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Matsumoto K, Fujimori N, Ichihara K, Takeno A, Murakami M, Ohno A, Kakehashi S, Teramatsu K, Ueda K, Nakata K, Sugahara O, Yamamoto T, Matsumoto A, Nakayama KI, Oda Y, Nakamura M, Ogawa Y. Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction. J Gastroenterol 2024; 59:629-640. [PMID: 38684511 PMCID: PMC11217054 DOI: 10.1007/s00535-024-02103-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 03/31/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Recently, two molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) have been proposed: the "Classical" and "Basal-like" subtypes, with the former showing better clinical outcomes than the latter. However, the "molecular" classification has not been applied in real-world clinical practice. This study aimed to establish patient-derived organoids (PDOs) for PDAC and evaluate their application in subtype classification and clinical outcome prediction. METHODS We utilized tumor samples acquired through endoscopic ultrasound-guided fine-needle biopsy and established a PDO library for subsequent use in morphological assessments, RNA-seq analyses, and in vitro drug response assays. We also conducted a prospective clinical study to evaluate whether analysis using PDOs can predict treatment response and prognosis. RESULTS PDOs of PDAC were established at a high efficiency (> 70%) with at least 100,000 live cells. Morphologically, PDOs were classified as gland-like structures (GL type) and densely proliferating inside (DP type) less than 2 weeks after tissue sampling. RNA-seq analysis revealed that the "morphological" subtype (GL vs. DP) corresponded to the "molecular" subtype ("Classical" vs. "Basal-like"). The "morphological" classification predicted the clinical treatment response and prognosis; the median overall survival of patients with GL type was significantly longer than that with DP type (P < 0.005). The GL type showed a better response to gemcitabine than the DP type in vitro, whereas the drug response of the DP type was improved by the combination of ERK inhibitor and chloroquine. CONCLUSIONS PDAC PDOs help in subtype determination and clinical outcome prediction, thereby facilitating the bench-to-bedside precision medicine for PDAC.
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Affiliation(s)
- Kazuhide Matsumoto
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Nao Fujimori
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
| | - Kazuya Ichihara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Ayumu Takeno
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masatoshi Murakami
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Akihisa Ohno
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Shotaro Kakehashi
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Katsuhito Teramatsu
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Keijiro Ueda
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Kohei Nakata
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Osamu Sugahara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeo Yamamoto
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Akinobu Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masafumi Nakamura
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan.
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Pulvirenti A, Barbagallo M, Putignano AR, Pea A, Polidori R, Upstill-Goddard R, Cortese N, Kunderfranco P, Brunelli L, De Simone G, Pastorelli R, Spaggiari P, Nappo G, Jamieson NB, Zerbi A, Chang DK, Capretti G, Marchesi F. Integrating metabolic profiling of pancreatic juice with transcriptomic analysis of pancreatic cancer tissue identifies distinct clinical subgroups. Front Oncol 2024; 14:1405612. [PMID: 38988711 PMCID: PMC11234733 DOI: 10.3389/fonc.2024.1405612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/31/2024] [Indexed: 07/12/2024] Open
Abstract
Introduction Metabolic reprogramming is a hallmark feature of pancreatic ductal adenocarcinoma (PDAC). A pancreatic juice (PJ) metabolic signature has been reported to be prognostic of oncological outcome for PDAC. Integration of PJ profiling with transcriptomic and spatial characterization of the tumor microenvironment would help in identifying PDACs with peculiar vulnerabilities. Methods We performed a transcriptomic analysis of 26 PDAC samples grouped into 3 metabolic clusters (M_CL) according to their PJ metabolic profile. We analyzed molecular subtypes and transcriptional differences. Validation was performed by multidimensional imaging on tumor slides. Results Pancreatic juice metabolic profiling was associated with PDAC transcriptomic molecular subtypes (p=0.004). Tumors identified as M_CL1 exhibited a non-squamous molecular phenotype and demonstrated longer survival. Enrichment analysis revealed the upregulation of immune genes and pathways in M_CL1 samples compared to M_CL2, the group with worse prognosis, a difference confirmed by immunofluorescence on tissue slides. Enrichment analysis of 39 immune signatures by xCell confirmed decreased immune signatures in M_CL2 compared to M_CL1 and allowed a stratification of patients associated with longer survival. Discussion PJ metabolic fingerprints reflect PDAC molecular subtypes and the immune microenvironment, confirming PJ as a promising source of biomarkers for personalized therapy.
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Affiliation(s)
- Alessandra Pulvirenti
- Section of Pancreatic Surgery, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
- Department of Surgical Oncological and Gastroenterological Sciences (DiSCOG), University of Padua, Padua, Italy
| | - Marialuisa Barbagallo
- Department of Immunology and Inflammation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Anna Rita Putignano
- Department of Immunology and Inflammation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Antonio Pea
- Department of General and Pancreatic Surgery-The Pancreas Institute, Verona University Hospital Trust, Verona, Italy
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rebecca Polidori
- Department of Immunology and Inflammation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Rosie Upstill-Goddard
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nina Cortese
- Department of Immunology and Inflammation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Paolo Kunderfranco
- Bioinformatics Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Laura Brunelli
- Laboratory of Metabolites and Proteins in Translational Research, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Giulia De Simone
- Laboratory of Metabolites and Proteins in Translational Research, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Roberta Pastorelli
- Laboratory of Metabolites and Proteins in Translational Research, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - Paola Spaggiari
- Pathology Department, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
| | - Gennaro Nappo
- Section of Pancreatic Surgery, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Nigel B. Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Alessandro Zerbi
- Section of Pancreatic Surgery, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Giovanni Capretti
- Section of Pancreatic Surgery, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Italy
| | - Federica Marchesi
- Department of Immunology and Inflammation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Rozzano, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
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van Eijck CWF, Real FX, Malats N, Vadgama D, van den Bosch TPP, Doukas M, van Eijck CHJ, Mustafa DAM. GATA6 identifies an immune-enriched phenotype linked to favorable outcomes in patients with pancreatic cancer undergoing upfront surgery. Cell Rep Med 2024; 5:101557. [PMID: 38733987 PMCID: PMC11148804 DOI: 10.1016/j.xcrm.2024.101557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/14/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
This study underscores GATA6's role in distinguishing classical and basal-like pancreatic ductal adenocarcinoma (PDAC) phenotypes. Retrospective studies associate GATA6 immunohistochemistry (IHC) expression with survival outcomes, warranting prospective validation. In a prospective treatment-naive cohort of patients with resected PDAC, GATA6 IHC proves a prognostic discriminator, associating high GATA6 expression with extended survival and the classical PDAC phenotype. However, GATA6's prognostic significance is numerically lower after gemcitabine-based neoadjuvant chemoradiotherapy compared to its significance in patients treated with upfront surgery. Furthermore, GATA6 is implicated in immunomodulation, although a comprehensive investigation of its immunological role is lacking. Treatment-naive PDAC tumors with varying GATA6 expression yield distinct immunological landscapes. Tumors highly expressing GATA6 show reduced infiltration of immunosuppressive regulatory T cells and M2 macrophages but increased infiltration of immune-stimulating, antigen-presenting, and activated T cells. Our findings caution against solely relying on GATA6 for molecular subtyping in clinical trials and open avenues for exploring immune-based combination therapies.
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Affiliation(s)
- Casper W F van Eijck
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain.
