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Kim SC, Seo HY, Lee JO, Maeng JE, Shin YK, Lee SH, Jang JY, Ku JL. Establishment, characterization, and biobanking of 36 pancreatic cancer organoids: prediction of metastasis in resectable pancreatic cancer. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00939-5. [PMID: 38619751 DOI: 10.1007/s13402-024-00939-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 04/16/2024] Open
Abstract
PURPOSE Early dissemination of primary pancreatic ductal adenocarcinoma (PDAC) is the main cause of dismal prognosis as it highly limits possible treatment options. A number of PDAC patients experience distant metastasis even after treatment due to the metastatic clones. We aimed to demonstrate the molecular architecture of borderline resectable PDAC manifests cancer dissemination of PDAC. METHODS Here, 36 organoids isolated from primary tumor masses of PDAC patients with diverse metastatic statues are presented. Whole-exome sequencing and RNA sequencing were performed and drug responses to clinically relevant 18 compounds were assessed. RESULTS Our results revealed that borderline resectable PDAC organoids exhibited distinct patterns according to their metastatic potency highlighted by multiple genetic and transcriptional factors and strong variances in drug responses. CONCLUSIONS These data suggest that the presence of metastatic PDAC can be identified by integrating molecular compositions and drug responses of borderline resectable PDAC.
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Affiliation(s)
- Soon-Chan Kim
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ha-Young Seo
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Ja-Oh Lee
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Ju Eun Maeng
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Young-Kyoung Shin
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Sang Hyub Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
| | - Jin-Young Jang
- Department of Surgery, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul, 03080, South Korea.
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Korea.
- Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
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Parise A, Magistrato A. Assessing the mechanism of fast-cycling cancer-associated mutations of Rac1 small Rho GTPase. Protein Sci 2024; 33:e4939. [PMID: 38501467 PMCID: PMC10949326 DOI: 10.1002/pro.4939] [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: 09/07/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 03/20/2024]
Abstract
Rho-GTPases proteins function as molecular switches alternating from an active to an inactive state upon Guanosine triphosphate (GTP) binding and hydrolysis to Guanosine diphosphate (GDP). Among them, Rac subfamily regulates cell dynamics, being overexpressed in distinct cancer types. Notably, these proteins are object of frequent cancer-associated mutations at Pro29 (P29S, P29L, and P29Q). To assess the impact of these mutations on Rac1 structure and function, we performed extensive all-atom molecular dynamics simulations on wild-type (wt) and oncogenic isoforms of this protein in GDP- and GTP-bound states. Our results unprecedentedly elucidate that P29Q/S-induced structural and dynamical perturbations of Rac1 core domain weaken the binding of the catalytic site Mg2+ ion, and reduce the GDP residence time within protein, enhancing the GDP/GTP exchange rate and Rac1 activity. This broadens our knowledge of the role of cancer-associated mutations on small GTPases mechanism supplying valuable information for future drug discovery efforts targeting specific Rac1 isoforms.
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Affiliation(s)
- Angela Parise
- Consiglio Nazionale delle ricerche (CNR)‐IOM c/o International School for Advanced Studies (SISSA/ISAS)TriesteItaly
| | - Alessandra Magistrato
- Consiglio Nazionale delle ricerche (CNR)‐IOM c/o International School for Advanced Studies (SISSA/ISAS)TriesteItaly
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Li J, Zhang H, Mu B, Zuo H, Zhou K. Identifying phenotype-associated subpopulations through LP_SGL. Brief Bioinform 2023; 25:bbad424. [PMID: 38008419 PMCID: PMC10753413 DOI: 10.1093/bib/bbad424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/28/2023] [Accepted: 10/31/2023] [Indexed: 11/28/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) enables the resolution of cellular heterogeneity in diseases and facilitates the identification of novel cell types and subtypes. However, the grouping effects caused by cell-cell interactions are often overlooked in the development of tools for identifying subpopulations. We proposed LP_SGL which incorporates cell group structure to identify phenotype-associated subpopulations by integrating scRNA-seq, bulk expression and bulk phenotype data. Cell groups from scRNA-seq data were obtained by the Leiden algorithm, which facilitates the identification of subpopulations and improves model robustness. LP_SGL identified a higher percentage of cancer cells, T cells and tumor-associated cells than Scissor and scAB on lung adenocarcinoma diagnosis, melanoma drug response and liver cancer survival datasets, respectively. Biological analysis on three original datasets and four independent external validation sets demonstrated that the signaling genes of this cell subset can predict cancer, immunotherapy and survival.
