, Nanchang, China
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Uccella S. Molecular Classification of Gastrointestinal and Pancreatic Neuroendocrine Neoplasms: Are We Ready for That? Endocr Pathol 2024; 35:91-106. [PMID: 38470548 PMCID: PMC11176254 DOI: 10.1007/s12022-024-09807-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
In the last two decades, the increasing availability of technologies for molecular analyses has allowed an insight in the genomic alterations of neuroendocrine neoplasms (NEN) of the gastrointestinal tract and pancreas. This knowledge has confirmed, supported, and informed the pathological classification of NEN, clarifying the differences between neuroendocrine carcinomas (NEC) and neuroendocrine tumors (NET) and helping to define the G3 NET category. At the same time, the identification genomic alterations, in terms of gene mutation, structural abnormalities, and epigenetic changes differentially involved in the pathogenesis of NEC and NET has identified potential molecular targets for precision therapy. This review critically recapitulates the available molecular features of digestive NEC and NET, highlighting their correlates with pathological aspects and clinical characteristics of these neoplasms and revising their role as predictive biomarkers for targeted therapy. In this context, the feasibility and applicability of a molecular classification of gastrointestinal and pancreatic NEN will be explored.
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Affiliation(s)
- Silvia Uccella
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072, Pieve Emanuele, Milan, Italy.
- Pathology Service IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano, Milan, Italy.
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Alcala N, Voegele C, Mangiante L, Sexton-Oates A, Clevers H, Fernandez-Cuesta L, Dayton TL, Foll M. Multi-omic dataset of patient-derived tumor organoids of neuroendocrine neoplasms. Gigascience 2024; 13:giae008. [PMID: 38451475 PMCID: PMC10919335 DOI: 10.1093/gigascience/giae008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/18/2023] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Organoids are 3-dimensional experimental models that summarize the anatomical and functional structure of an organ. Although a promising experimental model for precision medicine, patient-derived tumor organoids (PDTOs) have currently been developed only for a fraction of tumor types. RESULTS We have generated the first multi-omic dataset (whole-genome sequencing [WGS] and RNA-sequencing [RNA-seq]) of PDTOs from the rare and understudied pulmonary neuroendocrine tumors (n = 12; 6 grade 1, 6 grade 2) and provide data from other rare neuroendocrine neoplasms: small intestine (ileal) neuroendocrine tumors (n = 6; 2 grade 1 and 4 grade 2) and large-cell neuroendocrine carcinoma (n = 5; 1 pancreatic and 4 pulmonary). This dataset includes a matched sample from the parental sample (primary tumor or metastasis) for a majority of samples (21/23) and longitudinal sampling of the PDTOs (1 to 2 time points), for a total of n = 47 RNA-seq and n = 33 WGS. We here provide quality control for each technique and the raw and processed data as well as all scripts for genomic analyses to ensure an optimal reuse of the data. In addition, we report gene expression data and somatic small variant calls and describe how they were generated, in particular how we used WGS somatic calls to train a random forest classifier to detect variants in tumor-only RNA-seq. We also report all histopathological images used for medical diagnosis: hematoxylin and eosin-stained slides, brightfield images, and immunohistochemistry images of protein markers of clinical relevance. CONCLUSIONS This dataset will be critical to future studies relying on this PDTO biobank, such as drug screens for novel therapies and experiments investigating the mechanisms of carcinogenesis in these understudied diseases.
