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Wang Z, Zhang G, Fu J, Li G, Zhao Z, Choe H, Ding K, Ma J, Wei J, Shang D, Zhang L. Mechanism exploration and biomarker identification of glycemic deterioration in patients with diseases of the exocrine pancreas. Sci Rep 2024; 14:4374. [PMID: 38388766 PMCID: PMC10883946 DOI: 10.1038/s41598-024-52956-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
The damage to the endocrine pancreas among patients with diseases of the exocrine pancreas (DP) leads to reduced glycemic deterioration, ultimately resulting in diabetes of the exocrine pancreas (DEP). The present research aims to investigate the mechanism responsible for glycemic deterioration in DP patients, and to identify useful biomarkers, with the ultimate goal of enhancing clinical practice awareness. Gene expression profiles of patients with DP in this study were acquired from the Gene Expression Omnibus database. The original study defines DP patients to belong in one of three categories: non-diabetic (ND), impaired glucose tolerance (IGT) and DEP, which correspond to normoglycemia, early and late glycemic deterioration, respectively. After ensuring quality control, the discovery cohort included 8 ND, 20 IGT, and 12 DEP, while the validation cohort included 27 ND, 15 IGT, and 20 DEP. Gene set enrichment analysis (GSEA) employed differentially expressed genes (DEGs), while immunocyte infiltration was determined using single sample gene set enrichment analysis (ssGSEA). Additionally, correlation analysis was conducted to establish the link between clinical characteristics and immunocyte infiltration. The least absolute shrinkage and selection operator regression and random forest combined to identify biomarkers indicating glycemic deterioration in DP patients. These biomarkers were further validated through independent cohorts and animal experiments. With glycemic deterioration, biological processes in the pancreatic islets such as nutrient metabolism and complex immune responses are disrupted in DP patients. The expression of ACOT4, B2M, and ACKR2 was upregulated, whereas the expression of CACNA1F was downregulated. Immunocyte infiltration in the islet microenvironment showed a significant positive correlation with the age, body mass index (BMI), HbA1c and glycemia at the 2-h of patients. It was a crucial factor in glycemic deterioration. Additionally, B2M demonstrated a significant positive correlation with immunocyte infiltration and clinical features. Quantitative real-time PCR (qRT-PCR) and western blotting confirmed the upregulation in B2M. Immunofluorescent staining suggested the alteration of B2M was mainly in the alpha cells and beta cells. Overall, the study showed that gradually increased immunocyte infiltration was a significant contributor to glycemic deterioration in patients with DP, and it also highlighted B2M as a biomarker.
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Affiliation(s)
- Zhen Wang
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, China
| | - Guolin Zhang
- Department of Cardiology II, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116027, China
| | - Jixian Fu
- Department of Interventional Radiology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Guangxing Li
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Zhihao Zhao
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - HyokChol Choe
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
- Department of Clinical Medicine, Sinuiju Medical University, Sinuiju, Republic of Korea
| | - Kaiyue Ding
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Junnan Ma
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Jing Wei
- Department of Immunology, College of Basic Medical Science, Dalian Medical University, Dalian, 116044, China.
| | - Dong Shang
- Department of General Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, China.
| | - Lin Zhang
- Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China.