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Affiliation(s)
- Juntao Li
- College of Mathematics and Information Science, Henan Normal University, 46 Jianshe East Road, 453007, Xinxiang, China
| | - Hongmei Zhang
- College of Mathematics and Information Science, Henan Normal University, 46 Jianshe East Road, 453007, Xinxiang, China
| | - Bingyu Mu
- College of Arts and Design, Zhengzhou University of Light Industry, No. 5 Dongfeng Road, 450000, Zhengzhou, China
| | - Hongliang Zuo
- College of Mathematics and Information Science, Henan Normal University, 46 Jianshe East Road, 453007, Xinxiang, China
| | - Kanglei Zhou
- School of Computer Science and Engneering, Beihang University, 37 Xueyuan Road, Haidian District, 100191, Beijing, China
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Halder S, Basu S, Lal S, Ganti AK, Batra SK, Seshacharyulu P. Targeting the EGFR signaling pathway in cancer therapy: What's new in 2023? Expert Opin Ther Targets 2023; 27:305-324. [PMID: 37243489 PMCID: PMC10330690 DOI: 10.1080/14728222.2023.2218613] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023]
Abstract
INTRODUCTION Epidermal growth factor receptor (EGFR) is frequently amplified, overexpressed, and mutated in multiple cancers. In normal cell physiology, EGFR signaling controls cellular differentiation, proliferation, growth, and survival. During tumorigenesis, mutations in EGFR lead to increased kinase activity supporting survival, uncontrolled proliferation, and migratory functions of cancer cells. Molecular agents targeting the EGFR pathway have been discovered, and their efficacy has been demonstrated in clinical trials. To date, 14 EGFR-targeted agents have been approved for cancer treatments. AREAS COVERED This review describes the newly identified pathways in EGFR signaling, the evolution of novel EGFR-acquired and innate resistance mechanisms, mutations, and adverse side effects of EGFR signaling inhibitors. Subsequently, the latest EGFR/panEGFR inhibitors in preclinical and clinical studies have been summarized. Finally, the consequences of combining immune checkpoint inhibitors and EGFR inhibitors have also been discussed. EXPERT OPINION As new mutations are threatened against EGFR-tyrosine kinase inhibitors (TKIs), we suggest the development of new compounds targeting specific mutations without inducing new mutations. We discuss potential future research on developing EGFR-TKIs specific for exact allosteric sites to overcome acquired resistance and reduce adverse events. The rising trend of EGFR inhibitors in the pharma market and their economic impact on real-world clinical practice are discussed.
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Affiliation(s)
- Sushanta Halder
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Soumi Basu
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Shobhit Lal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Apar K. Ganti
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
- Eppley Institute for Research in Cancer and Allied Diseases
- Division of Oncology-Hematology, Department of Internal Medicine, VA Nebraska Western Iowa Health Care System, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
- Fred & Pamela Buffett Cancer Center University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
- Eppley Institute for Research in Cancer and Allied Diseases
- Fred & Pamela Buffett Cancer Center University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Parthasarathy Seshacharyulu
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
- Fred & Pamela Buffett Cancer Center University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
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Liu Q, Li R, Wu H, Liang Z. A novel cuproptosis-related gene model predicts outcomes and treatment responses in pancreatic adenocarcinoma. BMC Cancer 2023; 23:226. [PMID: 36894917 PMCID: PMC9999523 DOI: 10.1186/s12885-023-10678-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/24/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Cuproptosis is recently emerging as a hot spot in cancer research. However, its role in pancreatic adenocarcinoma (PAAD) has not yet been clarified. This study aimed to explore the prognostic and therapeutic implications of cuproptosis-related genes in PAAD. METHODS Two hundred thirteen PAAD samples from the International Cancer Genome Consortium (ICGC) were split into training and validation sets in the ratio of 7:3. The Cox regression analyses generated a prognostic model using the ICGC cohort for training (n = 152) and validation (n = 61). The model was externally tested on the Gene Expression Omnibus (GEO) (n = 80) and The Cancer Genome Atlas (TCGA) datasets (n = 176). The clinical characteristics, molecular mechanisms, immune landscape, and treatment responses in model-defined subgroups were explored. The expression of an independent prognostic gene TSC22D2 was confirmed by public databases, real-time quantitative PCR (RT-qPCR), western blot (WB), and immunohistochemistry (IHC). RESULTS A prognostic model was established based on three cuproptosis-related genes (TSC22D2, C6orf136, PRKDC). Patients were stratified into high- and low-risk groups using the risk score based on this model. PAAD