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Affiliation(s)
- Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon 69008, France
| | - Catherine Voegele
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon 69008, France
| | - Lise Mangiante
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon 69008, France
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Sexton-Oates
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon 69008, France
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, The Netherlands
- Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, The Netherlands
| | - Lynnette Fernandez-Cuesta
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon 69008, France
| | - Talya L Dayton
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, The Netherlands
- Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, The Netherlands
| | - Matthieu Foll
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research on Cancer/World Health Organization (IARC/WHO), Lyon 69008, France
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Chen S, Sun L, Chen H, Li J, Lu C, Yang Y, Sun Y. Clinicopathological and genetic characteristics of gastric neuroendocrine tumour (NET) G3 and comparisons with neuroendocrine carcinoma and NET G2. Histopathology 2023; 83:700-711. [PMID: 37403531 DOI: 10.1111/his.15002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/06/2023]
Abstract
AIMS To characterise the clinicopathological and genetic characteristics of gastric neuroendocrine tumour G3 (gNET G3) and to compare them with those of gastric neuroendocrine carcinoma (gNEC) and gNET G2. METHODS AND RESULTS A total of 115 gastric neuroendocrine neoplasms (NENs) were included, of which gNET G3 was different from gNET G1/G2 in terms of tumour location (P = 0.029), number (P = 0.003), size (P = 0.010), the Ki67 index (P < 0.001), lymph node metastasis (P < 0.001) and TNM stage (P = 0.011), and different from gNEC/gastric mixed neuroendocrine-non-neuroendocrine neoplasm (gMiNEN) in terms of tumour size (P = 0.010) and the Ki67 index (P = 0.001). High-resolution copy number (CN) profiling and validation experiments showed CN gains and high expression of DLL3 in gNET G3. Hierarchical clustering analysis based on CN characteristics showed that gNET G3 was separated from gNEC but mixed with gNET G2. In gene set enrichment analysis, eight pathways were significantly enriched in gNEC when comparing gNET G3 and gNEC (P < 0.05), while no pathways were enriched when comparing gNET G3 and gNET G2. Whole-exome sequencing and validation experiments showed nonsense mutation of TP53 in one gNET G3, with wild-type staining for p53. In gNEC, TP53 mutations were detected in four of eight cases, and abnormal expression of p53 was detected in all cases. CONCLUSION Gastric NET G3 is a distinct entity with unique genetic characteristics, which are different from those of gNEC than gNET G2. Our results provide insight into some molecular alterations that may contribute to the development and progression of gNET G3 and serve as potential therapeutic targets.
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Affiliation(s)
- Shuai Chen
- Department of Pathology, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Lin Sun
- Department of Pathology, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Haozhu Chen
- Department of Pathology, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jiaxin Li
- Department of Pathology, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Chenglu Lu
- Department of Pathology, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yichen Yang
- Department of Pathology, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yan Sun
- Department of Pathology, National Clinical Research Centre for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Centre for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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Postel MD, Darabi S, Howe JR, Liang WS, Craig DW, Demeure MJ. Multiomic sequencing of paired primary and metastatic small bowel carcinoids. F1000Res 2023; 12:417. [PMID: 37954063 PMCID: PMC10632590 DOI: 10.12688/f1000research.130251.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/15/2023] [Indexed: 11/14/2023] Open
Abstract
Background: Small bowel carcinoids are insidious tumors that are often metastatic when diagnosed. Limited mutation landscape studies of carcinoids indicate that these tumors have a relatively low mutational burden. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of carcinoid tumors. Methods: Whole exome and RNA sequencing of 5 matched sets of normal tissue, primary small intestine carcinoid tumors, and liver metastases were investigated. Germline and somatic variants included: single nucleotide variants (SNVs), insertions/deletions (indels), structural variants, and copy number alterations (CNAs). The functional impact of mutations was predicted using Ensembl Variant Effect Predictor. Results: Large-scale CNAs were observed including the loss of chromosome 18 in all 5 metastases and 3/5 primary tumors. Certain somatic SNVs were metastasis-specific; including mutations in ATRX, CDKN1B, MXRA5 (leading to the activation of a cryptic splice site and loss of mRNA), SMARCA2, and the loss of UBE4B. Additional mutations in ATRX, and splice site loss of PYGL, leading to intron retention observed in primary and metastatic tumors. Conclusions: We observed novel mutations in primary/metastatic carcinoid tumor pairs, and some have been observed in other types of neuroendocrine tumors. We confirmed a previously observed loss of chromosome 18 and CDKN1B. Transcriptome sequencing added relevant information that would not have been appreciated with DNA sequencing alone. The detection of several splicing mutations on the DNA level and their consequences at the RNA level suggests that RNA splicing aberrations may be an important mechanism underlying carcinoid tumors.
