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Ou G, Tian Z, Su M, Yu M, Gong J, Chen Y. Identification of gemcitabine resistance-related AHNAK2 gene associated with prognosis and immune infiltration in pancreatic cancer. Heliyon 2024; 10:e33687. [PMID: 39040243 PMCID: PMC11261888 DOI: 10.1016/j.heliyon.2024.e33687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 07/24/2024] Open
Abstract
Purpose Gemcitabine is a basic chemotherapy drug for pancreatic cancer (PC), but resistance is common and causes tumor recurrence and metastasis. Therefore, it is significant to explore gemcitabine resistance-related molecules for individualized treatment and prognosis assessment of PC. Methods In this study, transcriptome sequencing and TCGA database analysis were performed, and a differentiated gene AHNAK2 was screened. MEXPRESS database, tissue microarray analysis, and CIBERSORT and TIMER databases were used to correlate AHNAK2 expression with clinicopathological features and prognosis and immune infiltration of PC. Enrichment analysis was used to investigate the significant biological processes associated with AHNAK2. Results AHNAK2 was highly expressed in gemcitabine-resistant cells. High expression of AHNAK2 increased the risk of poor overall survival (OS) and progression-free survival (PFS) in PC. Clinicopathologic analysis revealed that AHNAK2 correlated with KRAS, TP53 mutations, histologic type, short OS, N stage, and elevated CA199 levels in PC. Knockdown of AHNAK2 inhibited the ability of cell proliferation and colony formation and enhanced the toxic effect of gemcitabine in PC. Meanwhile, the knockdown of AHNAK2 expression enhanced cell-ECM adhesion, inhibited cell-cell adhesion, and downregulated the KRAS/p53 signaling pathway in PC. Furthermore, AHNAK2 was correlated with immune infiltration, especially B cells and macrophages. Conclusions Our study unveils for the first time the pivotal role of AHNAK2 in PC, particularly its association with gemcitabine resistance, clinical prognosis, and immune infiltration. AHNAK2 not only drives the proliferation and drug resistance of PC cells by potentially activating the KRAS/p53 pathway but also significantly impacts cell-cell and cell- ECM adhesion. Additionally, AHNAK2 plays a crucial role in modulating the tumor immune microenvironment. These insights underscore AHNAK2's unique potential as a novel therapeutic target for overcoming gemcitabine resistance, offering new perspectives for PC treatment strategies.
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Affiliation(s)
- Guangsheng Ou
- Department of Gastrointestinal Surgery, the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510600, PR China
| | - Zhenfeng Tian
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
| | - Mingxin Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
| | - Miao Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
| | - Jin Gong
- Department of General Surgery, the First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China
| | - Yinting Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
- Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China
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2
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Lin W, Zhang S, Gu C, Zhu H, Liu Y. GLIPR2: a potential biomarker and therapeutic target unveiled - Insights from extensive pan-cancer analyses, with a spotlight on lung adenocarcinoma. Front Immunol 2024; 15:1280525. [PMID: 38476239 PMCID: PMC10929020 DOI: 10.3389/fimmu.2024.1280525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Background Glioma pathogenesis related-2 (GLIPR2), an emerging Golgi membrane protein implicated in autophagy, has received limited attention in current scholarly discourse. Methods Leveraging extensive datasets, including The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), Human Protein Atlas (HPA), and Clinical Proteomic Tumor Analysis Consortium (CPTAC), we conducted a comprehensive investigation into GLIPR2 expression across diverse human malignancies. Utilizing UALCAN, OncoDB, MEXPRESS and cBioPortal databases, we scrutinized GLIPR2 mutation patterns and methylation landscapes. The integration of bulk and single-cell RNA sequencing facilitated elucidation of relationships among cellular heterogeneity, immune infiltration, and GLIPR2 levels in pan-cancer. Employing ROC and KM analyses, we unveiled the diagnostic and prognostic potential of GLIPR2 across diverse cancers. Immunohistochemistry provided insights into GLIPR2 expression patterns in a multicenter cohort spanning various cancer types. In vitro functional experiments, including transwell assays, wound healing analyses, and drug sensitivity testing, were employed to delineate the tumor suppressive role of GLIPR2. Results GLIPR2 expression was significantly reduced in neoplastic tissues compared to its prevalence in healthy tissues. Copy number variations (CNV) and alterations in methylation patterns exhibited discernible correlations with GLIPR2 expression within tumor tissues. Moreover, GLIPR2 demonstrated diagnostic and prognostic implications, showing pronounced associations with the expression profiles of numerous immune checkpoint genes and the relative abundance of immune cells in the neoplastic microenvironment. This multifaceted influence was evident across various cancer types, with lung adenocarcinoma (LUAD) being particularly prominent. Notably, patients with LUAD exhibited a significant decrease in GLIPR2 expression within practical clinical settings. Elevated GLIPR2 expression correlated with improved prognostic outcomes specifically in LUAD. Following radiotherapy, LUAD cases displayed an increased presence of GLIPR2+ infiltrating cellular constituents, indicating a notable correlation with heightened sensitivity to radiation-induced therapeutic modalities. A battery of experiments validated the functional role of GLIPR2 in suppressing the malignant phenotype and enhancing treatment sensitivity. Conclusion In pan-cancer, particularly in LUAD, GLIPR2 emerges as a promising novel biomarker and tumor suppressor. Its involvement in immune cell infiltration suggests potential as an immunotherapeutic target.