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2
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Liu G, Zhang S, Lin R, Cao X, Yuan L. Anti-tumor target screening of sea cucumber saponin Frondoside A: a bioinformatics and molecular docking analysis. Front Oncol 2023; 13:1307838. [PMID: 38144520 PMCID: PMC10739435 DOI: 10.3389/fonc.2023.1307838] [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: 10/05/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Cancer remains the leading cause of death worldwide. In spite of significant advances in targeted and immunotherapeutic approaches, clinical outcomes for cancer remain poor. The aim of the present study was to investigate the potential mechanisms and therapeutic targets of Frondoside A for the treatment of liver, pancreatic, and bladder cancers. The data presented in our study demonstrated that Frondoside A reduced the viability and migration of HepG2, Panc02, and UM-UC-3 cancer cell in vitro. Moreover, we utilized the GEO database to screen and identify for differentially expressed genes (DEGs) in liver, pancreatic, and bladder cancers, which resulted in the identification of 714, 357, and 101 DEGs, respectively. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation were performed using the Metascape database for DEGs that were significantly associated with cancer development. The protein-protein interaction (PPI) networks of the identified DEGs in liver, pancreatic, and bladder cancers were analyzed using Cytoscape 3.9.0 software, and subsequently identified potential key genes that were associated with these networks. Subsequently, their prognostic values were assessed by gene expression level analysis and Kaplan-Meier survival analysis (GEPIA). Furthermore, we utilized TIMER 2.0 to investigate the correlation between the expression of the identified key gene and cancer immune infiltration. Finally, molecular docking simulations were performed to assess the affinity of Frondoside A and key genes. Our results showed a significant correlation between these DEGs and cancer progression. Combined, these analyses revealed that Frondoside A involves in the regulation of multiple pathways, such as drug metabolism, cell cycle in liver cancer by inhibiting the expression of CDK1, TOP2A, CDC20, and KIF20A, and regulates protein digestion and absorption, receptor interaction in pancreatic cancer by down-regulation of ASPM, TOP2A, DLGAP5, TPX2, KIF23, MELK, LAMA3, and ANLN. While in bladder cancer, Frondoside A regulates muscle contraction, complement and coagulation cascade by increase FLNC expression. In conclusion, the present study offers valuable insights into the molecular mechanism underlying the anticancer effects of Frondoside A, and suggests that Frondoside A can be used as a functional food supplement or further developed as a natural anti-cancer drug.
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Affiliation(s)
- Guangchun Liu
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Shenglin Zhang
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ruoyan Lin
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xudong Cao
- Deparment of Chemical and Biological Engineering, University of Ottawa, Ottawa, ON, Canada
| | - Lihong Yuan
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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Wang C, He Y, He Y, Liang W, Zhou C, Wu M, Meng Z, Li W, Cao J. Prognostic and biological function value of OSBPL3 in colorectal cancer analyzed by multi-omic data analysis. BMC Gastroenterol 2023; 23:270. [PMID: 37550605 PMCID: PMC10408063 DOI: 10.1186/s12876-023-02824-1] [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: 12/28/2022] [Accepted: 05/17/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignancies in the world. This study proposes to reveal prognostic biomarkers for the prognosis and treatment of CRC patients. METHODS Differential analysis of OSBPL3 was performed in pan-cancer, and the correlation between clinical stage and OSBPL3 was analyzed. Multiple omics analysis was used to compare the relationship between survival of patients and copy number variation, single nucleotide variant, and methylation status. Survival differences between high and low OSBPL3 expression groups were analyzed. Differentially expressed genes (DEGs) between high and low OSBPL3 expression groups were obtained, and functional enrichment analysis was implemented. Correlations between immune cells and OSBPL3 was analyzed. Drug sensitivity between the two OSBPL3 expression groups was compared. Moreover, the expression of OSBPL3 was verified by immunohistochemistry and real-time quantitative PCR. RESULTS OSBPL3 was differentially expressed in 13 tumors and had some correlations with T and N stages. OSBPL3 expression was regulated by methylation and higher OSBPL3 expression was associated with poorer prognosis in CRC. 128 DEGs were obtained and they were mainly involved in signaling receptor activator activity, aspartate and glutamate metabolism. T cell gamma delta and T cell follicular helper were significantly different in the high and low OSBPL3 expression groups. Moreover, OSBPL3 showed negative correlations with multiple drugs. OSBPL3 was significantly upregulated in CRC samples compared to normal samples. CONCLUSIONS A comprehensive analysis demonstrated that OSBPL3 had potential prognostic value, and guiding significance for CRC chemotherapeutic.
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Affiliation(s)
- Chengxing Wang
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Yaoming He
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Yu He
- National Drug Clinical Trial Institution, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Weijun Liang
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Chaorong Zhou
- Department of Gastrointestinal Surgery, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Meimei Wu
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Zijie Meng
- Clinical Experimental Center, Jiangmen Key Laboratory of Clinical Biobanks and Translational Research, Jiangmen Central Hospital, Jiangmen, 529000, Guangdong, China
| | - Wanglin Li
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China.
| | - Jie Cao
- The First Affiliated Hospital, Jinan University, Guangzhou, 529000, Guangdong, China.