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre, Madrid, Spain; Centro de Investigación Biomédica en Red-Cáncer, Madrid, Spain; Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain; Centro de Investigación Biomédica en Red-Cáncer, Madrid, Spain
| | - Disha Vadgama
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Thierry P P van den Bosch
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Michail Doukas
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Casper H J van Eijck
- Department of Surgery, Erasmus University Medical Centre, Rotterdam, the Netherlands; Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, Madrid, Spain
| | - Dana A M Mustafa
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Centre, Rotterdam, the Netherlands; The Tumor Immuno-Pathology Laboratory, Erasmus University Medical Centre, Rotterdam, the Netherlands.
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Lin J, Liu P, Sun K, Jiang L, Liu Y, Huang Y, Liu J, Shi M, Zhang J, Wang T, Shen B. Comprehensive analysis of KLF family reveals KLF6 as a promising prognostic and immune biomarker in pancreatic ductal adenocarcinoma. Cancer Cell Int 2024; 24:177. [PMID: 38773440 PMCID: PMC11106939 DOI: 10.1186/s12935-024-03369-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/11/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest tumors worldwide, with extremely aggressive and complicated biology. Krüppel-like factors (KLFs) encode a series of transcriptional regulatory proteins and play crucial roles in a variety of processes, including tumor cell differentiation and proliferation. However, the potential biological functions and possible pathways of KLFs in the progression of PDAC remain elusive. METHODS We systematically evaluated the transcriptional variations and expression patterns of KLFs in pancreatic cancer from the UCSC Xena. Based on difference analysis, the non-negative matrix factorization (NMF) algorithm was utilized to identify the immune characteristics and clinical significance of two different subtypes. The multivariate Cox regression was used to construct the risk model and then explore the differences in tumor immune microenvironment (TIME) and drug sensitivity between high and low groups. Through single-cell RNA sequencing (scRNA-seq) analysis, we screened KLF6 and further investigated its biological functions in pancreatic cancer and pan-cancer. RESULTS The KLFs exhibited differential expression and mutations in the transcriptomic profile of PDAC. According to the expression of KLFs, patients were classified into two distinct subtypes, each exhibiting significant differences in prognosis and TIME. Moreover, the KLF signature was developed using univariate Cox and Lasso regression, which proved to be a reliable and effective prognostic model. Furthermore, the KLF_Score was closely associated with immune infiltration, response to immunotherapy, and drug sensitivity and we screened small molecule compounds targeting prognostic genes separately. Through scRNA-seq analysis, KLF6 was selected to further demonstrate its role in the malignance of PC in vitro. Finally, pan-cancer analysis emphasized the biological significance of KLF6 in multiple types of tumors and its clinical utility in assessing cancer prognosis. CONCLUSION This study elucidated the pivotal role of KLF family genes in the malignant development of PC through comprehensive analysis and revealed that KLF6 would be a novel diagnostic biomolecule marker and potential therapeutic target for PDAC.
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Affiliation(s)
- Jiayu Lin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Pengyi Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Keyan Sun
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yang Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yishu Huang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jia Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Minmin Shi
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jun Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Pancreatic Neoplasms Translational Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiaotong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiaotong University, Shanghai, China
- Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ting Wang
- Department of Pathology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiaotong University, Shanghai, People's Republic of China.
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Zheng B, Li Y, Xiong G. Establishment and analysis of artificial neural network diagnosis model for coagulation-related molecular subgroups in coronary artery disease. Front Genet 2024; 15:1351774. [PMID: 38495669 PMCID: PMC10941628 DOI: 10.3389/fgene.2024.1351774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/20/2024] [Indexed: 03/19/2024] Open
Abstract
Background: Coronary artery disease (CAD) is the most common type of cardiovascular disease and cause significant morbidity and mortality. Abnormal coagulation cascade is one of the high-risk factors in CAD patients, but the molecular mechanism of coagulation in CAD is still limited. Methods: We clustered and categorized 352 CAD paitents based on the expression patterns of coagulation-related genes (CRGs), and then we explored the molecular and immunological variations across the subgroups to reveal the underlying biological characteristics of CAD patients. The feature genes between CRG-subgroups were further identified using a random forest model (RF) and least absolute shrinkage and selection operator (LASSO) regression, and an artificial neural network prediction model was constructed. Results: CAD patients could be divided into the C1 and C2 CRG-subgroups, with the C1 subgroup highly enriched in immune-related signaling pathways. The differential expressed genes between the two CRG-subgroups (DE-CRGs) were primarily enriched in signaling pathways connected to signal transduction and energy metabolism. Subsequently, 10 feature DE-CRGs were identified by RF and LASSO. We constructed a novel artificial neural network model using these 10 genes and evaluated and validated its diagnostic performance on a public dataset. Conclusion: Diverse molecular subgroups of CAD patients may each have a unique gene expression pattern. We may identify subgroups using a few feature genes, providing a theoretical basis for the precise treatment of CAD patients with different molecular subgroups.
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Affiliation(s)
- Biwei Zheng
- Department of Cardiology, Dongguan Hospital of Integrated Chinese and Western Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Dongguan, China
| | - Yujing Li
- Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
- Beijing University of Chinese Medicine Shenzhen Hospital (Longgang), Shenzhen, China
| | - Guoliang Xiong
- Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
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Wang L, Fu D, Weng S, Xu H, Liu L, Guo C, Ren Y, Liu Z, Han X. Genome-scale CRISPR-Cas9 screening stratifies pancreatic cancer with distinct outcomes and immunotherapeutic efficacy. Cell Signal 2023; 110:110811. [PMID: 37468054 DOI: 10.1016/j.cellsig.2023.110811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/02/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Pancreatic cancer (PC) was featured by dramatic heterogeneity and dismal outcomes. An ideal classification strategy capable of achieving risk stratification and individualized treatment is urgently needed to significantly improve prognosis. In this study, using the 105 prognostic cancer essential genes identified by genome-scale CRISPR-Cas9 screening and univariate Cox analysis, we established and verified three heterogeneous subtypes via non-negative matrix factorization (NMF) and nearest template prediction (NTP) algorithms in the TCGA-PAAD cohort (176 samples) and four multi-center cohorts (233 samples), respectively. Among them, C1 with the worst prognosis was enriched in immune-related pathways, possessed superior infiltration abundance of immune cells and immune checkpoint molecules expression, and might be most sensitive to immunotherapy. C3, owing a moderate prognosis, might be featured by proliferative biological function, and despite its highest immunogenicity, the defects in antigen processing and presentation ability coupled with barren immune environment render it ineffective for immunotherapy, while it had potential sensitivity to paclitaxel and methotrexate. Besides, C2 harbored the best prognosis and was characterized by metabolism-related functions. These results could deepen our understanding of PC molecular heterogeneity and provide a trustworthy reference for prognostic stratification management and precision medicine in clinical practice.
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Affiliation(s)
- Libo Wang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China; Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Deshuang Fu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China; Department of Dermatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Long Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China.
