1
|
Koca D, Abedi-Ardekani B, LeMaoult J, Guyon L. Peritumoral tissue (PTT): increasing need for naming convention. Br J Cancer 2024; 131:1111-1115. [PMID: 39223304 PMCID: PMC11443153 DOI: 10.1038/s41416-024-02828-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/19/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024] Open
Abstract
Various terms are used to describe non-malignant tissue located in the proximity of a tumor, belonging to the organ from which the tumor originated. Traditionally, these tissues, sometimes called "normal adjacent tissue" have been used as controls in cancer studies, and were considered representative of morphologically healthy, non-cancerous tissue. However, with the advancement of OMIC technologies, such tissues are increasingly recognized to be distinct from both tumor and healthy tissues. Furthermore, properties, characteristics, and role of these tissues in cancer formation and progression is increasingly studied. In order to make future research in this area more harmonized and more accessible, as well as to counter the widespread perception of normalcy, we are advocating the need for standardized naming convention. For this purpose, we propose the use of neutral and comprehensive term "Peritumoral Tissue" along with the acronym "PTT". While significant amount of data on these tissues are publicly available, reuse of such data remains limited due to a lack of information on sample collection procedures. In order to facilitate future reuse of the data, we suggest a list of features that should be documented during sample collection procedures. These recommendations can aid the definition of Standard Operating Procedures.
Collapse
Affiliation(s)
- Dzenis Koca
- Interdisciplinary Research Institute of Grenoble, IRIG-Biosanté, University Grenoble Alpes, CEA, INSERM, UMR 1292, F-38000, Grenoble, France.
| | - Behnoush Abedi-Ardekani
- International Agency for Research on Cancer (IARC/WHO), Genomic Epidemiology Branch, Lyon, France
| | - Joel LeMaoult
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF, Francois Jacob Institute of Biology, Hemato-Immunology Research Department, Saint-Louis Hospital, Paris, France
- INSERM U976 HIPI Unit, IRSL, Université Paris, Paris, France
| | - Laurent Guyon
- Interdisciplinary Research Institute of Grenoble, IRIG-Biosanté, University Grenoble Alpes, CEA, INSERM, UMR 1292, F-38000, Grenoble, France.
| |
Collapse
|
2
|
Wu Y, Seufert I, Al-Shaheri FN, Kurilov R, Bauer AS, Manoochehri M, Moskalev EA, Brors B, Tjaden C, Giese NA, Hackert T, Büchler MW, Hoheisel JD. DNA-methylation signature accurately differentiates pancreatic cancer from chronic pancreatitis in tissue and plasma. Gut 2023; 72:2344-2353. [PMID: 37709492 PMCID: PMC10715533 DOI: 10.1136/gutjnl-2023-330155] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy. Differentiation from chronic pancreatitis (CP) is currently inaccurate in about one-third of cases. Misdiagnoses in both directions, however, have severe consequences for patients. We set out to identify molecular markers for a clear distinction between PDAC and CP. DESIGN Genome-wide variations of DNA-methylation, messenger RNA and microRNA level as well as combinations thereof were analysed in 345 tissue samples for marker identification. To improve diagnostic performance, we established a random-forest machine-learning approach. Results were validated on another 48 samples and further corroborated in 16 liquid biopsy samples. RESULTS Machine-learning succeeded in defining markers to differentiate between patients with PDAC and CP, while low-dimensional embedding and cluster analysis failed to do so. DNA-methylation yielded the best diagnostic accuracy by far, dwarfing the importance of transcript levels. Identified changes were confirmed with data taken from public repositories and validated in independent sample sets. A signature of six DNA-methylation sites in a CpG-island of the protein kinase C beta type gene achieved a validated diagnostic accuracy of 100% in tissue and in circulating free DNA isolated from patient plasma. CONCLUSION The success of machine-learning to identify an effective marker signature documents the power of this approach. The high diagnostic accuracy of discriminating PDAC from CP could have tremendous consequences for treatment success, once the result from still a limited number of liquid biopsy samples would be confirmed in a larger cohort of patients with suspected pancreatic cancer.