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Bararia A, Chakraborty P, Roy P, Chattopadhay BK, Das A, Chatterjee A, Sikdar N. Emerging role of non-invasive and liquid biopsy biomarkers in pancreatic cancer. World J Gastroenterol 2023; 29:2241-2260. [PMID: 37124888 PMCID: PMC10134423 DOI: 10.3748/wjg.v29.i15.2241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
A global increase in the incidence of pancreatic cancer (PanCa) presents a major concern and health burden. The traditional tissue-based diagnostic techniques provided a major way forward for molecular diagnostics; however, they face limitations based on diagnosis-associated difficulties and concerns surrounding tissue availability in the clinical setting. Late disease development with asymptomatic behavior is a drawback in the case of existing diagnostic procedures. The capability of cell free markers in discriminating PanCa from autoimmune pancreatitis and chronic pancreatitis along with other precancerous lesions can be a boon to clinicians. Early-stage diagnosis of PanCa can be achieved only if these biomarkers specifically discriminate the non-carcinogenic disease stage from malignancy with respect to tumor stages. In this review, we comprehensively described the non-invasive disease detection approaches and why these approaches are gaining popularity for their early-stage diagnostic capability and associated clinical feasibility.
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Affiliation(s)
- Akash Bararia
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Prosenjeet Chakraborty
- Department of Molecular Biosciences, SVYASA School of Yoga and Naturopathy, Bangalore 560105, India
| | - Paromita Roy
- Department of Pathology, Tata Medical Center, Kolkata 700160, India
| | | | - Amlan Das
- Department of Biochemistry, Royal Global University, Assam 781035, India
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9061, New Zealand
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun 248007, India
| | - Nilabja Sikdar
- Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, India
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Liu L, Zhang T, Sui Y, Li G, Liu L, Lu T, Tan H, Sun B, Li X, Li L. Gut microbiota affects pancreatic fibrotic progression through immune modulation in chronic pancreatitis. Microb Pathog 2023; 177:106035. [PMID: 36828341 DOI: 10.1016/j.micpath.2023.106035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 12/02/2022] [Accepted: 02/19/2023] [Indexed: 02/25/2023]
Abstract
Chronic pancreatitis (CP) is characterized by chronic progressive pancreatic inflammation, which leads to the permanent damage of exocrine and endocrine cells. CP causes irreversible morphological and functional changes, and the clinical manifestations includes abdomen pain, steatorrhea and diabetes. CP induces changes in the composition of gut microbiota that could be used as potential biomarkers for pancreatic fibrosis evaluation. Gut microbiota has emerged as key regulator of immunomodulation and gut microbiota-induced immune activation has not been explored in CP. In current study, we profiled gut microbial signatures in mouse CP model, and found that higher proportion of Streptomyces, Turicibacter, Methylobacterium, Enterococcus and Candidatus_Paenicardiniummore were positively associated with the occurrence of pancreatic fibrosis. We then identified increased CD3+T cells and macrophage infiltration in mouse and human CP tissues by transcriptome sequencing data from GEO database. Subsequently, we demonstrated that fecal microbiota transplantation (FMT) from CP mouse (FMT-CP) exacerbated pancreatic fibrosis by increasing CD4+T cells and macrophage infiltration compared to fecal samples obtained from healthy mouse donor (FMT-HC). Our study describes the link between gut microbiota dysbiosis and immune activation in pancreatic fibrotic progression, and highlights the potential therapeutic roles of FMT and CP treatment.