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Zhang B, Huang B, Zhang X, Li S, Zhu J, Chen X, Song H, Shang D. PANoptosis-related molecular subtype and prognostic model associated with the immune microenvironment and individualized therapy in pancreatic cancer. Front Oncol 2023; 13:1217654. [PMID: 37519797 PMCID: PMC10382139 DOI: 10.3389/fonc.2023.1217654] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
Background PANoptosis is an inflammatory type of programmed cell death regulated by PANopotosome. Mounting evidence has shown that PANoptosis could be involved in cancer pathogenesis and the tumor immune microenvironment. Nevertheless, there have been no studies on the mechanism of PANoptosis on pancreatic cancer (PC) pathogenesis. Methods We downloaded the data on transcriptomic and clinical features of PC patients from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. Additionally, the data on copy number variation (CNV), methylation and somatic mutations of genes in 33 types of cancers were obtained from TCGA. Next, we identified the PANoptosis-related molecular subtype using the consensus clustering analysis, and constructed and validated the PANoptosis-related prognostic model using LASSO and Cox regression analyses. Moreover, RT-qPCR was performed to determine the expression of genes involved in the model. Results We obtained 66 PANoptosis-related genes (PANRGs) from published studies. Of these, 24 PC-specific prognosis-related genes were identified. Pan-cancer analysis revealed complex genetic changes, including CNV, methylation, and mutation in PANRGs were identified in various cancers. By consensus clustering analysis, PC patients were classified into two PANoptosis-related patterns: PANcluster A and B. In PANcluster A, the patient prognosis was significantly worse compared to PANcluster B. The CIBERSORT algorithm showed a significant increase in the infiltration of CD8+ T cells, monocytes, and naïve B cells, in patients in PANcluster B. Additionally, the infiltration of macrophages, activated mast cells, and dendritic cells were higher in patients in PANcluster A. Patients in PANcluster A were more sensitive to erlotinib, selumetinib and trametinib, whereas patients in PANcluster B were highly sensitive to irinotecan, oxaliplatin and sorafenib. Moreover, we constructed and validated the PANoptosis-related prognostic model to predict the patient's survival. Finally, the GEPIA and Human Protein Atlas databases were analyzed, and RT-qPCR was performed. Compared to normal tissues, a significant increase in CXCL10 and ITGB6 (associated with the model) expression was observed in PC tissues. Conclusion We first identified the PANoptosis-related molecular subtypes and established a PANoptosis-related prognostic model for predicting the survival of patients with PC. These results would aid in exploring the mechanisms of PANoptosis in PC pathogenesis.
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Affiliation(s)
- Biao Zhang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Bingqian Huang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Xiaonan Zhang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Shuang Li
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jingyi Zhu
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
| | - Xu Chen
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Huiyi Song
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dong Shang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, China
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, China
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8
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Saillard C, Delecourt F, Schmauch B, Moindrot O, Svrcek M, Bardier-Dupas A, Emile JF, Ayadi M, Rebours V, de Mestier L, Hammel P, Neuzillet C, Bachet JB, Iovanna J, Dusetti N, Blum Y, Richard M, Kermezli Y, Paradis V, Zaslavskiy M, Courtiol P, Kamoun A, Nicolle R, Cros J. Pacpaint: a histology-based deep learning model uncovers the extensive intratumor molecular heterogeneity of pancreatic adenocarcinoma. Nat Commun 2023; 14:3459. [PMID: 37311751 DOI: 10.1038/s41467-023-39026-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
Two tumor (Classical/Basal) and stroma (Inactive/active) subtypes of Pancreatic adenocarcinoma (PDAC) with prognostic and theragnostic implications have been described. These molecular subtypes were defined by RNAseq, a costly technique sensitive to sample quality and cellularity, not used in routine practice. To allow rapid PDAC molecular subtyping and study PDAC heterogeneity, we develop PACpAInt, a multi-step deep learning model. PACpAInt is trained on a multicentric cohort (n = 202) and validated on 4 independent cohorts including biopsies (surgical cohorts n = 148; 97; 126 / biopsy cohort n = 25), all with transcriptomic data (n = 598) to predict tumor tissue, tumor cells from stroma, and their transcriptomic molecular subtypes, either at the whole slide or tile level (112 µm squares). PACpAInt correctly predicts tumor subtypes at the whole slide level on surgical and biopsies specimens and independently predicts survival. PACpAInt highlights the presence of a minor aggressive Basal contingent that negatively impacts survival in 39% of RNA-defined classical cases. Tile-level analysis ( > 6 millions) redefines PDAC microheterogeneity showing codependencies in the distribution of tumor and stroma subtypes, and demonstrates that, in addition to the Classical and Basal tumors, there are Hybrid tumors that combine the latter subtypes, and Intermediate tumors that may represent a transition state during PDAC evolution.
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Affiliation(s)
| | - Flore Delecourt
- Université Paris Cité, Dpt of Pathology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France
| | | | | | - Magali Svrcek
- Dpt of Pathology, Saint-Antoine Hospital - Sorbonne Universités, Paris, France
| | | | - Jean Francois Emile
- Dpt of Pathology, Ambroise Paré Hospital - Université Saint Quentin en Yvelines, Paris, France
| | - Mira Ayadi
- Integragen, Genomic Services & Precision Medicine, Paris, France
| | - Vinciane Rebours
- Université Paris Cité, Dpt of Pancreatology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France
| | - Louis de Mestier
- Université Paris Cité, Dpt of Pancreatology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France
| | - Pascal Hammel
- Dpt of Medical oncology, Paul Brousse Hospital, Villejuif, France
| | | | - Jean Baptiste Bachet
- Dpt of Gastroenterology, Pitié-Salpêtrière Hospital - Sorbonne Universités, Paris, France
| | - Juan Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, Institut Paoli-Calmettes, Aix Marseille Université, CNRS UMR 7258, Marseille, France
| | - Nelson Dusetti
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, Institut Paoli-Calmettes, Aix Marseille Université, CNRS UMR 7258, Marseille, France
| | - Yuna Blum
- Institut Génétique et Développement de Rennes (IGDR), CNRS, Université de Rennes 1, UMR 6290, Rennes, France
| | - Magali Richard
- Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble (TIMC-IMAG), CNRS, Université Grenoble-Alpes, UMR5525, Grenoble, France
| | - Yasmina Kermezli
- Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble (TIMC-IMAG), CNRS, Université Grenoble-Alpes, UMR5525, Grenoble, France
| | - Valerie Paradis
- Université Paris Cité, Dpt of Pathology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France
| | | | | | | | - Remy Nicolle
- Université Paris Cité, FHU MOSAIC, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, F-75018, Paris, France
| | - Jerome Cros
- Université Paris Cité, Dpt of Pathology - FHU MOSAIC, Beaujon Hospital, INSERM U1149, Clichy, France.
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9
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Palma AM, Vudatha V, Peixoto ML, Madan E. Tumor heterogeneity: An oncogenic driver of PDAC progression and therapy resistance under stress conditions. Adv Cancer Res 2023; 159:203-249. [PMID: 37268397 DOI: 10.1016/bs.acr.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a clinically challenging disease usually diagnosed at advanced or metastasized stage. By this year end, there are an expected increase in 62,210 new cases and 49,830 deaths in the United States, with 90% corresponding to PDAC subtype alone. Despite advances in cancer therapy, one of the major challenges combating PDAC remains tumor heterogeneity between PDAC patients and within the primary and metastatic lesions of the same patient. This review describes the PDAC subtypes based on the genomic, transcriptional, epigenetic, and metabolic signatures observed among patients and within individual tumors. Recent studies in tumor biology suggest PDAC heterogeneity as a major driver of disease progression under conditions of stress including hypoxia and nutrient deprivation, leading to metabolic reprogramming. We therefore advance our understanding in identifying the underlying mechanisms that interfere with the crosstalk between the extracellular matrix components and tumor cells that define the mechanics of tumor growth and metastasis. The bilateral interaction between the heterogeneous tumor microenvironment and PDAC cells serves as another important contributor that characterizes the tumor-promoting or tumor-suppressing phenotypes providing an opportunity for an effective treatment regime. Furthermore, we highlight the dynamic reciprocating interplay between the stromal and immune cells that impact immune surveillance or immune evasion response and contribute towards a complex process of tumorigenesis. In summary, the review encapsulates the existing knowledge of the currently applied treatments for PDAC with emphasis on tumor heterogeneity, manifesting at multiple levels, impacting disease progression and therapy resistance under stress.