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Affiliation(s)
- Mackenzie D. Postel
- Institute of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Sourat Darabi
- Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA, 92663, USA
| | - James R. Howe
- Department of Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | - David W. Craig
- Institute of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michael J. Demeure
- Precision Medicine, Hoag Family Cancer Institute, Newport Beach, CA, 92663, USA
- Translational Genomics Research Institute, Phoenix, AZ, USA
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Lamberti G, Prinzi N, Bongiovanni A, Torniai M, Andrini E, de Biase D, Malvi D, Mosca M, Berardi R, Ibrahim T, Pusceddu S, Campana D. Targeted Genomic Profiling and Chemotherapy Outcomes in Grade 3 Gastro-Entero-Pancreatic Neuroendocrine Tumors (G3 GEP-NET). Diagnostics (Basel) 2023; 13:1595. [PMID: 37174986 PMCID: PMC10178589 DOI: 10.3390/diagnostics13091595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Grade 3 gastro-entero-pancreatic neuroendocrine tumors (G3 GEP-NET) are poorly characterized in terms of molecular features and response to treatments. METHODS Patients with G3 GEP-NET were included if they received capecitabine and temozolomide (CAPTEM) or oxaliplatin with either 5-fluorouracile (FOLFOX) or capecitabine (XELOX) as first-line treatment (chemotherapy cohort). G3 NET which successfully undergone next-generation sequencing (NGS) were included in the NGS cohort. RESULTS In total, 49 patients were included in the chemotherapy cohort: 15 received CAPTEM and 34 received FOLFOX/XELOX. Objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) were 42.9%, 9.0 months, and 33.6 months, respectively. Calculating a Ki67 cutoff using ROC curve analysis, tumors with Ki67 ≥ 40% had lower ORR (51.2% vs. 0%; p = 0.007) and shorter PFS (10.6 months vs. 4.4 months; p < 0.001) and OS (49.4 months vs. 10.0 months; p = 0.023). In patients who received FOLFOX/XELOX as a first-line treatment, ORR, PFS, and OS were 38.2%, 7.9 months, and 30.0 months, respectively. In the NGS cohort (N = 13), the most mutated genes were DAXX/ATRX (N = 5, 38%), MEN1 (N = 4, 31%), TP53 (N = 4, 31%), AKT1 (N = 2, 15%), and PIK3CA (N = 1, 8%). CONCLUSIONS FOLFOX/XELOX chemotherapy is active as the first-line treatment of patients with G3 GEP-NET. The mutational landscape of G3 NET is more similar to well-differentiated NETs than NECs.
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Affiliation(s)
- Giuseppe Lamberti
- Department of Medical or Surgical Sciences, University of Bologna, 40126 Bologna, Italy; (G.L.); (E.A.); (M.M.)
- Medical Oncology Department, IRCCS Azienda Ospedaliero-Universitaria Sant’Orsola-Malpighi di Bologna, 40138 Bologna, Italy
| | - Natalie Prinzi
- Medical Oncology, Foundation IRCCS National Cancer Institute, 20133 Milano, Italy; (N.P.); (S.P.)
| | - Alberto Bongiovanni
- Osteoncology and Rare Tumor Center (CDO-TR), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.B.); (T.I.)
| | - Mariangela Torniai
- Department of Oncology, Università Politecnica delle Marche-AOU delle Marche, 60126 Ancona, Italy; (M.T.); (R.B.)
| | - Elisa Andrini
- Department of Medical or Surgical Sciences, University of Bologna, 40126 Bologna, Italy; (G.L.); (E.A.); (M.M.)
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Deborah Malvi
- Pathology Unit, IRCCS Azienda-Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy;
| | - Mirta Mosca
- Department of Medical or Surgical Sciences, University of Bologna, 40126 Bologna, Italy; (G.L.); (E.A.); (M.M.)
| | - Rossana Berardi
- Department of Oncology, Università Politecnica delle Marche-AOU delle Marche, 60126 Ancona, Italy; (M.T.); (R.B.)
| | - Toni Ibrahim
- Osteoncology and Rare Tumor Center (CDO-TR), IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.B.); (T.I.)
| | - Sara Pusceddu
- Medical Oncology, Foundation IRCCS National Cancer Institute, 20133 Milano, Italy; (N.P.); (S.P.)
| | - Davide Campana
- Department of Medical or Surgical Sciences, University of Bologna, 40126 Bologna, Italy; (G.L.); (E.A.); (M.M.)