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Affiliation(s)
- Lu Liu
- Department of Pharmacy, The First Hospital of Qiqihar, Qiqihar, Heilongjiang, China
| | - Tao Zhang
- Department of General Surgery, Beijing Chaoyang Hospital of Capital Medical University, Beijing, China
| | - Yuhang Sui
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Guanqun Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Liwei Liu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Tianqi Lu
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongtao Tan
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Bei Sun
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xina Li
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
| | - Le Li
- Department of Pancreatic and Biliary Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China; Key Laboratory of Hepatosplenic Surgery, Ministry of Education, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
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6
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Choi J, Oh TG, Jung HW, Park KY, Shin H, Jo T, Kang DS, Chanda D, Hong S, Kim J, Hwang H, Ji M, Jung M, Shoji T, Matsushima A, Kim P, Mun JY, Paik MJ, Cho SJ, Lee IK, Whitcomb DC, Greer P, Blobner B, Goodarzi MO, Pandol SJ, Rotter JI, Fan W, Bapat SP, Zheng Y, Liddle C, Yu RT, Atkins AR, Downes M, Yoshihara E, Evans RM, Suh JM. Estrogen-Related Receptor γ Maintains Pancreatic Acinar Cell Function and Identity by Regulating Cellular Metabolism. Gastroenterology 2022; 163:239-256. [PMID: 35461826 PMCID: PMC9233018 DOI: 10.1053/j.gastro.2022.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/22/2022] [Accepted: 04/03/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Mitochondrial dysfunction disrupts the synthesis and secretion of digestive enzymes in pancreatic acinar cells and plays a primary role in the etiology of exocrine pancreas disorders. However, the transcriptional mechanisms that regulate mitochondrial function to support acinar cell physiology are poorly understood. Here, we aim to elucidate the function of estrogen-related receptor γ (ERRγ) in pancreatic acinar cell mitochondrial homeostasis and energy production. METHODS Two models of ERRγ inhibition, GSK5182-treated wild-type mice and ERRγ conditional knock-out (cKO) mice, were established to investigate ERRγ function in the exocrine pancreas. To identify the functional role of ERRγ in pancreatic acinar cells, we performed histologic and transcriptome analysis with the pancreas isolated from ERRγ cKO mice. To determine the relevance of these findings for human disease, we analyzed transcriptome data from multiple independent human cohorts and conducted genetic association studies for ESRRG variants in 2 distinct human pancreatitis cohorts. RESULTS Blocking ERRγ function in mice by genetic deletion or inverse agonist treatment results in striking pancreatitis-like phenotypes accompanied by inflammation, fibrosis, and cell death. Mechanistically, loss of ERRγ in primary acini abrogates messenger RNA expression and protein levels of mitochondrial oxidative phosphorylation complex genes, resulting in defective acinar cell energetics. Mitochondrial dysfunction due to ERRγ deletion further triggers autophagy dysfunction, endoplasmic reticulum stress, and production of reactive oxygen species, ultimately leading to cell death. Interestingly, ERRγ-deficient acinar cells that escape cell death acquire ductal cell characteristics, indicating a role for ERRγ in acinar-to-ductal metaplasia. Consistent with our findings in ERRγ cKO mice, ERRγ expression was significantly reduced in patients with chronic pancreatitis compared with normal subjects. Furthermore, candidate locus region genetic association studies revealed multiple single nucleotide variants for ERRγ that are associated with chronic pancreatitis. CONCLUSIONS Collectively, our findings highlight an essential role for ERRγ in maintaining the transcriptional program that supports acinar cell mitochondrial function and organellar homeostasis and provide a novel molecular link between ERRγ and exocrine pancreas disorders.
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Affiliation(s)
- Jinhyuk Choi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Tae Gyu Oh
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Hee-Won Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kun-Young Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hyemi Shin
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Taehee Jo
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Du-Seock Kang
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Dipanjan Chanda
- Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, Republic of Korea; Bio-Medical Research Institute, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Sujung Hong
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jina Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Hayoung Hwang
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Moongi Ji
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Takashi Shoji
- Department of Medicine, Kyoto University, Kyoto, Japan
| | - Ayami Matsushima
- Laboratory of Structure-Function Biochemistry, Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Pilhan Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Man-Jeong Paik
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Sung Jin Cho
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - In-Kyu Lee
- Leading-Edge Research Center for Drug Discovery and Development for Diabetes and Metabolic Disease, Kyungpook National University Hospital, Daegu, Republic of Korea; Bio-Medical Research Institute, Kyungpook National University Hospital, Daegu, Republic of Korea; Research Institute of Aging and Metabolism, Kyungpook National University, Daegu, Republic of Korea; Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - David C Whitcomb
- Ariel Precision Medicine, Pittsburgh, Pennsylvania; Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Cell Biology and Molecular Physiology and the Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Phil Greer
- Ariel Precision Medicine, Pittsburgh, Pennsylvania; Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brandon Blobner
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Stephen J Pandol
- Cedars-Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, California; Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California; Departments of Pediatrics and Human Genetics, David Geffen School of Medicine at University of California-Los Angeles, Los Angeles, California
| | - Weiwei Fan
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Sagar P Bapat
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California; Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California; Diabetes Center, University of California-San Francisco, San Francisco, California; Nomis Laboratories for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California
| | - Ye Zheng
- Nomis Laboratories for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California
| | - Chris Liddle
- Storr Liver Centre, Westmead Institute for Medical Research and Sydney School of Medicine, University of Sydney, Westmead, New South Wales, Australia
| | - Ruth T Yu
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Annette R Atkins
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Michael Downes
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Eiji Yoshihara
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California; The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California; David Geffen School of Medicine at University of California-Los Angeles, Los Angeles, California.