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Affiliation(s)
- Wei Lin
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou, China
| | - Siming Zhang
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Chunyan Gu
- Department of Pathology, Affiliated Nantong Hospital 3 of Nantong University (Nantong Third People’s Hospital), Nantong, China
| | - Haixia Zhu
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, China
| | - Yuan Liu
- Cancer Research Center Nantong, Affiliated Tumor Hospital of Nantong University, Nantong, China
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3
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Wu C, Yang J, Ding R, Li X, Yang Z, Zhu M, Liu Z. Identification of a costimulatory molecule-based signature to predict prognostic risk of pancreatic adenocarcinoma. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2090450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Chao Wu
- Department of Oncology, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Jingyue Yang
- Department of Oncology, Xijing Hospital, Air Force Military Medical University, Xi’an, People’s Republic of China
| | - Rui Ding
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Military Medical University, Xi’an, People’s Republic of China
| | - Xiao Li
- Department of Hepatobiliary Surgery, Xijing Hospital, Air Force Military Medical University, Xi’an, People’s Republic of China
| | - Zhi Yang
- The IVD Medical Marketing Department, 3D Medicines Inc., Shanghai, People’s Republic of China
| | - Min Zhu
- Department of Oncology, The Fifth medical center, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Zhengcai Liu
- Department of Hepatopancreatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
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4
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Dai M, Liu M, Yang H, Küçük C, You H. New insights into epigenetic regulation of resistance to PD-1/PD-L1 blockade cancer immunotherapy: mechanisms and therapeutic opportunities. Exp Hematol Oncol 2022; 11:101. [PMID: 36384676 PMCID: PMC9667634 DOI: 10.1186/s40164-022-00356-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/17/2022] Open
Abstract
Programmed cell death protein 1(PD-1) is a type of immune-inhibitory checkpoint protein, which delivers inhibitory signals to cytotoxic T cells by binding to the programmed death ligand-1 (PD-L1) displayed on the surface of cancer cells. Antibodies blocking PD-1/PD-L1 interaction have been extensively used in treatment of human malignancies and have achieved promising outcomes in recent years. However, gradual development of resistance to PD-1/PD-L1 blockade has decreased the effectiveness of this immunotherapy in cancer patients. The underlying epigenetic mechanisms need to be elucidated for application of novel strategies overcoming this immunotherapy resistance. Epigenetic aberrations contribute to cancerogenesis by promoting different hallmarks of cancer. Moreover, these alterations may lead to therapy resistance, thereby leading to poor prognosis. Recently, the epigenetic regulatory drugs have been shown to decrease the resistance to PD-1/PD-L1 inhibitors in certain cancer patients. Inhibitors of the non-coding RNAs, DNA methyltransferases, and histone deacetylases combined with PD-1/PD-L1 inhibitors have shown considerable therapeutic efficacy against carcinomas as well as blood cancers. Importantly, DNA methylation-mediated epigenetic silencing can inhibit antigen processing and presentation, which promotes cancerogenesis and aggravates resistance to PD-1/PD-L1 blockade immunotherapy. These observations altogether suggest that the combination of the epigenetic regulatory drugs with PD-1/PD-L1 inhibitors may present potential solution to the resistance caused by monotherapy of PD-1/PD-L1 immunotherapy.