patients in the high-risk group had a worse prognosis. The risk score was statistically significantly correlated with most clinicopathological characteristics. The risk score based on this model was an independent predictor of overall survival (OS) (HR = 10.7, p < 0.001), and was utilized to create a scoring nomogram with excellent prognostic value. High-risk patients had a higher TP53 mutation rate and a superior response to multiple targeted therapies and chemotherapeutic drugs, but might obtain fewer benefits from immunotherapy. Moreover, elevated TSC22D2 expression was discovered to be an independent prognostic predictor for OS (p < 0.001). Data from public databases and our own experiments showed that TSC22D2 expression was significantly higher in pancreatic cancer tissues/cells compared to normal tissues/cells. CONCLUSION This novel model based on cuproptosis-related genes provided a robust biomarker for predicting the prognosis and treatment responses of PAAD. The potential roles and underlying mechanisms of TSC22D2 in PAAD need further explored.
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Affiliation(s)
- Qixian Liu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Ruiyu Li
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Huanwen Wu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
| | - Zhiyong Liang
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China.
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6
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Zhang Z, Zhang H, Liao X, Tsai HI. KRAS mutation: The booster of pancreatic ductal adenocarcinoma transformation and progression. Front Cell Dev Biol 2023; 11:1147676. [PMID: 37152291 PMCID: PMC10157181 DOI: 10.3389/fcell.2023.1147676] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/10/2023] [Indexed: 05/09/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer. It has a poor response to conventional therapy and has an extremely poor 5-year survival rate. PDAC is driven by multiple oncogene mutations, with the highest mutation frequency being observed in KRAS. The KRAS protein, which binds to GTP, has phosphokinase activity, which further activates downstream effectors. KRAS mutation contributes to cancer cell proliferation, metabolic reprogramming, immune escape, and therapy resistance in PDAC, acting as a critical driver of the disease. Thus, KRAS mutation is positively associated with poorer prognosis in pancreatic cancer patients. This review focus on the KRAS mutation patterns in PDAC, and further emphases its role in signal transduction, metabolic reprogramming, therapy resistance and prognosis, hoping to provide KRAS target therapy strategies for PDAC.
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Affiliation(s)
- Zining Zhang
- Institute of Medical Imaging and Artificial Intelligence, Jiangsu University, Zhenjiang, China
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Heng Zhang
- Institute of Medical Imaging and Artificial Intelligence, Jiangsu University, Zhenjiang, China
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiang Liao
- Institute of Medical Imaging and Artificial Intelligence, Jiangsu University, Zhenjiang, China
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Xiang Liao, ; Hsiang-i Tsai,
| | - Hsiang-i Tsai
- Institute of Medical Imaging and Artificial Intelligence, Jiangsu University, Zhenjiang, China
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, China
- *Correspondence: Xiang Liao, ; Hsiang-i Tsai,
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Zheng M, Wang W, Bu Y, Liu J, Ma J, Wang R, Ren X, Lu Z, Li J, Cai J. Pan-Cancer Analysis of the Roles and Driving Forces of RAB42. Biomolecules 2022; 13:biom13010043. [PMID: 36671428 PMCID: PMC9855782 DOI: 10.3390/biom13010043] [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: 10/28/2022] [Revised: 12/14/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
RAB42 is a member of the RAS family. However, the roles and driving forces for RAB42 in tumors remain elusive. In this study, we performed a comprehensive pan-cancer analysis of the roles and regulatory mechanisms of RAB42 using bioinformatics and experiments. Online databases such as Sanger Box, ACLBI and TIDE were used to search for the expression levels, prognostic value and immune features of RAB42. We observed that RAB42 expression was upregulated in most tumors and was closely associated with poor prognosis. Enrichment analysis indicated that RAB42 was related to multiple biological functions, especially the immune process. RAB42 expression had a positive correlation with immune cell infiltration and immune checkpoint gene expression. RAB42 had a high predictive value for immunotherapy efficiency. Our study screened out susceptible drugs for the RAB42 protein by sensitivity analysis and virtual screening. Many key driver genes such as TP53 contributed to RAB42 expression. DNA methylation, super-enhancer and non-coding RNAs were the epigenetic factors responsible for RAB42 expression. In brief, RAB42 could serve as a diagnostic and prognostic biomarker in many tumor types. RAB42 might be a predictive biomarker and a new target for immunotherapy. Genetic and epigenetic factors were essential for RAB42 overexpression in tumors.