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Affiliation(s)
| | - Vignesh Vudatha
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | | | - Esha Madan
- Champalimaud Centre for the Unknown, Lisbon, Portugal; Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States.
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10
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Jeong YJ, Knutsdottir H, Shojaeian F, Lerner MG, Wissler MF, Henriet E, Ng T, Datta S, Navarro-Serer B, Chianchiano P, Kinny-Köster B, Zimmerman JW, Stein-O’Brien G, Gaida MM, Eshleman JR, Lin MT, Fertig EJ, Ewald AJ, Bader JS, Wood LD. Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion. J Clin Invest 2023; 133:e162054. [PMID: 36881486 PMCID: PMC10104894 DOI: 10.1172/jci162054] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) frequently presents with metastasis, but the molecular programs in human PDAC cells that drive invasion are not well understood. Using an experimental pipeline enabling PDAC organoid isolation and collection based on invasive phenotype, we assessed the transcriptomic programs associated with invasion in our organoid model. We identified differentially expressed genes in invasive organoids compared with matched noninvasive organoids from the same patients, and we confirmed that the encoded proteins were enhanced in organoid invasive protrusions. We identified 3 distinct transcriptomic groups in invasive organoids, 2 of which correlated directly with the morphological invasion patterns and were characterized by distinct upregulated pathways. Leveraging publicly available single-cell RNA-sequencing data, we mapped our transcriptomic groups onto human PDAC tissue samples, highlighting differences in the tumor microenvironment between transcriptomic groups and suggesting that non-neoplastic cells in the tumor microenvironment can modulate tumor cell invasion. To further address this possibility, we performed computational ligand-receptor analysis and validated the impact of multiple ligands (TGF-β1, IL-6, CXCL12, MMP9) on invasion and gene expression in an independent cohort of fresh human PDAC organoids. Our results identify molecular programs driving morphologically defined invasion patterns and highlight the tumor microenvironment as a potential modulator of these programs.
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Affiliation(s)
- Yea Ji Jeong
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hildur Knutsdottir
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
| | - Fatemeh Shojaeian
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael G. Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana, USA
| | - Maria F. Wissler
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Tammy Ng
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shalini Datta
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Bernat Navarro-Serer
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter Chianchiano
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Jacquelyn W. Zimmerman
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Genevieve Stein-O’Brien
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthias M. Gaida
- Department of Pathology, University of Mainz, Mainz, Germany
- TRON, Translational Oncology at the University Medical Center, Mainz, Germany
- Research Center for Immunotherapy, University Medical Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
| | - James R. Eshleman
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
| | - Ming-Tseh Lin
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Elana J. Fertig
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew J. Ewald
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
- Department of Cell Biology
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
| | - Joel S. Bader
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
| | - Laura D. Wood
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, and
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11
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Williams HL, Dias Costa A, Zhang J, Raghavan S, Winter PS, Kapner KS, Ginebaugh SP, Väyrynen SA, Väyrynen JP, Yuan C, Navia AW, Wang J, Yang A, Bosse TL, Kalekar RL, Lowder KE, Lau MC, Elganainy D, Morales-Oyarvide V, Rubinson DA, Singh H, Perez K, Cleary JM, Clancy TE, Wang J, Mancias JD, Brais LK, Hill ER, Kozak MM, Linehan DC, Dunne RF, Chang DT, Koong AC, Hezel AF, Hahn WC, Shalek AK, Aguirre AJ, Nowak JA, Wolpin BM. Spatially Resolved Single-Cell Assessment of Pancreatic Cancer Expression Subtypes Reveals Co-expressor Phenotypes and Extensive Intratumoral Heterogeneity. Cancer Res 2023; 83:441-455. [PMID: 36459568 PMCID: PMC10548885 DOI: 10.1158/0008-5472.can-22-3050] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has been classified into classical and basal-like transcriptional subtypes by bulk RNA measurements. However, recent work has uncovered greater complexity to transcriptional subtypes than was initially appreciated using bulk RNA expression profiling. To provide a deeper understanding of PDAC subtypes, we developed a multiplex immunofluorescence (mIF) pipeline that quantifies protein expression of six PDAC subtype markers (CLDN18.2, TFF1, GATA6, KRT17, KRT5, and S100A2) and permits spatially resolved, single-cell interrogation of pancreatic tumors from resection specimens and core needle biopsies. Both primary and metastatic tumors displayed striking intratumoral subtype heterogeneity that was associated with patient outcomes, existed at the scale of individual glands, and was significantly reduced in patient-derived organoid cultures. Tumor cells co-expressing classical and basal markers were present in > 90% of tumors, existed on a basal-classical polarization continuum, and were enriched in tumors containing a greater admixture of basal and classical cell populations. Cell-cell neighbor analyses within tumor glands further suggested that co-expressor cells may represent an intermediate state between expression subtype poles. The extensive intratumoral heterogeneity identified through this clinically applicable mIF pipeline may inform prognosis and treatment selection for patients with PDAC. SIGNIFICANCE A high-throughput pipeline using multiplex immunofluorescence in pancreatic cancer reveals striking expression subtype intratumoral heterogeneity with implications for therapy selection and identifies co-expressor cells that may serve as intermediates during subtype switching.