| | - Ronald M Evans
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, California.
| | - Jae Myoung Suh
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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Hu C, Yin L, Chen Z, Waldron RT, Lugea A, Lin Y, Zhai X, Wen L, Han YP, Pandol SJ, Deng L, Xia Q. The unique pancreatic stellate cell gene expression signatures are associated with the progression from acute to chronic pancreatitis. Comput Struct Biotechnol J 2021; 19:6375-6385. [PMID: 34938413 PMCID: PMC8649580 DOI: 10.1016/j.csbj.2021.11.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 02/05/2023] Open
Abstract
Early recognition of chronic pancreatitis (CP) is still lacking. In the setting of CP injury, activated pancreatic stellate cell (PSC) is the central mediator of pancreatic fibrosis. We systematically define highly and uniquely expressed PSC genes and show that these genes are enriched in pancreatic diseases. Unresolved or recurrent injury causes dysregulation of biological process following AP, which would cause CP. We demonstrated subset genes that may be associated with the progression from AP to CP. Furthermore, SPARC was identified as a candidate marker for the disease progression. Increased expression of SPARC and canonical PSC genes were verified during AP recovery, especially in recurrent AP mice models.
Chronic pancreatitis (CP) is characterized by irreversible fibro-inflammatory changes induced by pancreatic stellate cell (PSC). Unresolved or recurrent injury causes dysregulation of biological process following AP, which would cause CP. Here, we systematically identify genes whose expressions are unique to PSC by comparing transcriptome profiles among total pancreas, pancreatic stellate, acinar, islet and immune cells. We then identified candidate genes and correlated them with the pancreatic disease continuum by performing intersection analysis among total PSC and activated PSC genes, and genes persistently differentially expressed during acute pancreatitis (AP) recovery. Last, we examined the association between candidate genes and AP, and substantiated their potential as biomarkers in experimental AP and recurrent AP (RAP) models. A total of 68 genes were identified as highly and uniquely expressed in PSC. The PSC signatures were highly enriched with extracellular matrix remodeling genes and were significantly enriched in AP pancreas compared to healthy control tissues. Among PSC signature genes that comprised a fibrotic phenotype, 10 were persistently differentially expressed during AP recovery. SPARC was determined as a candidate marker for the pancreatic disease continuum, which was not only persistently differentially expressed even five days after AP injury, but also highly expressed in two clinical datasets of CP. Sparc was also validated as highly elevated in RAP compared to AP mice. This work highlights the unique transcriptional profiles of PSC. These PSC signatures’ expression may help to identify patients with high risk of AP progression to CP.
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Affiliation(s)
- Cheng Hu
- Department and Laboratory of Integrated Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis Center and West China-Liverpool Biomedical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Liyuan Yin
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyao Chen
- Department and Laboratory of Integrated Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis Center and West China-Liverpool Biomedical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Richard T Waldron
- Department of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Aurelia Lugea
- Department of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Yiyun Lin
- Graduate School of Biomedical Sciences, UT MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Xiaoqian Zhai
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Li Wen
- Department of Gastroenterology and Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuan-Ping Han
- Center for Growth, Metabolism and Aging, College of Life Sciences, Sichuan University, Chengdu, China
| | - Stephen J Pandol
- Department of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United States.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Lihui Deng
- Department and Laboratory of Integrated Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis Center and West China-Liverpool Biomedical Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qing Xia
- Department and Laboratory of Integrated Traditional Chinese and Western Medicine, Sichuan Provincial Pancreatitis Center and West China-Liverpool Biomedical Research Center, West China Hospital, Sichuan University, Chengdu, China