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Affiliation(s)
- Mengyuan Dai
- Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology, Department of Hematology and Oncology, Pediatric Research Institute, Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation base of Child development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, 136 Zhongshan Second Rd., Yuzhong District, 401122, Chongqing, China
| | - Miao Liu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
| | - Hua Yang
- Department of Basic Medicine and Biomedical Engineering, School of Medical, Foshan University, Foshan, China
| | - Can Küçük
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, İzmir, Türkiye
- Basic and Translational Research Program, İzmir Biomedicine and Genome Center, İzmir, Türkiye
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, İzmir, Türkiye
| | - Hua You
- Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology, Department of Hematology and Oncology, Pediatric Research Institute, Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation base of Child development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, 136 Zhongshan Second Rd., Yuzhong District, 401122, Chongqing, China.
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5
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Chi H, Peng G, Wang R, Yang F, Xie X, Zhang J, Xu K, Gu T, Yang X, Tian G. Cuprotosis Programmed-Cell-Death-Related lncRNA Signature Predicts Prognosis and Immune Landscape in PAAD Patients. Cells 2022; 11:cells11213436. [PMID: 36359832 PMCID: PMC9658590 DOI: 10.3390/cells11213436] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/22/2022] [Accepted: 10/28/2022] [Indexed: 12/03/2022] Open
Abstract
In terms of mortality and survival, pancreatic cancer is one of the worst malignancies. Known as a unique type of programmed cell death, cuprotosis contributes to tumor cell growth, angiogenesis, and metastasis. Cuprotosis programmed-cell-death-related lncRNAs (CRLs) have been linked to PAAD, although their functions in the tumor microenvironment and prognosis are not well understood. This study included data from the TCGA-PAAD cohort. Random sampling of PAAD data was conducted, splitting the data into two groups for use as a training set and test set (7:3). We searched for differentially expressed genes that were substantially linked to prognosis using univariate Cox and Lasso regression analysis. Through the use of multivariate Cox proportional risk regression, a risk-rating system for prognosis was developed. Correlations between the CRL signature and clinicopathological characteristics, tumor microenvironment, immunotherapy response, and chemotherapy sensitivity were further evaluated. Lastly, qRT-PCR was used to compare CRL expression in healthy tissues to that in tumors. Some CRLs are thought to have strong correlations with PAAD outcomes. These CRLs include AC005332.6, LINC02041, LINC00857, and AL117382.1. The CRL-based signature construction exhibited outstanding predictive performance and offers a fresh approach to evaluating pre-immune effectiveness, paving the way for future studies in precision immuno-oncology.
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Affiliation(s)
- Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Gaoge Peng
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Rui Wang
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou 646000, China
- Academician (Expert) Workstation of Sichuan Province, Luzhou 646000, China
| | - Fengyi Yang
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou 646000, China
- Academician (Expert) Workstation of Sichuan Province, Luzhou 646000, China
| | - Xixi Xie
- School of Stomatology, Southwest Medical University, Luzhou 646000, China
| | - Jinhao Zhang
- School of Stomatology, Southwest Medical University, Luzhou 646000, China
| | - Ke Xu
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Tao Gu
- Clinical Medical College, Southwest Medical University, Luzhou 646000, China
| | - Xiaoli Yang
- Department of General Surgery (Hepatobiliary Surgery), The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Luzhou 646000, China
- Academician (Expert) Workstation of Sichuan Province, Luzhou 646000, China
- Correspondence: (X.Y.); (G.T.); Tel.: +86-150-8687-8251 (X.Y.); +86-182-4436-2063 (G.T.)
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China
- Correspondence: (X.Y.); (G.T.); Tel.: +86-150-8687-8251 (X.Y.); +86-182-4436-2063 (G.T.)