Collapse
Affiliation(s)
- Yenan Wu
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Isabelle Seufert
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Roman Kurilov
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mehdi Manoochehri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Evgeny A Moskalev
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christin Tjaden
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Nathalia A Giese
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Thilo Hackert
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus W Büchler
- Department of Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
3
|
Wu Y, Kröller L, Miao B, Boekhoff H, Bauer AS, Büchler MW, Hackert T, Giese NA, Taipale J, Hoheisel JD. Promoter Hypermethylation Promotes the Binding of Transcription Factor NFATc1, Triggering Oncogenic Gene Activation in Pancreatic Cancer. Cancers (Basel) 2021; 13:4569. [PMID: 34572796 PMCID: PMC8471171 DOI: 10.3390/cancers13184569] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/14/2021] [Accepted: 09/08/2021] [Indexed: 01/01/2023] Open
Abstract
Studies have indicated that some genes involved in carcinogenesis are highly methylated in their promoter regions but nevertheless strongly transcribed. It has been proposed that transcription factors could bind specifically to methylated promoters and trigger transcription. We looked at this rather comprehensively for pancreatic ductal adenocarcinoma (PDAC) and studied some cases in more detail. Some 2% of regulated genes in PDAC exhibited higher transcription coupled to promoter hypermethylation in comparison to healthy tissue. Screening 661 transcription factors, several were found to bind specifically to methylated promoters, in particular molecules of the NFAT family. One of them-NFATc1-was substantially more strongly expressed in PDAC than control tissue and exhibited a strong oncogenic role. Functional studies combined with computational analyses allowed determining affected genes. A prominent one was gene ALDH1A3, which accelerates PDAC metastasis and correlates with a bad prognosis. Further studies confirmed the direct up-regulation of ALDH1A3 transcription by NFATc1 promoter binding in a methylation-dependent process, providing insights into the oncogenic role of transcription activation in PDAC that is promoted by DNA methylation.
Collapse
Affiliation(s)
- Yenan Wu
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Lea Kröller
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Beiping Miao
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
- Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Henning Boekhoff
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Andrea S. Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
| | - Markus W. Büchler
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany; (M.W.B.); (T.H.); (N.A.G.)
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany; (M.W.B.); (T.H.); (N.A.G.)
| | - Nathalia A. Giese
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany; (M.W.B.); (T.H.); (N.A.G.)
| | - Jussi Taipale
- Division of Functional Genomics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 65 Solna, Sweden;
| | - Jörg D. Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; (Y.W.); (L.K.); (B.M.); (H.B.); (A.S.B.)
| |
Collapse
|
4
|
Knolle M, Kaissis G, Jungmann F, Ziegelmayer S, Sasse D, Makowski M, Rueckert D, Braren R. Efficient, high-performance semantic segmentation using multi-scale feature extraction. PLoS One 2021; 16:e0255397. [PMID: 34411138 PMCID: PMC8375977 DOI: 10.1371/journal.pone.0255397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/15/2021] [Indexed: 11/19/2022] Open
Abstract
The success of deep learning in recent years has arguably been driven by the availability of large datasets for training powerful predictive algorithms. In medical applications however, the sensitive nature of the data limits the collection and exchange of large-scale datasets. Privacy-preserving and collaborative learning systems can enable the successful application of machine learning in medicine. However, collaborative protocols such as federated learning require the frequent transfer of parameter updates over a network. To enable the deployment of such protocols to a wide range of systems with varying computational performance, efficient deep learning architectures for resource-constrained environments are required. Here we present MoNet, a small, highly optimized neural-network-based segmentation algorithm leveraging efficient multi-scale image features. MoNet is a shallow, U-Net-like architecture based on repeated, dilated convolutions with decreasing dilation rates. We apply and test our architecture on the challenging clinical tasks of pancreatic segmentation in computed tomography (CT) images as well as brain tumor segmentation in magnetic resonance imaging (MRI) data. We assess our model's segmentation performance and demonstrate that it provides performance on par with compared architectures while providing superior out-of-sample generalization performance, outperforming larger architectures on an independent validation set, while utilizing significantly fewer parameters. We furthermore confirm the suitability of our architecture for federated learning applications by demonstrating a substantial reduction in serialized model storage requirement as a surrogate for network data transfer. Finally, we evaluate MoNet's inference latency on the central processing unit (CPU) to determine its utility in environments without access to graphics processing units. Our implementation is publicly available as free and open-source software.