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Affiliation(s)
- Mingzhu Zheng
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Wenhao Wang
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Yulan Bu
- Department of Radiotherapy, Affiliated Hospital of Weifang Medical University, Weifang 261031, China
| | - Jing Liu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Jingang Ma
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Rui Wang
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Xiaomin Ren
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Zhong Lu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, School of Clinical Medicine, Weifang Medical University, Weifang 261031, China
| | - Jiaqiu Li
- Jinming Yu Academician Workstation of Oncology, Clinical Research Center, Affiliated Hospital of Weifang Medical University, Weifang 261031, China
- Correspondence: (J.L.); (J.C.)
| | - Jinwei Cai
- Department of Oncology, People’s Hospital of Kecheng District, Quzhou 324000, China
- Correspondence: (J.L.); (J.C.)
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Kori M, Ozdemir GE, Arga KY, Sinha R. A Pan-Cancer Atlas of Differentially Interacting Hallmarks of Cancer Proteins. J Pers Med 2022; 12:1919. [PMID: 36422095 PMCID: PMC9695992 DOI: 10.3390/jpm12111919] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 10/21/2023] Open
Abstract
Cancer hallmark genes and proteins orchestrate and drive carcinogenesis to a large extent, therefore, it is important to study these features in different cancer types to understand the process of tumorigenesis and discover measurable indicators. We performed a pan-cancer analysis to map differentially interacting hallmarks of cancer proteins (DIHCP). The TCGA transcriptome data associated with 12 common cancers were analyzed and the differential interactome algorithm was applied to determine DIHCPs and DIHCP-centric modules (i.e., DIHCPs and their interacting partners) that exhibit significant changes in their interaction patterns between the tumor and control phenotypes. The diagnostic and prognostic capabilities of the identified modules were assessed to determine the ability of the modules to function as system biomarkers. In addition, the druggability of the prognostic and diagnostic DIHCPs was investigated. As a result, we found a total of 30 DIHCP-centric modules that showed high diagnostic or prognostic performance in any of the 12 cancer types. Furthermore, from the 16 DIHCP-centric modules examined, 29% of these were druggable. Our study presents candidate systems' biomarkers that may be valuable for understanding the process of tumorigenesis and improving personalized treatment strategies for various cancers, with a focus on their ten hallmark characteristics.