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6
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Gong X, Liu Y, Zheng C, Tian P, Peng M, Pan Y, Li X. Establishment of a 4-miRNA Prognostic Model for Risk Stratification of Patients With Pancreatic Adenocarcinoma. Front Oncol 2022; 12:827259. [PMID: 35186758 PMCID: PMC8851918 DOI: 10.3389/fonc.2022.827259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/17/2022] [Indexed: 12/12/2022] Open
Abstract
Pancreatic adenocarcinomas (PAADs) often remain undiagnosed until later stages, limiting treatment options and leading to poor survival. The lack of robust biomarkers complicates PAAD prognosis, and patient risk stratification remains a major challenge. To address this issue, we established a panel constructed by four miRNAs (miR-4444-2, miR-934, miR-1301 and miR-3655) based on The Cancer Genome Atlas (TCGA) and Human Cancer Metastasis Database (HCMDB) to predicted the prognosis of PAAD patients. Then, a risk prediction model of these four miRNAs was constructed by using Cox regression analysis with the least absolute shrinkage and selection operator (LASSO) regression analysis. This model stratified TCGA PAAD cohort into the low-risk and high-risk groups based on the panel-based risk score, which was significantly associated with 1-, 2-, 3-year OS (AUC=0.836, AUC=0.844, AUC=0.952, respectively). The nomogram was then established with a robust performance signature for predicting prognosis compared to clinical characteristics of pancreatic cancer (PC) patients, including age, gender and clinical stage. Moreover, two GSE data were validated the expressions of 4 miRNAs with prognosis/survival outcome in PC. In the external clinical sample validation, the high-risk group with the upregulated expressions of miR-934/miR-4444-2 and downregulated expressions of miR-1301/miR-3655 were indicated a poor prognosis. Furthermore, the cell counting kit-8 (CCK-8) assay, clone formation, transwell and wound healing assay also confirmed the promoting effect of miR-934/miR-4444-2 and the inhibiting effect of miR-1301/miR-3655 in PC cell proliferation and migration. Taken together, we identified a new 4-miRNA risk stratification model could be used in predicting prognosis in PAAD.
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Affiliation(s)
- Xun Gong
- Department of Hepatobiliary Surgery, Shenzhen Key Laboratory, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, China.,College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China
| | - Yuchen Liu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Big Data Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Chenglong Zheng
- Department of Hepatobiliary Surgery, Shenzhen Key Laboratory, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, China
| | - Peikai Tian
- Department of Hepatobiliary Surgery, Shenzhen Key Laboratory, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, China
| | - Minjie Peng
- Department of Hepatobiliary Surgery, Shenzhen Key Laboratory, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, China
| | - Yihang Pan
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Big Data Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiaowu Li
- Department of Hepatobiliary Surgery, Shenzhen Key Laboratory, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen, China
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7
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Tan M, Brusgaard K, Gerdes AM, Mortensen MB, Detlefsen S, Schaffalitzky de Muckadell OB, Joergensen MT. Whole genome sequencing identifies rare germline variants enriched in cancer related genes in first degree relatives of familial pancreatic cancer patients. Clin Genet 2021; 100:551-562. [PMID: 34313325 PMCID: PMC9291090 DOI: 10.1111/cge.14038] [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: 05/05/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/20/2022]
Abstract
First-degree relatives (FDRs) of familial pancreatic cancer (FPC) patients have increased risk of developing pancreatic ductal adenocarcinoma (PDAC). Investigating and understanding the genetic basis for PDAC susceptibility in FPC predisposed families may contribute toward future risk-assessment and management of high-risk individuals. Using a Danish cohort of 27 FPC families, we performed whole-genome sequencing of 61 FDRs of FPC patients focusing on rare genetic variants that may contribute to familial aggregation of PDAC. Statistical analysis was performed using the gnomAD database as external controls. Through analysis of heterozygous premature truncating variants (PTV), we identified cancer-related genes and cancer-driver genes harboring multiple germline mutations. Association analysis detected 20 significant genes with false discovery rate, q < 0.05 including: PALD1, LRP1B, COL4A2, CYLC2, ZFYVE9, BRD3, AHDC1, etc. Functional annotation showed that the significant genes were enriched by gene clusters encoding for extracellular matrix and associated proteins. PTV genes were over-represented by functions related to transport of small molecules, innate immune system, ion channel transport, and stimuli-sensing channels. In conclusion, FDRs of FPC patients carry rare germline variants related to cancer pathogenesis that may contribute to increased susceptibility to PDAC. The identified variants may potentially be useful for risk prediction of high-risk individuals in predisposed families.