Collapse
Affiliation(s)
- Moritz Knolle
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Artificial Intelligence and Informatics in Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Georgios Kaissis
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Artificial Intelligence and Informatics in Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- OpenMined
- Department of Computing, Imperial College London, London, United Kingdom
| | - Friederike Jungmann
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian Ziegelmayer
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Daniel Sasse
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Marcus Makowski
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Daniel Rueckert
- Institute for Artificial Intelligence and Informatics in Medicine, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Computing, Imperial College London, London, United Kingdom
| | - Rickmer Braren
- Department of Diagnostic and Interventional Radiology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| |
Collapse
|
5
|
Gopalan V, Singh A, Rashidi Mehrabadi F, Wang L, Ruppin E, Arda HE, Hannenhalli S. A Transcriptionally Distinct Subpopulation of Healthy Acinar Cells Exhibit Features of Pancreatic Progenitors and PDAC. Cancer Res 2021; 81:3958-3970. [PMID: 34049974 PMCID: PMC8338776 DOI: 10.1158/0008-5472.can-21-0427] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/19/2021] [Accepted: 05/26/2021] [Indexed: 12/30/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) tumors can originate either from acinar or ductal cells in the adult pancreas. We re-analyze multiple pancreas and PDAC single-cell RNA-seq datasets and find a subset of nonmalignant acinar cells, which we refer to as acinar edge (AE) cells, whose transcriptomes highly diverge from a typical acinar cell in each dataset. Genes upregulated among AE cells are enriched for transcriptomic signatures of pancreatic progenitors, acinar dedifferentiation, and several oncogenic programs. AE-upregulated genes are upregulated in human PDAC tumors, and consistently, their promoters are hypomethylated. High expression of these genes is associated with poor patient survival. The fraction of AE-like cells increases with age in healthy pancreatic tissue, which is not explained by clonal mutations, thus pointing to a nongenetic source of variation. The fraction of AE-like cells is also significantly higher in human pancreatitis samples. Finally, we find edge-like states in lung, liver, prostate, and colon tissues, suggesting that subpopulations of healthy cells across tissues can exist in pre-neoplastic states. SIGNIFICANCE: These findings show "edge" epithelial cell states with oncogenic transcriptional activity in human organs without oncogenic mutations. In the pancreas, the fraction of acinar cells increases with age.
Collapse
Affiliation(s)
- Vishaka Gopalan
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland.
| | - Arashdeep Singh
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland
| | - Farid Rashidi Mehrabadi
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland
- Department of Computer Science, Indiana University, Bloomington, Indiana
| | - Li Wang
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland
| | - H Efsun Arda
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland.
| |
Collapse
|
6
|
Xia J, Zhang H, Guan Q, Wang S, Li Y, Xie J, Li M, Huang H, Yan H, Chen T. Qualitative diagnostic signature for pancreatic ductal adenocarcinoma based on the within-sample relative expression orderings. J Gastroenterol Hepatol 2021; 36:1714-1720. [PMID: 33150986 DOI: 10.1111/jgh.15326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/18/2020] [Accepted: 10/24/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) accounts for about 90% of pancreatic cancer, which is one of the most aggressive malignant neoplasms with a 9.3% five-year survival rate. The pathological biopsy is the current golden standard for confirming suspicious lesions of PDAC, but it is not entirely reliable because of the insufficient sampling amount and inaccurate sampling location. Therefore, developing a robust signature to aid the accurate diagnosis of PDAC is critical. METHODS Based on the within-sample relative expression orderings of gene pairs, we identified a qualitative signature to discriminate both PDAC and adjacent samples from both chronic pancreatitis and normal samples in the training datasets and validated it in other independent datasets produced by different laboratories with different measuring platforms. RESULTS A six-gene-pair signature was identified in the training data and validated in eight independent datasets. For surgical samples, 96.63% of 356 PDAC tissues, 100% of 11 pancreatitis tissues of non-cancer patients, and 23 of 24 normal pancreatic tissues were correctly classified. Especially, 59 of 60 cancer-adjacent normal tissues of PDAC patients were correctly identified as PDAC. For biopsy samples, all of 11 PDAC biopsy tissues were correctly classified as PDAC. CONCLUSION The signature can distinguish both PDAC and PDAC-adjacent normal tissues from both chronic pancreatitis and normal tissues of non-cancer patients even when the sampling locations are inaccurate, which can aid the diagnosis of PDAC.