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Affiliation(s)
- Hannah L. Williams
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Andressa Dias Costa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Jinming Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Srivatsan Raghavan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter S. Winter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin S. Kapner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Scott P. Ginebaugh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sara A. Väyrynen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Juha P. Väyrynen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Cancer and Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew W. Navia
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Junning Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Annan Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Radha L. Kalekar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristen E. Lowder
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mai Chan Lau
- Department of Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Dalia Elganainy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Vicente Morales-Oyarvide
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Douglas A. Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Perez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Thomas E. Clancy
- Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Jiping Wang
- Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Joseph D. Mancias
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Harvard Medical School; Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Lauren K. Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Emma R. Hill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Margaret M. Kozak
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford, CA, USA
| | - David C. Linehan
- Department of Surgery, University of Rochester Medical Center, Rochester, NY, USA
| | - Richard F. Dunne
- Department of Medicine, Division of Hematology and Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Daniel T. Chang
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford, CA, USA
| | - Albert C. Koong
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aram F. Hezel
- Department of Medicine, Division of Hematology and Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - William C. Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alex K. Shalek
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew J. Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan A. Nowak
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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12
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Kokumai T, Omori Y, Ishida M, Ohtsuka H, Mizuma M, Nakagawa K, Maeda C, Ono Y, Mizukami Y, Miura S, Kume K, Masamune A, Morikawa T, Unno M, Furukawa T. GATA6 and CK5 Stratify the Survival of Patients With Pancreatic Cancer Undergoing Neoadjuvant Chemotherapy. Mod Pathol 2023; 36:100102. [PMID: 36788090 DOI: 10.1016/j.modpat.2023.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/13/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023]
Abstract
Relevant protein expression of GATA6, CK5, vimentin, and mucins using immunohistochemistry was assessed for predicting the prognosis of and chemotherapy efficacy in patients with pancreatic cancers (PCs). The protein expression was examined in 159 PCs resected after neoadjuvant chemotherapy (NAC-PCs) and compared with that of 120 matched biopsy specimens taken before NAC. KRAS mutations were assessed by digital PCR. NAC-PCs were classified by GATA6 expression initially and CK5 expression subsequently into 4 types: classical-type (n = 22) with GATA6-high (≥50%)/CK5-low (<10%) PCs; hybrid-type (n = 45) with GATA6-high/CK5-high (≥10%) PCs; basal-like-type (n = 53) with GATA6-low (<50%)/CK5-high (≥30%) PCs; and null-type (n = 39) with GATA6-low/CK5-low (<30%) PCs, which resulted in clear stratification of patient prognosis. The classical-type was associated with the most favorable prognosis, whereas the null-type was associated with the worst prognosis (multivariate hazard ratio: 3.56; 95% CI: 1.63-7.77; P = .0015). The hybrid and basal-like types correlated with in-between levels of prognosis. The risk of hepatic recurrence was lower in the classical-type than in null (multivariate odds ratio [mOR]: 0.18; 95% CI: 0.04-0.96; P = .0449) and basal-like (mOR: 0.24; 95% CI: 0.05-1.16; P =.0750) types. By contrast, the risk of locoregional recurrence was higher in the classical-type than in the basal-like-type (mOR: 5.03; 95% CI: 1.20-21.1; P = .0272). The hybrid-type was subclassified into transition and coexpression patterns with different gastric mucin expression levels. High levels of vimentin (≥10%, n = 30) in pre-NAC-PC tissues was associated with poor prognosis (P = .0256). Phenotypic transitions between pre-NAC and post-NAC-PCs were common (73/120; 61%). PCs with NAC regression grades 2 and 3 showed a transition to poorer prognostic phenotypes (P = .0497). KRAS mutations were not associated with these phenotypes. In conclusion, GATA6 and CK5 immunohistochemical expression phenotypes may stratify the survival of patients with NAC-PCs and reflect post-NAC phenotypic transitions associated with poor prognosis. Prompt evaluation of immunohistochemical phenotypes may contribute to designing a precision therapeutic strategy for patients with PCs.
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Affiliation(s)
- Takashi Kokumai
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuko Omori
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan; Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Masaharu Ishida
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hideo Ohtsuka
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masamichi Mizuma
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kei Nakagawa
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Chiho Maeda
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, Japan
| | - Shin Miura
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kiyoshi Kume
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takanori Morikawa
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toru Furukawa
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, Japan.
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13
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Wisniewski L, Braak S, Klamer Z, Gao C, Shi C, Allen P, Haab BB. Heterogeneity of Glycan Biomarker Clusters as an Indicator of Recurrence in Pancreatic Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.05.522607. [PMID: 36711795 PMCID: PMC9881915 DOI: 10.1101/2023.01.05.522607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Outcomes following tumor resection vary dramatically among patients with pancreatic cancer. A challenge in defining predictive biomarkers is to discern within the complex tumor tissue the specific subpopulations and relationships that drive recurrence. Multiplexed immunofluorescence is valuable for such studies when supplied with markers of relevant subpopulations and analysis methods to sort out the intra-tumor relationships that are informative of tumor behavior. We hypothesized that the glycan biomarkers CA19-9 and STRA, which detect separate subpopulations of cancer cells, define intra-tumoral features associated with recurrence. We probed this question using automated signal thresholding and spatial cluster analysis applied to the immunofluorescence images of the STRA and CA19-9 glycan biomarkers in whole-block tumor sections. The tumors (N = 22) displayed extreme diversity between them in the amounts of the glycans and in the levels of spatial clustering, but neither the amounts nor the clusters of the individual and combined glycans associated with recurrence. The combined glycans, however, marked divergent types of spatial clusters, alternatively only STRA, only CA19-9, or both. The co-occurrence of more than one cluster type within a tumor associated significantly with disease recurrence, in contrast to the independent occurrence of each type of cluster. In addition, intra-tumoral regions with heterogeneity in biomarker clusters spatially aligned with pathology-confirmed cancer cells, whereas regions with homogeneous biomarker clusters aligned with various non-cancer cells. Thus, the STRA and CA19-9 glycans are markers of distinct and co-occurring subpopulations of cancer cells that in combination are associated with recurrence. Furthermore, automated signal thresholding and spatial clustering provides a tool for quantifying intra-tumoral subpopulations that are informative of outcome.
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14
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Wisniewski L, Braak S, Klamer Z, Gao C, Shi C, Allen P, Haab BB. Heterogeneity of glycan biomarker clusters as an indicator of recurrence in pancreatic cancer. Front Oncol 2023; 13:1135405. [PMID: 37124496 PMCID: PMC10130372 DOI: 10.3389/fonc.2023.1135405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/17/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction Outcomes following tumor resection vary dramatically among patients with pancreatic ductal adenocarcinoma (PDAC). A challenge in defining predictive biomarkers is to discern within the complex tumor tissue the specific subpopulations and relationships that drive recurrence. Multiplexed immunofluorescence is valuable for such studies when supplied with markers of relevant subpopulations and analysis methods to sort out the intra-tumor relationships that are informative of tumor behavior. We hypothesized that the glycan biomarkers CA19-9 and STRA, which detect separate subpopulations of cancer cells, define intra-tumoral features associated with recurrence. Methods We probed this question using automated signal thresholding and spatial cluster analysis applied to the immunofluorescence images of the STRA and CA19-9 glycan biomarkers in whole-block sections of PDAC tumors collected from curative resections. Results The tumors (N = 22) displayed extreme diversity between them in the amounts of the glycans and in the levels of spatial clustering, but neither the amounts nor the clusters of the individual and combined glycans associated with recurrence. The combined glycans, however, marked divergent types of spatial clusters, alternatively only STRA, only CA19-9, or both. The co-occurrence of more than one cluster type within a tumor associated significantly with disease recurrence, in contrast to the independent occurrence of each type of cluster. In addition, intra-tumoral regions with heterogeneity in biomarker clusters spatially aligned with pathology-confirmed cancer cells, whereas regions with homogeneous biomarker clusters aligned with various non-cancer cells. Conclusion Thus, the STRA and CA19-9 glycans are markers of distinct and co-occurring subpopulations of cancer cells that in combination are associated with recurrence. Furthermore, automated signal thresholding and spatial clustering provides a tool for quantifying intra-tumoral subpopulations that are informative of outcome.