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Affiliation(s)
- Ming Tan
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
| | - Klaus Brusgaard
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Michael Bau Mortensen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark.,Department of Surgery, Odense University Hospital, Odense, Denmark
| | - Sönke Detlefsen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark.,Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Ove B Schaffalitzky de Muckadell
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
| | - Maiken Thyregod Joergensen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
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8
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Wang W, Yan L, Guan X, Dong B, Zhao M, Wu J, Tian X, Hao C. Identification of an Immune-Related Signature for Predicting Prognosis in Patients With Pancreatic Ductal Adenocarcinoma. Front Oncol 2021; 10:618215. [PMID: 33718118 PMCID: PMC7945593 DOI: 10.3389/fonc.2020.618215] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/31/2020] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is one of the highest fatality rate cancers with poor survival rates. The tumor microenvironment (TME) is vital for tumor immune responses, leading to resistance to chemotherapy and poor prognosis of PDAC patients. This study aimed to provide a comprehensive evaluation of the immune genes and microenvironment in PDAC that might help in predicting prognosis and guiding clinical treatments. METHODS We developed a prognosis-associated immune signature (i.e., PAIS) based on immune-associated genes to predict the overall survival of patients with PDAC. The clinical significance and immune landscapes of the signature were comprehensively analyzed. RESULTS Owing to gene expression profiles from TCGA database, functional enrichment analysis revealed a significant difference in the immune response between PDAC and normal pancreas. Using transcriptome data analysis of a training set, we identified an immune signature represented by 5 genes (ESR2, IDO1, IL20RB, PPP3CA, and PLAU) related to the overall survival of patients with PDAC, significantly. This training set was well-validated in a test set. Our results indicated a clear association between a high-risk score and a very poor prognosis. Stratification analysis and multivariate Cox regression analysis revealed that PAIS was an important prognostic factor. We also found that the risk score was positively correlated with the inflammatory response, antigen-presenting process, and expression level of some immunosuppressive checkpoint molecules (e.g., CD73, PD-L1, CD80, and B7-H3). These results suggested that high-risk patients had a suppressed immune response. However, they could respond better to chemotherapy. In addition, PAIS was positively correlated with the infiltration of M2 macrophages in PDAC. CONCLUSIONS This study highlighted the relationship between the immune response and prognosis in PDAC and developed a clinically feasible signature that might serve as a powerful prognostic tool and help further optimize the cancer therapy paradigm.
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Affiliation(s)
- Weijia Wang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Liang Yan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaoya Guan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Bin Dong
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Central Laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Min Zhao
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Pathology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jianhui Wu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiuyun Tian
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Chunyi Hao
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Hepato-Pancreato-Biliary Surgery, Peking University Cancer Hospital & Institute, Beijing, China
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9
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Huang H, Zhou W, Chen R, Xiang B, Zhou S, Lan L. CXCL10 is a Tumor Microenvironment and Immune Infiltration Related Prognostic Biomarker in Pancreatic Adenocarcinoma. Front Mol Biosci 2021; 8:611508. [PMID: 33681290 PMCID: PMC7930611 DOI: 10.3389/fmolb.2021.611508] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/11/2021] [Indexed: 01/18/2023] Open
Abstract
Pancreatic adenocarcinoma (PAAD) is the 10th most common cancer worldwide and the outcomes for patients with the disease remain extremely poor. Precision biomarkers are urgently needed to increase the efficiency of early diagnosis and to improve the prognosis of patients. The tumor microenvironment (TME) and tumor immune infiltration are thought to impact the occurrence, progression, and prognosis of PAAD. Novel biomarkers excavated originating from the TME and immune infiltration may be effective in predicting the prognosis of PAAD patients. In the current study, the ESTIMATE and CIBERSORT algorithms were applied to estimate the division of immune and stromal components and the proportion of tumor-infiltrating immune cells in 182 PAAD cases downloaded from The Cancer Genome Atlas database. Intersection analyses of the Protein-Protein Interaction networks and Cox regression analysis identified the chemokine (CXC-motif) ligand 10 (CXCL10) as a predictive biomarker. We verified that CXCL10 in the TME negatively correlates with prognosis in PAAD and positively correlates with tumor cell differentiation. GSE62452 from the GEO database and cumulative survival analysis were performed to validate CXCL10 expression as an independent prognostic indicator. We also found that memory B cells, regulatory T cells, and macrophages M0 and M1 were correlated with the expression of CXCL10 indicating that expression of CXCL10 influenced the immune activity of the TME. Our data suggest that CXCL10 is beneficial as a prognostic indicator in PAAD patients and highlights the potential for immune targeted therapy in the treatment of PAAD.