Collapse
Affiliation(s)
- Jie Xia
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Huarong Zhang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qingzhou Guan
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Shanshan Wang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yawei Li
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jiajing Xie
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Meifeng Li
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Haiyan Huang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Haidan Yan
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Ting Chen
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| |
Collapse
|
7
|
Al-Shaheri FN, Alhamdani MSS, Bauer AS, Giese N, Büchler MW, Hackert T, Hoheisel JD. Blood biomarkers for differential diagnosis and early detection of pancreatic cancer. Cancer Treat Rev 2021; 96:102193. [PMID: 33865174 DOI: 10.1016/j.ctrv.2021.102193] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
Pancreatic cancer is currently the most lethal tumor entity and case numbers are rising. It will soon be the second most frequent cause of cancer-related death in the Western world. Mortality is close to incidence and patient survival after diagnosis stands at about five months. Blood-based diagnostics could be one crucial factor for improving this dismal situation and is at a stage that could make this possible. Here, we are reviewing the current state of affairs with its problems and promises, looking at various molecule types. Reported results are evaluated in the overall context. Also, we are proposing steps toward clinical utility that should advance the development toward clinical application by improving biomarker quality but also by defining distinct clinical objectives and the respective diagnostic accuracies required to achieve them. Many of the discussed points and conclusions are highly relevant to other solid tumors, too.
Collapse
Affiliation(s)
- Fawaz N Al-Shaheri
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany.
| | - Mohamed S S Alhamdani
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Andrea S Bauer
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Markus W Büchler
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| |
Collapse
|
8
|
Barrera LN, Evans A, Lane B, Brumskill S, Oldfield FE, Campbell F, Andrews T, Lu Z, Perez-Mancera PA, Liloglou T, Ashworth M, Jalali M, Dawson R, Nunes Q, Phillips PA, Timms JF, Halloran C, Greenhalf W, Neoptolemos JP, Costello E. Fibroblasts from Distinct Pancreatic Pathologies Exhibit Disease-Specific Properties. Cancer Res 2020; 80:2861-2873. [PMID: 32393661 DOI: 10.1158/0008-5472.can-19-3534] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/14/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022]
Abstract
Although fibrotic stroma forms an integral component of pancreatic diseases, whether fibroblasts programmed by different types of pancreatic diseases are phenotypically distinct remains unknown. Here, we show that fibroblasts isolated from patients with pancreatic ductal adenocarcinoma (PDAC), chronic pancreatitis (CP), periampullary tumors, and adjacent normal (NA) tissue (N = 34) have distinct mRNA and miRNA profiles. Compared with NA fibroblasts, PDAC-associated fibroblasts were generally less sensitive to an antifibrotic stimulus (NPPB) and more responsive to positive regulators of activation such as TGFβ1 and WNT. Of the disease-associated fibroblasts examined, PDAC- and CP-derived fibroblasts shared greatest similarity, yet PDAC-associated fibroblasts expressed higher levels of tenascin C (TNC), a finding attributable to miR-137, a novel regulator of TNC. TNC protein and transcript levels were higher in PDAC tissue versus CP tissue and were associated with greater levels of stromal activation, and conditioned media from TNC-depleted PDAC-associated fibroblasts modestly increased both PDAC cell proliferation and PDAC cell migration, indicating that stromal TNC may have inhibitory effects on PDAC cells. Finally, circulating TNC levels were higher in patients with PDAC compared with CP. Our characterization of pancreatic fibroblast programming as disease-specific has consequences for therapeutic targeting and for the manner in which fibroblasts are used in research. SIGNIFICANCE: Primary fibroblasts derived from various types of pancreatic diseases possess and retain distinct molecular and functional characteristics in culture, providing a series of cellular models for treatment development and disease-specific research.