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Affiliation(s)
- Luke Wisniewski
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Samuel Braak
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Zachary Klamer
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - ChongFeng Gao
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
| | - Chanjuan Shi
- Department of Pathology, Duke University School of Medicine, Durham, NC, United States
| | - Peter Allen
- Department of Surgery, Duke University School of Medicine, Durham, NC, United States
| | - Brian B. Haab
- Department of Cell Biology, Van Andel Institute, Grand Rapids, MI, United States
- *Correspondence: Brian B. Haab,
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15
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The Microbiome in PDAC-Vantage Point for Future Therapies? Cancers (Basel) 2022; 14:cancers14235974. [PMID: 36497456 PMCID: PMC9739548 DOI: 10.3390/cancers14235974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/10/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Microorganisms have been increasingly implicated in the pathogenesis of malignant diseases, potentially affecting different hallmarks of cancer. Despite the fact that we have recently gained tremendous insight into the existence and interaction of the microbiome with neoplastic cells, we are only beginning to understand and exploit this knowledge for the treatment of human malignancies. Pancreatic ductal adenocarcinoma (PDAC) is an aggressive solid tumor with limited therapeutic options and a poor long-term survival. Recent data have revealed fascinating insights into the role of the tumoral microbiome in PDAC, with profound implications for survival and potentially therapeutic outcomes. In this review, we outline the current scientific knowledge about the clinical and translational role of the microbiome in PDAC. We describe the microbial compositions in healthy and tumoral pancreatic tissue and point out four major aspects of the microbiome in PDAC: pathogenesis, diagnosis, treatment, and prognosis. However, caution must be drawn to inherent pitfalls in analyzing the intratumoral microbiome. Among others, contamination with environmental microbes is one of the major challenges. To this end, we discuss different decontamination approaches that are crucial for clinicians and scientists alike to foster applicability and physiological relevance in this translational field. Without a definition of an exact and reproducible intratumoral microbial composition, the exploitation of the microbiome as a diagnostic or therapeutic tool remains theoretical.
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16
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Lautizi M, Baumbach J, Weichert W, Steiger K, List M, Pfarr N, Kacprowski T. The limits of molecular signatures for pancreatic ductal adenocarcinoma subtyping. NAR Cancer 2022; 4:zcac030. [PMID: 36267208 PMCID: PMC9575186 DOI: 10.1093/narcan/zcac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 09/27/2022] [Indexed: 11/22/2022] Open
Abstract
Molecular signatures have been suggested as biomarkers to classify pancreatic ductal adenocarcinoma (PDAC) into two, three, four or five subtypes. Since the robustness of existing signatures is controversial, we performed a systematic evaluation of four established signatures for PDAC stratification across nine publicly available datasets. Clustering revealed inconsistency of subtypes across independent datasets and in some cases a different number of PDAC subgroups than in the original study, casting doubt on the actual number of existing subtypes. Next, we built sixteen classification models to investigate the ability of the signatures for tumor subtype prediction. The overall classification performance ranged from ∼35% to ∼90% accuracy, suggesting instability of the signatures. Notably, permuted subtypes and random gene sets achieved very similar performance. Cellular decomposition and functional pathway enrichment analysis revealed strong tissue-specificity of the predicted classes. Our study highlights severe limitations and inconsistencies that can be attributed to technical biases in sample preparation and tumor purity, suggesting that PDAC molecular signatures do not generalize across datasets. How stromal heterogeneity and immune compartment interplay in the diverging development of PDAC is still unclear. Therefore, a more mechanistic or a cross-platform multi-omic approach seems necessary to extract more robust and clinically exploitable insights.
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Affiliation(s)
- Manuela Lautizi
- Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany,Computational BioMedicine, University of Southern Denmark, Odense, Denmark
| | - Wilko Weichert
- Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany,Bavarian Cancer Consortium (BZKF), Munich, Germany
| | - Katja Steiger
- Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Markus List
- To whom correspondence should be addressed. Tel: +49 8161 712761;
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17
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Topham JT, Tsang ES, Karasinska JM, Metcalfe A, Ali H, Kalloger SE, Csizmok V, Williamson LM, Titmuss E, Nielsen K, Negri GL, Spencer Miko SE, Jang GH, Denroche RE, Wong HL, O'Kane GM, Moore RA, Mungall AJ, Loree JM, Notta F, Wilson JM, Bathe OF, Tang PA, Goodwin R, Morin GB, Knox JJ, Gallinger S, Laskin J, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma. Nat Commun 2022; 13:5941. [PMID: 36209277 PMCID: PMC9547977 DOI: 10.1038/s41467-022-33718-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/29/2022] [Indexed: 11/15/2022] Open
Abstract
Oncogenic KRAS mutations are absent in approximately 10% of patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) and may represent a subgroup of mPDAC with therapeutic options beyond standard-of-care cytotoxic chemotherapy. While distinct gene fusions have been implicated in KRAS wildtype mPDAC, information regarding other types of mutations remain limited, and gene expression patterns associated with KRAS wildtype mPDAC have not been reported. Here, we leverage sequencing data from the PanGen trial to perform comprehensive characterization of the molecular landscape of KRAS wildtype mPDAC and reveal increased frequency of chr1q amplification encompassing transcription factors PROX1 and NR5A2. By leveraging data from colorectal adenocarcinoma and cholangiocarcinoma samples, we highlight similarities between cholangiocarcinoma and KRAS wildtype mPDAC involving both mutation and expression-based signatures and validate these findings using an independent dataset. These data further establish KRAS wildtype mPDAC as a unique molecular entity, with therapeutic opportunities extending beyond gene fusion events. KRAS wildtype metastatic pancreatic ductal adenocarcinoma (mPDAC) could represent a distinct molecular entity from other PDACs. Here, the authors analyse KRAS wildtype mPDAC tumours using genomics and transcriptomics and find molecular similarities with cholangiocarcinomas.
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Affiliation(s)
| | - Erica S Tsang
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | | | - Hassan Ali
- Pancreas Centre BC, Vancouver, BC, Canada
| | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Veronika Csizmok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Karina Nielsen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Hui-Li Wong
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Oliver F Bathe
- Departments of Surgery and Oncology, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Patricia A Tang
- Departments of Surgery and Oncology, Cummings School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rachel Goodwin
- The Ottawa Hospital Cancer Centre, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Jennifer J Knox
- University Health Network, University of Toronto, Toronto, ON, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, ON, Canada.,University Health Network, University of Toronto, Toronto, ON, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada.,Division of Anatomic Pathology, Vancouver General Hospital, Vancouver, BC, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC, Canada. .,Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada. .,Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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18
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Wood LD, Canto MI, Jaffee EM, Simeone DM. Pancreatic Cancer: Pathogenesis, Screening, Diagnosis, and Treatment. Gastroenterology 2022; 163:386-402.e1. [PMID: 35398344 PMCID: PMC9516440 DOI: 10.1053/j.gastro.2022.03.056] [Citation(s) in RCA: 226] [Impact Index Per Article: 113.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/13/2022] [Accepted: 03/25/2022] [Indexed: 12/13/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a clinically challenging cancer, due to both its late stage at diagnosis and its resistance to chemotherapy. However, recent advances in our understanding of the biology of PDAC have revealed new opportunities for early detection and targeted therapy of PDAC. In this review, we discuss the pathogenesis of PDAC, including molecular alterations in tumor cells, cellular alterations in the tumor microenvironment, and population-level risk factors. We review the current status of surveillance and early detection of PDAC, including populations at high risk and screening approaches. We outline the diagnostic approach to PDAC and highlight key treatment considerations, including how therapeutic approaches change with disease stage and targetable subtypes of PDAC. Recent years have seen significant improvements in our approaches to detect and treat PDAC, but large-scale, coordinated efforts will be needed to maximize the clinical impact for patients and improve overall survival.