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8
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Mukherjee M, Goswami S. Identification of Key Deregulated RNA-Binding Proteins in Pancreatic Cancer by Meta-Analysis and Prediction of Their Role as Modulators of Oncogenesis. Front Cell Dev Biol 2021; 9:713852. [PMID: 34912796 PMCID: PMC8667787 DOI: 10.3389/fcell.2021.713852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play a significant role in multiple cellular processes with their deregulations strongly associated with cancer. However, there are not adequate evidences regarding global alteration and functions of RBPs in pancreatic cancer, interrogated in a systematic manner. In this study, we have prepared an exhaustive list of RBPs from multiple sources, downloaded gene expression microarray data from a total of 241 pancreatic tumors and 124 normal pancreatic tissues, performed a meta-analysis, and obtained differentially expressed RBPs (DE-RBPs) using the Limma package of R Bioconductor. The results were validated in microarray datasets and the Cancer Genome Atlas (TCGA) RNA sequencing dataset for pancreatic adenocarcinoma (PAAD). Pathway enrichment analysis was performed using DE-RBPs, and we also constructed the protein-protein interaction (PPI) network to detect key modules and hub-RBPs. Coding and noncoding targets for top altered and hub RBPs were identified, and altered pathways modulated by these targets were also investigated. Our meta-analysis identified 45 upregulated and 15 downregulated RBPs as differentially expressed in pancreatic cancer, and pathway enrichment analysis demonstrated their important contribution in tumor development. As a result of PPI network analysis, 26 hub RBPs were detected and coding and noncoding targets for all these RBPs were categorized. Functional exploration characterized the pathways related to epithelial-to-mesenchymal transition (EMT), cell migration, and metastasis to emerge as major pathways interfered by the targets of these RBPs. Our study identified a unique meta-signature of 26 hub-RBPs to primarily modulate pancreatic tumor cell migration and metastasis in pancreatic cancer. IGF2BP3, ISG20, NIP7, PRDX1, RCC2, RUVBL1, SNRPD1, PAIP2B, and SIDT2 were found to play the most prominent role in the regulation of EMT in the process. The findings not only contribute to understand the biology of RBPs in pancreatic cancer but also to evaluate their candidature as possible therapeutic targets.
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Affiliation(s)
| | - Srikanta Goswami
- National Institute of Biomedical Genomics, Kalyani, India.,Regional Centre for Biotechnology, Faridabad, India
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Li H, Weng Y, Wang S, Wang F, Wang Y, Kong P, Zhang L, Cheng C, Cui H, Xu E, Wei S, Guo D, Chen F, Bi Y, Meng Y, Cheng X, Cui Y. CDCA7 Facilitates Tumor Progression by Directly Regulating CCNA2 Expression in Esophageal Squamous Cell Carcinoma. Front Oncol 2021; 11:734655. [PMID: 34737951 PMCID: PMC8561731 DOI: 10.3389/fonc.2021.734655] [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: 08/03/2021] [Accepted: 09/27/2021] [Indexed: 01/14/2023] Open
Abstract
Background CDCA7 is a copy number amplified gene identified not only in esophageal squamous cell carcinoma (ESCC) but also in various cancer types. Its clinical relevance and underlying mechanisms in ESCC have remained unknown. Methods Tissue microarray data was used to analyze its expression in 179 ESCC samples. The effects of CDCA7 on proliferation, colony formation, and cell cycle were tested in ESCC cells. Real-time PCR and Western blot were used to detect the expression of its target genes. Correlation of CDCA7 with its target genes in ESCC and various SCC types was analyzed using GSE53625 and TCGA data. The mechanism of CDCA7 was studied by chromatin immunoprecipitation (ChIP), luciferase reporter assays, and rescue assay. Results The overexpression of CDCA7 promoted proliferation, colony formation, and cell cycle in ESCC cells. CDCA7 affected the expression of cyclins in different cell phases. GSE53625 and TCGA data showed CCNA2 expression was positively correlated with CDCA7. The knockdown of CCNA2 reversed the malignant phenotype induced by CDCA7 overexpression. Furthermore, CDCA7 was found to directly bind to CCNA2, thus promoting its expression. Conclusions Our results reveal a novel mechanism of CDCA7 that it may act as an oncogene by directly upregulating CCNA2 to facilitate tumor progression in ESCC.