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Affiliation(s)
- Huimin Huang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wangxiao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Renpin Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bingfeng Xiang
- Department of Emergency Intensive Care Unit, The Cangnan Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shipeng Zhou
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Linhua Lan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Multi-omics analysis of copy number variations of RNA regulatory genes in soft tissue sarcoma. Life Sci 2020; 265:118734. [PMID: 33166590 DOI: 10.1016/j.lfs.2020.118734] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 12/11/2022]
Abstract
AIMS RNA regulatory genes were closely associated with tumorigenesis and prognosis in multiple tumors. Copy number variation (CNV) is a frequent characteristic in soft tissue sarcomas (STS). However, little is known regarding their possible roles in STS. MAIN METHODS RNA sequence profiles and CNV data of 255 STS patients were downloaded from the Cancer Genome Atlas (TCGA). The correlation analysis involved CNVs of RNA regulatory genes, patient survival, immune infiltration, and DNA methylation. Drug sensitivity (IC50) was analyzed and validated by MTT assays in STS cell lines. KEY FINDINGS CNV events were frequently observed in all kinds (m6A, m5C, ac4C, m1A, m3C, m6Am, m7G, and Ψ) of RNA regulatory genes. Diploid copy number (CN) of METTL4 was associated with better overall survival (OS) in STS and the subtypes (leiomyosarcoma, LMS; dedifferentiated liposarcoma, DDLPS). In STS and LMS, diploid CN of METTL4 was significantly associated with higher infiltration fraction of resting mast cells. In STS and DDLPS, diploid CN of METTL4 possessed lower methylation level in CpG site of cg12105018, which represented better OS. Besides, sensitive drugs for STS cell lines were analyzed according to lower IC50 for the loss CN of METTL4. Temozolomide and Olaparib were identified. Further validation by MTT assays demonstrated that GCT was the most sensitive cell line to both Temozolomide and Olaparib. SIGNIFICANCE CNV of METTL4 could be a prognostic biomarker for STS by potentially influencing mast cell infiltration and DNA methylation. Besides, STS with loss CN of METTL4 would be sensitive to Temozolomide and Olaparib.
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Pu N, Chen Q, Gao S, Liu G, Zhu Y, Yin L, Hu H, Wei L, Wu Y, Maeda S, Lou W, Yu J, Wu W. Genetic landscape of prognostic value in pancreatic ductal adenocarcinoma microenvironment. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:645. [PMID: 31930046 DOI: 10.21037/atm.2019.10.91] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background The prognosis of pancreatic ductal adenocarcinoma (PDAC) remains dismally poor and is widely considered as an intricate genetic disorder. The mutational landscape of PDAC may directly reflect cancer immunogenicity and dictate the extent and phenotype of immune cell infiltration. In adverse, the microenvironment may also effect the gene expression of cancer cells, which is associated with clinical prognosis. Thus, it is crucial to identify genomic alterations in PDAC microenvironment and its impacts on clinical prognosis. Methods The gene expression profiles, mutation data and clinical information of 179 pancreatic cancer patients with an initial pathologic diagnosis ranging from 2001 to 2013 were retrieved from The Cancer Genome Atlas (TCGA) database. The MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm for calculating immune scores and stromal scores and Tumor IMmune Estimation Resource (TIMER) resource for cell infiltrations were applied in this study. Results The average immune score or stromal score of PDAC subtype was significantly higher than that of other specific subtypes. KRAS mutant cases had significantly lower immune scores (P=0.001) and stromal scores (P=0.007), in concert with lower immune scores in TP53 mutant cases (P=0.030). However, no significant difference was found in SMAD4 and CDKN2A mutations. In the cohort OS/RFS, the infiltration levels of CD8+ T cells, B cells, Macrophages, Neutrophils and DCs in high stromal score group were higher than those in the low score group (all P<0.001), as well as in immune score groups except for Macrophages in the cohort RFS. In the cohort OS/RFS, 317/379 upregulated genes and 9/6 downregulated genes were observed in the high immune score group, while 227/205 upregulated genes and 17/6 downregulated genes in the high stromal score group. With the analysis for prognostic value of DEGs, 82 and 58 DEGs respectively in the high immune and stromal score group were verified to be significantly associated with better OS (P<0.05), while 53 and 17 DEGs respectively with longer RFS (P<0.05). Functional enrichment analysis showed genes of prognostic values were significantly related to immune response. Conclusions A list of genes with prognostic value in PDAC microenvironment were obtained from functional enrichment analysis based on immune and stromal scores, which indicates a series of potential auxiliary prognostic biomarkers for PDAC are available. Further research on these genes may be valuable and helpful to understand the crosstalk between tumor and microenvironment, new immune evasion mechanisms and underlying novel therapeutic targets in an integrated manner.