- Medical Oncology Department, IRCCS Azienda Ospedaliero-Universitaria Sant’Orsola-Malpighi di Bologna, 40138 Bologna, Italy
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Vesely C, Wong YNS, Childs A, Akarca AU, Dhami P, Vaikkinen H, Conde L, Herrero J, Ogunbiyi O, Gander A, Luong TV, Thirlwell C, Caplin M, Toumpanakis C, Peggs K, Quezada SA, Marafioti T, Meyer T. Systematic Evaluation of the Immune Environment of Small Intestinal Neuroendocrine Tumors. Clin Cancer Res 2022; 28:2657-2668. [PMID: 35320356 PMCID: PMC9359734 DOI: 10.1158/1078-0432.ccr-21-4203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/01/2022] [Accepted: 03/21/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE The immune tumor microenvironment and the potential therapeutic opportunities for immunotherapy in small intestinal neuroendocrine tumors (siNET) have not been fully defined. EXPERIMENTAL DESIGN Herein, we studied 40 patients with primary and synchronous metastatic siNETs, and matched blood and normal tissue obtained during surgery. We interrogated the immune checkpoint landscape using multi-parametric flow cytometry. In addition, matched FFPE tissue was obtained for multi-parametric IHC to determine the relative abundance and distribution of T-cell infiltrate. Tumor mutational burden (TMB) was also assessed and correlated with immune infiltration. RESULTS Effector tumor-infiltrating lymphocytes (TIL) had a higher expression of PD-1 in the tumor microenvironment compared with the periphery. In addition, CD8+ TILs had a significantly higher co-expression of PD-1/ICOS and PD-1/CTLA-4 (cytotoxic T lymphocyte antigen-4) and higher levels of PD-1 expression compared with normal tissue. IHC revealed that the majority of cases have ≤10% intra-tumoral T cells but a higher number of peri-tumoral T cells, demonstrating an "exclusion" phenotype. Finally, we confirmed that siNETs have a low TMB compared with other tumor types in the TCGA database but did not find a correlation between TMB and CD8/Treg ratio. CONCLUSIONS Taken together, these results suggest that a combination therapy approach will be required to enhance the immune response, using PD-1 as a checkpoint immunomodulator backbone in combination with other checkpoint targeting molecules (CTLA-4 or ICOS), or with drugs targeting other pathways to recruit "excluded" T cells into the tumor microenvironment to treat patients with siNETs.
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Affiliation(s)
- Clare Vesely
- UCL Cancer Institute, UCL, London, United Kingdom
| | - Yien Ning Sophia Wong
- UCL Cancer Institute, UCL, London, United Kingdom.,Cancer Immunology Unit, Research Department of Hematology, UCL Cancer Institute, UCL, London, United Kingdom
| | - Alexa Childs
- UCL Cancer Institute, UCL, London, United Kingdom.,Royal Free Hospital, Pond Street, London, United Kingdom
| | | | - Pawan Dhami
- UCL Cancer Institute, UCL, London, United Kingdom
| | | | - Lucia Conde
- UCL Cancer Institute, UCL, London, United Kingdom
| | | | | | - Amir Gander
- Royal Free Hospital, Pond Street, London, United Kingdom
| | - Tu Vinh Luong
- Royal Free Hospital, Pond Street, London, United Kingdom
| | - Chrissie Thirlwell
- UCL Cancer Institute, UCL, London, United Kingdom.,The University of Exeter Medical School, Exeter, United Kingdom
| | - Martyn Caplin
- Royal Free Hospital, Pond Street, London, United Kingdom
| | | | - Karl Peggs
- UCL Cancer Institute, UCL, London, United Kingdom.,Cancer Immunology Unit, Research Department of Hematology, UCL Cancer Institute, UCL, London, United Kingdom
| | - Sergio A. Quezada
- UCL Cancer Institute, UCL, London, United Kingdom.,Cancer Immunology Unit, Research Department of Hematology, UCL Cancer Institute, UCL, London, United Kingdom
| | | | - Tim Meyer
- UCL Cancer Institute, UCL, London, United Kingdom.,Royal Free Hospital, Pond Street, London, United Kingdom.,Corresponding Author: Tim Meyer, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD. Phone: 44-207-679-6731; E-mail;
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10