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Affiliation(s)
- Medi Kori
- Department of Bioengineering, Marmara University, Istanbul 34854, Turkey
| | - Gullu Elif Ozdemir
- Department of Bioengineering, Marmara University, Istanbul 34854, Turkey
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Istanbul 34854, Turkey
- Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul 34854, Turkey
| | - Raghu Sinha
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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Li W, Zhang X, Li Y, Yue Q, Cui M, Liu J. Prognostic Value of KRAS Mutations in the Peripheral Blood of Patients with Pancreatic Cancer: a Systematic Review and Meta-analysis. Indian J Surg 2022. [DOI: 10.1007/s12262-021-03142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Wang R, Guo Y, Ma P, Song Y, Min J, Zhao T, Hua L, Zhang C, Yang C, Shi J, Zhu L, Gan D, Li S, Li J, Su H. Comprehensive Analysis of 5-Methylcytosine (m 5C) Regulators and the Immune Microenvironment in Pancreatic Adenocarcinoma to Aid Immunotherapy. Front Oncol 2022; 12:851766. [PMID: 35433474 PMCID: PMC9009261 DOI: 10.3389/fonc.2022.851766] [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: 01/10/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
Abstract
Background Pancreatic adenocarcinoma (PAAD) is one of the most malignant cancers and has a poor prognosis. As a critical RNA modification, 5-methylcytosine (m5C) has been reported to regulate tumor progression, including PAAD progression. However, a comprehensive analysis of m5C regulators in PAAD is lacking. Methods In the present study, PAAD datasets were obtained from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and ArrayExpress databases. The expression pattern of m5C regulators were analyzed and patients were divided into different m5C clusters according to consensus clustering based on m5C regulators. Additionally, m5C differentially expressed genes (DEGs) were determined using Limma package. Based on m5C DEGs, patients were divided into m5C gene clusters. Moreover, m5C gene signatures were derived from m5C DEGs and a quantitative indicator, the m5C score, was developed from the m5C gene signatures. Results Our study showed that m5C regulators were differentially expressed in patients with PAAD. The m5C clusters and gene clusters based on m5C regulators and m5C DEGs were related to immune cell infiltration, immune-related genes and patient survival status, indicating that m5C modification play a central role in regulating PAAD development partly by modulating immune microenvironment. Additionally, a quantitative indicator, the m5C score, was also developed and was related to a series of immune-related indicators. Moreover, the m5C score precisely predicted the immunotherapy response and prognosis of patients with PAAD. Conclusion In summary, we confirmed that m5C regulators regulate PAAD development by modulating the immune microenvironment. In addition, a quantitative indicator, the m5C score, was developed to predict immunotherapy response and prognosis and assisted in identifying PAAD patients suitable for tailored immunotherapy strategies.
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Affiliation(s)
- Ronglin Wang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Yongdong Guo
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Peixiang Ma
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Yang Song
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Jie Min
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Ting Zhao
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Lei Hua
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Chao Zhang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Cheng Yang
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Jingjie Shi
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Liaoliao Zhu
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Dongxue Gan
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Shanshan Li
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Junqiang Li
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Haichuan Su
- Department of Oncology, Tangdu Hospital, Air Force Medical University, Xi'an, China
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Zhang T, Zhu L, Cai J, He J. Four drug metabolism-related subgroups of pancreatic adenocarcinoma in prognosis, immune infiltration, and gene mutation. Open Med (Wars) 2022; 17:427-440. [PMID: 35340619 PMCID: PMC8898926 DOI: 10.1515/med-2022-0433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/14/2022] [Accepted: 01/14/2022] [Indexed: 11/15/2022] Open
Abstract
We aimed to screen the drug metabolism-related subgroups of pancreatic adenocarcinoma (PAAD) and to study the prognosis, clinical features, immune infiltration, and gene mutation differences of different subtypes in PAAD patients. All 181 cases of PAAD samples and clinical characteristics data were downloaded from The Cancer Genome Atlas (TCGA). After matching the drug metabolism-related genes downloaded from PMID 33202946 with the TCGA dataset, the drug metabolism-related genes were initially obtained. Besides, univariate Cox regression analysis was used to screen the drug metabolism genes related to the prognosis of PAAD. Moreover, the construction of the protein–protein interaction (PPI) network and gene ontology were performed. The four subgroups of PAAD obtained from unsupervised clustering analysis were systematically analyzed, including prognostic, GSVA, immune infiltration, and gene mutation analysis. A total of 83 drug metabolism genes related to the prognosis of PAAD were obtained and enriched in 16 pathways. The PPI network was composed of 248 relationship pairs. Four subgroups that can identify different subtypes of PPAD were obtained, and there were significant differences in survival and clinical characteristics, mutation types, and immune infiltration abundance between subgroups. A total of 17 different pathways among the four subgroups involved in cell cycle, response to stimulants such as drugs, and transmembrane transport. In this study, the four subgroups related to the drug metabolism of PAAD were comprehensively analyzed, and the important role of drug metabolism-related genes in the immune infiltration and prognosis of PAAD were emphasized.