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Affiliation(s)
- Ning Pu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China.,Department of Surgery and The Pancreatic Cancer Precision Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qiangda Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shanshan Gao
- Department of Surgery and The Pancreatic Cancer Precision Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Gao Liu
- Department of Liver Surgery and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yayun Zhu
- Department of Surgery and The Pancreatic Cancer Precision Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Liver Surgery and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lingdi Yin
- Department of Surgery and The Pancreatic Cancer Precision Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, and Pancreas Institute of Nanjing Medical University, Nanjing 210029, China
| | - Haijie Hu
- Department of Surgery and The Pancreatic Cancer Precision Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biliary Surgery, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Li Wei
- Department of Liver Surgery and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yong Wu
- Department of Surgery and The Pancreatic Cancer Precision Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Shimpei Maeda
- Department of Surgery and The Pancreatic Cancer Precision Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Wenhui Lou
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jun Yu
- Department of Surgery and The Pancreatic Cancer Precision Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wenchuan Wu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Hayashi H, Tanishima S, Fujii K, Mori R, Okamura Y, Yanagita E, Matsuoka R, Amano T, Kinoshita I, Komatsu Y, Dosaka-Akita H, Nishihara H. Genomic testing for pancreatic cancer in clinical practice as real-world evidence. Pancreatology 2018; 18:647-654. [PMID: 30055942 DOI: 10.1016/j.pan.2018.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/20/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Precision medicine guided by comprehensive genome sequencing represents a potential treatment strategy for pancreatic cancer. However, clinical sequencing for pancreatic cancer entails several practical difficulties. We have launched an in-house clinical sequencing system and started genomic testing for patients with cancer in clinical practice. We have analyzed the clinical utility of this system in pancreatic cancer. METHODS We retrospectively reviewed 20 patients with pancreatic cancer who visited our division. Genomic DNA was extracted from both tumor tissue and peripheral blood mononuclear cells obtained from the patients. We performed a comprehensive genomic testing using targeted amplicon sequencing for 160 cancer-related genes. The primary endpoints were the detection rates of potential actionable and druggable gene alterations. The secondary endpoints were the detection rate of secondary germline findings, the rate of re-biopsy required for genome sequencing, survival time after the initial visit (post-sequencing survival time), and turnaround time. RESULTS Although re-biopsy was required for 25% (5/20) of all patients, genomic testing was performed in all patients. Actionable and druggable gene alterations were detected in 100% (20/20) and 35% (7/20) of patients, respectively, whereas secondary germline findings were detected in 5% (1/20) of patients. The median turnaround times for physicians and patients were 20 and 26 days, respectively. The median post-sequencing survival time was 10.3 months. Only 10% (2/20) of all patients were treated with therapeutic agents based on the outcomes of genomic testing. CONCLUSIONS The clinical application of comprehensive genomic testing for pancreatic cancer was feasible and promising in clinical practice.
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Affiliation(s)
- Hideyuki Hayashi
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan.
| | - Shigeki Tanishima
- Department of Biomedical Informatics Development, Mitsubishi Space Software Co., Ltd, Tokyo, Japan
| | - Kyoko Fujii
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Ryo Mori
- Department of Biomedical Informatics Development, Mitsubishi Space Software Co., Ltd, Tokyo, Japan
| | - Yasunobu Okamura
- Department of Biomedical Informatics Development, Mitsubishi Space Software Co., Ltd, Tokyo, Japan
| | - Emmy Yanagita
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Ryosuke Matsuoka
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
| | - Toraji Amano
- Hokkaido University Hospital Clinical Research and Medical Innovation Center, Sapporo, Japan
| | - Ichiro Kinoshita
- Department of Medical Oncology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yoshito Komatsu
- Department of Cancer Chemotherapy, Hokkaido University Hospital Cancer Center, Sapporo, Japan
| | - Hirotoshi Dosaka-Akita
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan; Department of Medical Oncology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hiroshi Nishihara
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Japan
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