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Affiliation(s)
- Laura D Wood
- Departments of Pathology and Oncology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Marcia Irene Canto
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth M Jaffee
- Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreatic Cancer Research and Clinical Care, Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Diane M Simeone
- Departments of Surgery and Pathology, Perlmutter Cancer Center, NYU Langone Health, New York, New York
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19
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Hyun S, Park D. Challenges in genomic analysis of model systems and primary tumors of pancreatic ductal adenocarcinoma. Comput Struct Biotechnol J 2022; 20:4806-4815. [PMID: 36147673 PMCID: PMC9464644 DOI: 10.1016/j.csbj.2022.08.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/28/2022] [Accepted: 08/28/2022] [Indexed: 11/24/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by aggressive tumor behavior and poor prognosis. Recent next-generation sequencing (NGS)-based genomic studies have provided novel treatment modes for pancreatic cancer via the identification of cancer driver variants and molecular subtypes in PDAC. Genome-wide approaches have been extended to model systems such as patient-derived xenografts (PDXs), organoids, and cell lines for pre-clinical purposes. However, the genomic characteristics vary in the model systems, which is mainly attributed to the clonal evolution of cancer cells during their construction and culture. Moreover, fundamental limitations such as low tumor cellularity and the complex tumor microenvironment of PDAC hinder the confirmation of genomic features in the primary tumor and model systems. The occurrence of these phenomena and their associated complexities may lead to false insights into the understanding of mechanisms and dynamics in tumor tissues of patients. In this review, we describe various model systems and discuss differences in the results based on genomics and transcriptomics between primary tumors and model systems. Finally, we introduce practical strategies to improve the accuracy of genomic analysis of primary tissues and model systems.
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20
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PRMT5: An Emerging Target for Pancreatic Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13205136. [PMID: 34680285 PMCID: PMC8534199 DOI: 10.3390/cancers13205136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The burden of pancreatic ductal adenocarcinoma (PDAC) increases with rising incidence, yet 5-year overall survival remains poor at 17%. Routine comprehensive genomic profiling of PDAC only finds 2.5% of patients who may benefit and receive matched targeted therapy. Protein arginine methyltransferase 5 (PRMT5) as an anti-cancer target has gained significant interest in recent years and high levels of PRMT5 protein are associated with worse survival outcomes across multiple cancer types. Inhibition of PRMT5 in pre-clinical models can lead to cancer growth inhibition. However, PRMT5 is involved in multiple cellular processes, thus determining its mechanism of action is challenging. While past reviews on PRMT5 have focused on its role in diverse cellular processes and past research studies have focused mainly on haematological malignancies and glioblastoma, this review provides an overview of the possible biological mechanisms of action of PRMT5 inhibition and its potential as a treatment in pancreatic cancer. Abstract The overall survival of pancreatic ductal adenocarcinoma (PDAC) remains poor and its incidence is rising. Targetable mutations in PDAC are rare, thus novel therapeutic approaches are needed. Protein arginine methyltransferase 5 (PRMT5) overexpression is associated with worse survival and inhibition of PRMT5 results in decreased cancer growth across multiple cancers, including PDAC. Emerging evidence also suggests that altered RNA processing is a driver in PDAC tumorigenesis and creates a partial dependency on this process. PRMT5 inhibition induces altered splicing and this vulnerability can be exploited as a novel therapeutic approach. Three possible biological pathways underpinning the action of PRMT5 inhibitors are discussed; c-Myc regulation appears central to its action in the PDAC setting. Whilst homozygous MTAP deletion and symmetrical dimethylation levels are associated with increased sensitivity to PRMT5 inhibition, neither measure robustly predicts its growth inhibitory response. The immunomodulatory effect of PRMT5 inhibitors on the tumour microenvironment will also be discussed, based on emerging evidence that PDAC stroma has a significant bearing on disease behaviour and response to therapy. Lastly, with the above caveats in mind, current knowledge gaps and the implications and rationales for PRMT5 inhibitor development in PDAC will be explored.
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21
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Zhao S, Nicolle R, Augustin J, Svrcek M, de Mestier L, Le Corre D, Pietrasz D, Caliez O, Cros J, Laurent-Puig P, Bachet JB. Prognostic Relevance of Pancreatic Adenocarcinoma Whole-Tumor Transcriptomic Subtypes and Components. Clin Cancer Res 2021; 27:6491-6499. [PMID: 34518308 DOI: 10.1158/1078-0432.ccr-21-1907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/15/2021] [Accepted: 09/03/2021] [Indexed: 12/09/2022]
Abstract
PURPOSE Our team previously defined six quantitative transcriptomic components, and a classification in five subtypes by association of these components. In this study, we compared the robustness of quantitative components and qualitative classifications from different transcriptomic profiling techniques, investigated their clinical relevance, and proposed a new prognostic model. EXPERIMENTAL DESIGN A total of 210 patients from a multicentric cohort and 149 patients from a monocentric cohort were included in this study. RNA microarray profiles were obtained from 165 patients of the multicentric cohort. RNA sequencing (RNA-seq) profiles were obtained from all the patients. RESULTS For the patients with both RNA microarray and RNA-seq profiles, the concordance in subtype assignment was partial with an 82.4% coherence rate. The correlation between the two technique projections of the six components ranged from 0.85 to 0.95, demonstrating an advantage of robustness. On the basis of the Akaike information criterion, the RNA components showed more prognostic value in univariate or multivariate models than the subtypes. Using the monocentric cohort for training, we developed a multivariate Cox regression model using all six components and clinicopathologic characteristics (node invasion and resection margins) on disease-free survival (DFS). This prognostic model was highly associated with DFS (P < 0.001). The evaluation of the model in the multicentric cohort showed significant association with DFS and overall survival (P < 0.001). CONCLUSIONS We described the advantage of the prognostic value and robustness of the whole-tumor transcriptomic components than subtypes. We created and validated a new DFS-based multivariate Cox regression prognostic model, including six pancreatic adenocarcinoma transcriptomic component levels and pathologic characteristics.