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Affiliation(s)
- Tongyi Zhang
- Department of General Surgery, Huadong Hospital Affiliated to Fudan University , Jing’an District, 200040 , Shanghai , China
| | - Liyong Zhu
- Department of General Surgery, Huadong Hospital Affiliated to Fudan University , Jing’an District, 200040 , Shanghai , China
| | - Jianhua Cai
- Department of General Surgery, Huadong Hospital Affiliated to Fudan University , Jing’an District, 200040 , Shanghai , China
| | - Jiaqi He
- Department of General Surgery, Huadong Hospital Affiliated to Fudan University , No. 221 Yan’an West Road, Jing’an District, 200040 , Shanghai , China
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Zhang F, Wang Y, Yang F, Zhang Y, Jiang M, Zhang X. The Efficacy and Safety of PD-1 Inhibitors Combined with Nab-Paclitaxel Plus Gemcitabine versus Nab-Paclitaxel Plus Gemcitabine in the First-Line Treatment of Advanced Pancreatic Cancer: A Retrospective Monocentric Study. Cancer Manag Res 2022; 14:535-546. [PMID: 35173487 PMCID: PMC8841313 DOI: 10.2147/cmar.s349442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/22/2022] [Indexed: 12/12/2022] Open
Abstract
Purpose The purpose of this study was to evaluate the efficacy and safety of PD-1 inhibitor combined with nab-paclitaxel plus gemcitabine (AG) chemotherapy versus AG chemotherapy in the first-line treatment of advanced pancreatic cancer. Patients and Methods This study included the application of AG treatment and PD-1 combined with AG treatment with advanced pancreatic ductal adenocarcinoma at the Affiliated Hospital of Qingdao University from September 2018 to July 2020. Clinical information and next-generation sequencing (NGS) reports of patients were collected to compare the effectiveness and adverse events of the two treatments and analyze the risk factors affecting the prognosis of patients. Results There was no difference in PFS between the AG group and the PD-1+AG group (4.9 months vs 5.0 months, P = 0.154), but the difference in OS was statistically significant (9.3 months vs 12.1 months, P < 0.001). Compared with the AG group, the PD-1+AG group reduced the risk of death about 20.0% (HR = 0.203, 95% CI, 0.090−0.459, P < 0.001). In terms of safety, the incidence of hypothyroidism and reactive skin capillary hyperplasia in PD-1 + AG group was higher than that in AG group (P < 0.050) in grade 1–2; grade 3–4 adverse reactions were mainly hematologic AEs and abnormal liver function. The incidence of grade 3–4 adverse reactions in the two groups was 38.7% (95% CI, 20.5–56.9%) and 35.3% (95% CI, 10.0–60.6%), respectively. In addition, PD-1+ AG regimen improved the OS of patients with KRAS and TP53 co-mutations (8.0months vs 10.2 months, P = 0.004). Conclusion PD-1 inhibitors combined with AG chemotherapy have shown good efficacy and safety in the first-line treatment of patients with advanced pancreatic ductal adenocarcinoma. This regimen similarly improved OS in patients with KRAS and TP53 co-mutations.
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Affiliation(s)
- Feng Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People’s Republic of China
| | - Yuyang Wang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People’s Republic of China
| | - Fangfang Yang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People’s Republic of China
| | - Yuming Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People’s Republic of China
| | - Man Jiang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People’s Republic of China
- Correspondence: Man Jiang; Xiaochun Zhang, Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, 59Haier Road, LaoShan District, Qingdao, 266003, People’s Republic of China, Tel/Fax +86053282913271, Email ;
| | - Xiaochun Zhang
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, People’s Republic of China
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Chen J, Zeng Q, Wang W, Hu Q, Bao H. Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes. RSC Adv 2022; 12:1742-1757. [PMID: 35425180 PMCID: PMC8978876 DOI: 10.1039/d1ra07936k] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/19/2022] Open
Abstract
Understanding the molecular mechanism of the GTP-KRAS binding is significant for improving the target roles of KRAS in cancer treatment. In this work, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations were applied to decode the effect of Q61A, Q61H and Q61L on the activity of KRAS. Dynamics analyses based on MR-GaMD trajectory reveal that motion modes and dynamics behavior of the switch domain in KRAS are heavily affected by the three Q61 mutants. Information of free energy landscapes (FELs) shows that Q61A, Q61H and Q61L induce structural disorder of the switch domain and disturb the activity of KRAS. Analysis of the interaction network uncovers that the decrease in the stability of hydrogen bonding interactions (HBIs) of GTP with residues V29 and D30 induced by Q61A, Q61H and Q61L is responsible for the structural disorder of the switch-I and that in the occupancy of the hydrogen bond between GTP and residue G60 leads to the structural disorder of the switch-II. Thus, the high disorder of the switch domain caused by three current Q61 mutants produces a significant effect on binding of KRAS to its effectors. This work is expected to provide useful information for further understanding function and target roles of KRAS in anti-cancer drug development.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Qingkai Zeng