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Affiliation(s)
- Hongyi Li
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Yongjia Weng
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Shaojie Wang
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Fang Wang
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Yanqiang Wang
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Pengzhou Kong
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Ling Zhang
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Caixia Cheng
- Department of Pathology, the First Hospital, Shanxi Medical University, Taiyuan, China
| | - Heyang Cui
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Enwei Xu
- Department of Pathology, Shanxi Province Cancer Hospital, Taiyuan, China
| | - Shuqing Wei
- Department of Thoracic Surgery (Ⅰ), Shanxi Province Cancer Hospital, Taiyuan, China
| | - Dinghe Guo
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Fei Chen
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Yanghui Bi
- The Science Research Center, Shanxi Bethone Hospital, Taiyuan, China
| | - Yongsheng Meng
- Tumor Biobank, Shanxi Province Cancer Hospital, Taiyuan, China
| | - Xiaolong Cheng
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
| | - Yongping Cui
- Department of Pathology & Shanxi Key Laboratory of Carcinogenesis and Translational Research of Esophageal Cancer, Shanxi Medical University, Taiyuan, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, China
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Huang X, Zhang G, Tang T, Liang T. Identification of tumor antigens and immune subtypes of pancreatic adenocarcinoma for mRNA vaccine development. Mol Cancer 2021; 20:44. [PMID: 33648511 PMCID: PMC7917175 DOI: 10.1186/s12943-021-01310-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/08/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Although mRNA vaccines have been effective against multiple cancers, their efficacy against pancreatic adenocarcinoma (PAAD) remains undefined. Accumulating evidence suggests that immunotyping can indicate the comprehensive immune status in tumors and their immune microenvironment, which is closely associated with therapeutic response and vaccination potential. The aim of this study was to identify potent antigens in PAAD for mRNA vaccine development, and further distinguish immune subtypes of PAAD to construct an immune landscape for selecting suitable patients for vaccination. METHODS Gene expression profiles and clinical information of 239 PAAD datasets were extracted from ICGC, and RNA-Seq data of 103 samples were retrieved from TCGA. GEPIA was used to calculate differential expression levels and prognostic indices, cBioPortal program was used to compare genetic alterations, and TIMER was used to explore correlation between genes and immune infiltrating cells. Consensus cluster was used for consistency matrix construction and data clustering, DAVID was used for functional annotation, and graph learning-based dimensional reduction was used to depict immune landscape. RESULTS Six overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in PAAD, including ADAM9, EFNB2, MET, TMOD3, TPX2, and WNT7A. Furthermore, five immune subtypes (IS1-IS5) and nine immune gene modules of PAAD were identified that were consistent in both patient cohorts. The immune subtypes showed distinct molecular, cellular and clinical characteristics. IS1 and IS2 exhibited immune-activated phenotypes and correlated to better survival compared to the other subtypes. IS4 and IS5 tumors were immunologically cold and associated with higher tumor mutation burden. Immunogenic cell death modulators, immune checkpoints, and CA125 and CA199, were also differentially expressed among the five immune subtypes. Finally, the immune landscape of PAAD showed a high degree of heterogeneity between individual patients. CONCLUSIONS ADAM9, EFNB2, MET, TMOD3, TPX2, and WNT7A are potent antigens for developing anti-PAAD mRNA vaccine, and patients with IS4 and IS5 tumors are suitable for vaccination.
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Affiliation(s)
- Xing Huang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003 Hangzhou China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003 Hangzhou China
- Innovation Center for the Study of Pancreatic Diseases, Zhejiang Province, Zhejiang, 310003 Hangzhou China
- Zhejiang University Cancer Center, Zhejiang, 310003 Hangzhou China
- Research Center for Healthcare Data Science, Zhejiang Lab, Zhejiang, 310003 Hangzhou China
| | - Gang Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003 Hangzhou China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003 Hangzhou China
- Innovation Center for the Study of Pancreatic Diseases, Zhejiang Province, Zhejiang, 310003 Hangzhou China
- Zhejiang University Cancer Center, Zhejiang, 310003 Hangzhou China
- Research Center for Healthcare Data Science, Zhejiang Lab, Zhejiang, 310003 Hangzhou China
| | - Tianyu Tang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003 Hangzhou China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003 Hangzhou China
- Innovation Center for the Study of Pancreatic Diseases, Zhejiang Province, Zhejiang, 310003 Hangzhou China
- Zhejiang University Cancer Center, Zhejiang, 310003 Hangzhou China
- Research Center for Healthcare Data Science, Zhejiang Lab, Zhejiang, 310003 Hangzhou China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003 Hangzhou China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang, 310003 Hangzhou China
- Innovation Center for the Study of Pancreatic Diseases, Zhejiang Province, Zhejiang, 310003 Hangzhou China
- Zhejiang University Cancer Center, Zhejiang, 310003 Hangzhou China
- Research Center for Healthcare Data Science, Zhejiang Lab, Zhejiang, 310003 Hangzhou China
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