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van der Graaf W, Tesselaar M, McVeigh T, Oyen W, Fröhling S. Biology-Guided Precision Medicine in Rare Cancers: Lessons from Sarcomas and Neuroendocrine Tumours. Semin Cancer Biol 2022; 84:228-241. [DOI: 10.1016/j.semcancer.2022.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/26/2022]
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11
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Metastatic Neuroendocrine Neoplasms of Unknown Primary: Clues from Pathology Workup. Cancers (Basel) 2022; 14:cancers14092210. [PMID: 35565339 PMCID: PMC9100271 DOI: 10.3390/cancers14092210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary While most neuroendocrine neoplasms are indolent and slow-growing tumors, subsets of cases will spread beyond the tissue of origin. Given the rather slow progress, some lesions are incidentally discovered as metastatic deposits rather than primary masses. In these cases, a biopsy is often taken to allow the pathologist to identify the tumor type and possibly the primary tumor site via microscopic examination. In this review, the authors present a simplified guide on how to approach metastatic neuroendocrine tumors from a pathologist’s perspective. Abstract Neuroendocrine neoplasms (NENs) are diverse tumors arising in various anatomical locations and may therefore cause a variety of symptoms leading to their discovery. However, there are instances in which a NEN first presents clinically as a metastatic deposit, while the associated primary tumor is not easily identified using conventional imaging techniques because of small primary tumor sizes. In this setting (which is referred to as a “NEN of unknown primary”; NEN-UP), a tissue biopsy is often procured to allow the surgical pathologist to diagnose the metastatic lesion. If indeed a metastatic NEN-UP is found, several clues can be obtained from morphological assessment and immunohistochemical staining patterns that individually or in concert may help identify the primary tumor site. Herein, histological and auxiliary analyses of value in this context are discussed in order to aid the pathologist when encountering these lesions in clinical practice.
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12
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Couvelard A, Cros J. An update on the development of concepts, diagnostic criteria, and challenging issues for neuroendocrine neoplasms across different digestive organs. Virchows Arch 2022; 480:1129-1148. [PMID: 35278097 DOI: 10.1007/s00428-022-03306-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/11/2022] [Accepted: 02/27/2022] [Indexed: 12/16/2022]
Abstract
Digestive neuroendocrine neoplasms (NENs) are a group of heterogeneous neoplasms found throughout the digestive tract, with different behaviour and genetic background. In the last few years, nomenclature and WHO/UICC classifications of digestive NENs have changed, and molecular classifications have emerged, especially in pancreatic locations. Increasing patho-molecular details are needed to diagnose the different categories of NEN, including the use of helpful immunohistochemical markers. In this review, we address these topics in three successive chapters. We first briefly review recent updates in classifications, discuss important grading and proliferating issues and advances in the molecular understanding of NEN. Then, we provide an update on diagnosis, including the most important differential diagnoses of NEN, with a focus on high-grade neoplasms and mixed tumours. Finally, we highlight a variety of currently used and next-generation predictive and prognostic biomarkers as well as biomarkers of tumour origin and describe some site specificities of gastrointestinal NEN. We specifically focus on biomarkers available to pathologists with the potential to change the way patients with NEN are diagnosed and treated.
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Affiliation(s)
- Anne Couvelard
- Department of Pathology of Bichat and Beaujon AP-HP Hospitals, ENETS Centre of Excellence, Université Paris Cité, 46 Rue Henri Huchard, 75018, Paris, France.