Collapse
Affiliation(s)
- Lawrence N Barrera
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Anthony Evans
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Brian Lane
- School of Medical Sciences, Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Sarah Brumskill
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Frances E Oldfield
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Fiona Campbell
- Department of Histopathology, Royal Liverpool University Hospital, Liverpool, United Kingdom
| | - Timothy Andrews
- Department of Histopathology, Royal Liverpool University Hospital, Liverpool, United Kingdom
| | - Zipeng Lu
- Pancreas Center, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Pedro A Perez-Mancera
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Triantafillos Liloglou
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Milton Ashworth
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Mehdi Jalali
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Rebecca Dawson
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Quentin Nunes
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Phoebe A Phillips
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, School of Medical Sciences, University of New South Wales (UNSW Sydney), Sydney, Australia
| | - John F Timms
- Institute for Women's Health, University College London, London, United Kingdom
| | - Christopher Halloran
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - William Greenhalf
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - John P Neoptolemos
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Eithne Costello
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom.
| |
Collapse
|
9
|
Manoochehri M, Wu Y, Giese NA, Strobel O, Kutschmann S, Haller F, Hoheisel JD, Moskalev EA, Hackert T, Bauer AS. SST gene hypermethylation acts as a pan-cancer marker for pancreatic ductal adenocarcinoma and multiple other tumors: toward its use for blood-based diagnosis. Mol Oncol 2020; 14:1252-1267. [PMID: 32243066 PMCID: PMC7266283 DOI: 10.1002/1878-0261.12684] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 03/07/2020] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
Aberrant DNA methylation is often involved in carcinogenesis. Our initial goal was to identify DNA methylation biomarkers associated with pancreatic cancer. A genomewide methylation study was performed on DNA from pancreatic ductal adenocarcinoma (PDAC) and endocrine pancreas tumors. Validation of DNA methylation patterns and concomitant alterations in expression of gene candidates was performed on patient samples and pancreatic cancer cell lines. Furthermore, validation was done on independent data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Finally, droplet digital PCR was employed to detect DNA methylation marks in cell-free (cf) DNA isolated from plasma samples of PDAC patients and cancer-free blood donors. Hypermethylation of the SST gene (encoding somatostatin) and concomitant downregulation of its expression were discovered in PDAC and endocrine tumor tissues while not being present in chronic pancreatitis (inflamed) tissues and normal pancreas. Fittingly, treatment with a somatostatin agonist (octreotide) reduced cell proliferation and migration of pancreatic cancer cells. Diagnostic performance of SST methylation in a receiver operating characteristic curve analysis was 100% and 89% for tissue and plasma samples, respectively. A large body of TCGA and GEO data confirmed SST hypermethylation and downregulation in PDAC and showed a similar effect in a broad spectrum of other tumor entities. SST promoter methylation represents a sensitive and promising molecular, pan-cancer biomarker detectable in tumor tissue, and liquid biopsy samples.
Collapse
Affiliation(s)
- Mehdi Manoochehri
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Molecular Genetics of Breast CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Yenan Wu
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | | | - Oliver Strobel
- Department of General SurgeryUniversity Hospital HeidelbergGermany
| | - Stefanie Kutschmann
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Florian Haller
- Diagnostic Molecular PathologyInstitute of PathologyFriedrich‐Alexander UniversityErlangenGermany
| | - Jörg D. Hoheisel
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Evgeny A. Moskalev
- Diagnostic Molecular PathologyInstitute of PathologyFriedrich‐Alexander UniversityErlangenGermany
| | - Thilo Hackert
- Department of General SurgeryUniversity Hospital HeidelbergGermany
| | - Andrea S. Bauer
- Division of Functional Genome AnalysisGerman Cancer Research Center (DKFZ)HeidelbergGermany
| |
Collapse
|