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Affiliation(s)
- Shulin Zhao
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France.,Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Rémy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Jérémy Augustin
- Sorbonne Université, Assistance Publique - Hôpitaux de Paris, Department of Pathology, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Magali Svrcek
- Sorbonne Université, UPMC Université, IUC, Paris, France.,Assistance Publique - Hôpitaux de Paris, Department of pathology, Hôpital Saint Antoine, Paris, France
| | - Louis de Mestier
- Assistance Publique - Hôpitaux de Paris, Department of Gastroenterology and Pancreatology, and INSERM U1149, Hôpital Beaujon, Clichy, France
| | - Delphine Le Corre
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France
| | - Daniel Pietrasz
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France.,Paris-Saclay University, Assistance Publique - Hôpitaux de Paris, Department of digestive surgery, Paul Brousse Hospital, Villejuif, France
| | - Olivier Caliez
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France.,Sorbonne Université, UPMC Université, IUC, Paris, France.,Assistance Publique - Hôpitaux de Paris, Department of Hepato-gastroenterology, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Jérôme Cros
- Assistance Publique - Hôpitaux de Paris, INSERM, Université de Paris, Department of Pathology, Hôpital Beaujon, Clichy, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France.,Assistance Publique - Hôpitaux de Paris, Department of biochemistry, Hôpital Européen Georges Pompidou, Paris, France
| | - Jean-Baptiste Bachet
- Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France. .,Sorbonne Université, UPMC Université, IUC, Paris, France.,Assistance Publique - Hôpitaux de Paris, Department of Hepato-gastroenterology, Groupe Hospitalier Pitié Salpêtrière, Paris, France
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22
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Gutiérrez ML, Muñoz-Bellvís L, Orfao A. Genomic Heterogeneity of Pancreatic Ductal Adenocarcinoma and Its Clinical Impact. Cancers (Basel) 2021; 13:4451. [PMID: 34503261 PMCID: PMC8430663 DOI: 10.3390/cancers13174451] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the leading causes of cancer death due to limited advances in recent years in early diagnosis and personalized therapy capable of overcoming tumor resistance to chemotherapy. In the last decades, significant advances have been achieved in the identification of recurrent genetic and molecular alterations of PDAC including those involving the KRAS, CDKN2A, SMAD4, and TP53 driver genes. Despite these common genetic traits, PDAC are highly heterogeneous tumors at both the inter- and intra-tumoral genomic level, which might contribute to distinct tumor behavior and response to therapy, with variable patient outcomes. Despite this, genetic and genomic data on PDAC has had a limited impact on the clinical management of patients. Integration of genomic data for classification of PDAC into clinically defined entities-i.e., classical vs. squamous subtypes of PDAC-leading to different treatment approaches has the potential for significantly improving patient outcomes. In this review, we summarize current knowledge about the most relevant genomic subtypes of PDAC including the impact of distinct patterns of intra-tumoral genomic heterogeneity on the classification and clinical and therapeutic management of PDAC.
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Affiliation(s)
- María Laura Gutiérrez
- Department of Medicine and Cytometry Service (NUCLEUS), Universidad de Salamanca, 37007 Salamanca, Spain;
- Cancer Research Center (IBMCC-CSIC/USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, 28029 Madrid, Spain
| | - Luis Muñoz-Bellvís
- Cancer Research Center (IBMCC-CSIC/USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, 28029 Madrid, Spain
- Service of General and Gastrointestinal Surgery, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and Cytometry Service (NUCLEUS), Universidad de Salamanca, 37007 Salamanca, Spain;
- Cancer Research Center (IBMCC-CSIC/USAL), 37007 Salamanca, Spain;
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, 28029 Madrid, Spain
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23
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Melendez-Zajgla J, Maldonado V. The Role of lncRNAs in the Stem Phenotype of Pancreatic Ductal Adenocarcinoma. Int J Mol Sci 2021; 22:6374. [PMID: 34203589 PMCID: PMC8232220 DOI: 10.3390/ijms22126374] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 12/17/2022] Open
Abstract
Pancreatic ductal adenocarcinoma is one of the deadliest tumors. This neoplasia is characterized by an important cellular and phenotypic heterogeneity. In particular, it has been shown that at least two subtypes can be found: basal-like, which presents stem-like properties, and classical. Cancer stem cells have been isolated and characterized from these tumors, showing their dependance on general and tissue-specific stem transcription factors and signaling pathways. Nevertheless, little is known about their tissue microenvironment and cell non-autonomous regulators, such as long-non-coding RNAs. (lncRNAs). In this review, we summarize the current knowledge about the positive and negative effects of lncRNAs in the stemness phenotype of pancreatic ductal adenocarcinoma cancer (PDAC).
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Affiliation(s)
- Jorge Melendez-Zajgla
- Functional Genomics Laboratory, Instituto Nacional de Medicina Genomica, Periferico Sur 4809, Tlalpan, Mexico City 14610, Mexico;
| | - Vilma Maldonado
- Epigenomics Laboratory, Instituto Nacional de Medicina Genomica, Periferico Sur 4809, Tlalpan, Mexico City 14610, Mexico
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Hilmi M, Cros J, Puleo F, Augustin J, Emile JF, Svrcek M, Hammel P, Arsenijevic T, Van Laethem JL, Bachet JB, Nicolle R. Tumour and stroma RNA signatures predict more accurately distant recurrence than clinicopathological factors in resected pancreatic adenocarcinoma. Eur J Cancer 2021; 148:171-180. [PMID: 33743485 DOI: 10.1016/j.ejca.2021.01.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/19/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Few patients with pancreatic adenocarcinoma (PAC) are eligible for surgery. Patients with early relapse have a poor prognosis and might be better candidates for a medical approach. Clinical and pathological parameters only partially predict recurrence and are only obtained after surgery. PAC subtypes based on gene expression were proposed, and we assessed if they could predict the risk and type of recurrence independently of clinicopathological parameters. METHODS Patients with curative-intent surgery for PAC without pretreatment were selected and divided into two independent cohorts defined as discovery (n = 381) and validation (n = 149) cohorts. Transcriptomic analyses were performed on formalin-fixed paraffin-embedded surgical samples to characterise tumour and stroma compartments using previously defined signatures. We associated molecular and clinicopathological characteristics with general, distant, and local recurrences using Cox regression analyses. RESULTS We found that tumour biology predicted distant recurrence contrary to local recurrence, which was directly related to resection margin status. Pure basal-like and stroma-activated subtypes were strongly associated with distant recurrence, independently of clinicopathological factors (hazard ratios [HRs] = 5.85, p < 0.001 and HR = 1.75, p = 0.007, respectively). By dissecting tumoural and stromal compartments, we demonstrated that the basal-like tumour component positively correlated with distant recurrence in both cohorts (HR = 1.45, p < 0.001 and HR = 1.90, p < 0.001), whereas the inactive structural stroma component was protective against distant recurrence (HR = 0.68, p < 0.001 and HR = 0.72, p < 0.001). CONCLUSIONS In addition to suggesting a different mechanism for local and distant relapse (incomplete resection and high metastatic potential, respectively), our results show the potency of molecular phenotype to predict patient outcome regarding distant recurrences.
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Affiliation(s)
- Marc Hilmi
- Programme Cartes D'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France.
| | - Jérôme Cros
- Department of Pathology, Assistance Publique Hopitaux de Paris, Beaujon Hopsital, INSERM U1149, Université de Paris, Clichy, France
| | - Francesco Puleo
- Department of Gastroenterology and Medical Oncology, Delta Hospital CHIREC, Brussels, Belgium
| | - Jeremy Augustin
- Department of Pathology, Assistance Publique Hopitaux de Paris, Pitié Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - Jean-Francois Emile
- Department of Pathology, Assistance Publique Hopitaux de Paris, Ambroise Paré Hospital, Université de Versailles Saint Quentin-En-Yvelines, Boulogne-Billancourt, France
| | - Magali Svrcek
- Department of Pathology, Assistance Publique Hopitaux de Paris, Saint-Antoine Hospital, Sorbonne Université, Paris, France
| | - Pascal Hammel
- Department of Pancreatology, Assistance Publique Hopitaux de Paris, Beaujon Hopsital, University Paris VII, Clichy, France
| | - Tatjana Arsenijevic
- Department of Gastroenterology and Medical Oncology, Hôpital Erasme and Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Van Laethem
- Department of Gastroenterology and Medical Oncology, Hôpital Erasme and Laboratory of Experimental Gastroenterology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Baptiste Bachet
- Department of Hepato-Gastroenterology, Assistance Publique Hopitaux de Paris, Pitié Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - Remy Nicolle
- Programme Cartes D'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
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