| | - Jérôme Cros
- Department of Pathology of Bichat and Beaujon AP-HP Hospitals, ENETS Centre of Excellence, Université Paris Cité, 46 Rue Henri Huchard, 75018, Paris, France
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13
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Nieboer MM, Nguyen L, de Ridder J. Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning. Sci Rep 2021; 11:14411. [PMID: 34257393 PMCID: PMC8277903 DOI: 10.1038/s41598-021-93917-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
Over the past years, large consortia have been established to fuel the sequencing of whole genomes of many cancer patients. Despite the increased abundance in tools to study the impact of SNVs, non-coding SVs have been largely ignored in these data. Here, we introduce svMIL2, an improved version of our Multiple Instance Learning-based method to study the effect of somatic non-coding SVs disrupting boundaries of TADs and CTCF loops in 1646 cancer genomes. We demonstrate that svMIL2 predicts pathogenic non-coding SVs with an average AUC of 0.86 across 12 cancer types, and identifies non-coding SVs affecting well-known driver genes. The disruption of active (super) enhancers in open chromatin regions appears to be a common mechanism by which non-coding SVs exert their pathogenicity. Finally, our results reveal that the contribution of pathogenic non-coding SVs as opposed to driver SNVs may highly vary between cancers, with notably high numbers of genes being disrupted by pathogenic non-coding SVs in ovarian and pancreatic cancer. Taken together, our machine learning method offers a potent way to prioritize putatively pathogenic non-coding SVs and leverage non-coding SVs to identify driver genes. Moreover, our analysis of 1646 cancer genomes demonstrates the importance of including non-coding SVs in cancer diagnostics.
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Affiliation(s)
- Marleen M Nieboer
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Luan Nguyen
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
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14
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Hiltunen N, Väyrynen JP, Böhm J, Helminen O. CD3 +, CD8 +, CD4 + and FOXP3 + T Cells in the Immune Microenvironment of Small Bowel Neuroendocrine Tumors. Diseases 2021; 9:diseases9020042. [PMID: 34208144 PMCID: PMC8293127 DOI: 10.3390/diseases9020042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 12/24/2022] Open
Abstract
The role of inflammation in neuroendocrine tumors is poorly known. The purpose of this study was to characterize the densities of CD3+, CD8+, CD4+ and FOXP3+ T cells in small bowel neuroendocrine tumors (SB-NETs), SB-NET lymph node metastases and gastric neuroendocrine tumors (G-NETs) to assess the prognostic role of immune cell infiltrates in SB-NETs. The final cohort included 113 SB-NETs, 75 SB-NET lymph node metastases and 19 G-NETs from two Finnish hospitals. CD3+- and CD8+-based immune cell score (ICS), and other T cell densities were evaluated. Survival analyses of SB-NETs and SB-NET lymph node metastases were performed with the Kaplan-Meier method and Cox regression adjusted for confounders. The primary outcome was disease-specific survival (DSS). No significant difference in DSS was seen between low and high ICS groups in SB-NETs at 5 years (92.6% vs. 87.8%) or 10 years (53.8% vs. 79.4%), p = 0.507, or in SB-NET lymph node metastases at 5 years (88.9% vs. 90.4%) or 10 years (71.1% vs. 59.8%), p = 0.466. Individual densities of the examined T cell types showed no correlation with prognosis either. SB-NETs and lymph node metastases had similar inflammatory cell profiles, whereas in G-NETs CD3+ and CD8+ T cells were particularly more abundant. In SB-NETs, ICS or T cell densities showed no correlation with prognosis.
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Affiliation(s)
- Niko Hiltunen
- Cancer and Translational Medicine Research Unit, Medical Research Center, University of Oulu, Oulu University Hospital, 90220 Oulu, Finland; (J.P.V.); (O.H.)
- Correspondence:
| | - Juha P. Väyrynen
- Cancer and Translational Medicine Research Unit, Medical Research Center, University of Oulu, Oulu University Hospital, 90220 Oulu, Finland; (J.P.V.); (O.H.)
- Department of Pathology, Central Finland Central Hospital, 40620 Jyväskylä, Finland;
| | - Jan Böhm
- Department of Pathology, Central Finland Central Hospital, 40620 Jyväskylä, Finland;
| | - Olli Helminen
- Cancer and Translational Medicine Research Unit, Medical Research Center, University of Oulu, Oulu University Hospital, 90220 Oulu, Finland; (J.P.V.); (O.H.)
- Surgery Research Unit, Medical Research Center, University of Oulu, Oulu University Hospital, 90220 Oulu, Finland
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