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Wei Wang
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Qingquan Hu
- School of Science, Shandong Jiaotong University Jinan 250357 China
| | - Huayin Bao
- School of Pharmacy, Shandong University of Traditional Chinese Medicine Jinan 250355 China
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14
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Chen J, Zhang S, Wang W, Pang L, Zhang Q, Liu X. Mutation-Induced Impacts on the Switch Transformations of the GDP- and GTP-Bound K-Ras: Insights from Multiple Replica Gaussian Accelerated Molecular Dynamics and Free Energy Analysis. J Chem Inf Model 2021; 61:1954-1969. [PMID: 33739090 DOI: 10.1021/acs.jcim.0c01470] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mutations yield significant effect on the structural flexibility of two switch domains, SW1 and SW2, in K-Ras, which is considered as an important target of anticancer drug design. To unveil a molecular mechanism with regard to mutation-mediated tuning on the activity of K-Ras, multiple replica Gaussian accelerated molecular dynamics (MR-GaMD) simulations followed by analysis of free energy landscapes (FELs) are performed on the GDP- and GTP-bound wild-type (WT), G12V, and D33E K-Ras. The results suggest that G12V and D33E not only evidently change the flexibility of SW1 and SW2 but also greatly affect correlated motions of SW1 and SW2 separately relative to the P-loop and SW1, which exerts a certain tuning on the activity of K-Ras. The information stemming from the analyses of FELs reveals that the conformations of SW1 and SW2 are in high disorders in the GDP- and GTP-associated WT and mutated K-Ras, possibly producing significant effect on binding of guanine nucleotide exchange factors or effectors to K-Ras. The interaction networks of GDP and GTP with K-Ras are identified and the results uncover that the instability in hydrogen-bonding interactions of SW1 with GDP and GTP is mostly responsible for conformational disorder of SW1 and SW2 as well as tunes the activity of oncogenic K-Ras.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Laixue Pang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China
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15
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Li R, Guo C, Li Y, Liang X, Su M. Functional benefit and molecular mechanism of vitamin C against perfluorooctanesulfonate-associated leukemia. CHEMOSPHERE 2021; 263:128242. [PMID: 33297189 DOI: 10.1016/j.chemosphere.2020.128242] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 06/12/2023]
Abstract
Perfluorooctanesulfonate (PFOS) is a persistent pollutant that can induce toxic effects, including leukemia, on blood cells. Vitamin C (VC), a functional nutrient, has been found to possess potent cytoprotective effects. However, there are currently no reports on its ability to treat PFOS-associated leukemia. This study used a molecular networking analysis to reveal the functional action and pharmacological mechanism of VC against PFOS-associated leukemia. The biological informatics findings revealed a total of 17 intersection targets against PFOS-associated leukemia. In addition, seven core-functional targets, including tumor protein p53 (TP53), mitogen-activated protein kinase 1 (MAPK1), estrogen receptor 1 (ESR1), sirtuin 1 (SIRT1), nitric oxide synthase 3 (NOS3), myeloid cell leukemia-1 (MCL1), and telomerase reverse transcriptase (TERT), were screened and identified. Notably, the molecular docking findings indicated that TP53, MAPK1, and ESR1 were potent pharmacological targets of VC against PFOS-associated leukemia. Moreover, the pharmacological functions including biological processes, cell components, and molecular pathways of VC against PFOS-associated leukemia were determined. According to the computational findings, we conclude that VC protects against PFOS-associated leukemia action by suppressing leukemia-associated cell proliferation and tumor growth. The validated genes of TP53, MAPK1, ESR1 may become potential biomarkers for monitoring and treating PFOS-associated leukemia.
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Affiliation(s)
- Rong Li
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
| | - Chao Guo
- Department of Pharmacy, Guigang City People's Hospital, The Eighth Affiliated Hospital of Guangxi Medical University, Guigang, Guangxi, PR China
| | - Yu Li
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
| | - Xiao Liang
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China
| | - Min Su
- Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, China.
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