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Zhu G, Wang L, Wang X, Dong X, Yang S, Wang J, Xu S, Zeng Y. Comparative Proteomics Identified EXOSC1 as a Target Protein of Anticancer Peptide LVTX-8 in Nasopharyngeal Carcinoma Cells. J Proteome Res 2024. [PMID: 38700954 DOI: 10.1021/acs.jproteome.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Nasopharyngeal carcinoma (NPC) is a prevalent malignancy that usually occurs among the nose and throat. Due to mild initial symptoms, most patients are diagnosed in the late stage, and the recurrence rate of tumors is high, resulting in many deaths every year. Traditional radiotherapy and chemotherapy are prone to causing drug resistance and significant side effects. Therefore, searching for new bioactive drugs including anticancer peptides is necessary and urgent. LVTX-8 is a peptide toxin synthesized from the cDNA library of the spider Lycosa vittata, which is consisting of 25 amino acids. In this study, a series of in vitro cell experiments such as cell toxicity, colony formation, and cell migration assays were performed to exam the anticancer activity of LVTX-8 in NPC cells (5-8F and CNE-2). The results suggested that LVTX-8 significantly inhibited cell proliferation and migration of NPC cells. To find the potential molecular targets for the anticancer capability of LVTX-8, high-throughput proteomic and bioinformatics analysis were conducted on NPC cells. The results identified EXOSC1 as a potential target protein with significantly differential expression levels under LVTX-8+/LVTX-8- conditions. The results in this research indicate that spider peptide toxin LVTX-8 exhibits significant anticancer activity in NPC, and EXOSC1 may serve as a target protein for its anticancer activity. These findings provide a reference for the development of new therapeutic drugs for NPC and offer new ideas for the discovery of biomarkers related to NPC diagnosis. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (https://proteomecentral.proteomexchange.org) via the iProX partner repository with the data set identifier PXD050542.
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Affiliation(s)
- Ganghua Zhu
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Lingxiang Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xingyao Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xiaoping Dong
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Shu Yang
- Department of Otolaryngology-Head and Neck Surgery, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Jiaqi Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Siyuan Xu
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
| | - Yong Zeng
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
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Zhu M, Zhu Z, Zhang N, Ma J, Huang N, He S, Lu X. Identification of miRNA, lncRNA and circRNA associated with gastric cancer metabolism through sequencing and bioinformatics analysis. Pathol Res Pract 2024; 254:155151. [PMID: 38290402 DOI: 10.1016/j.prp.2024.155151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/09/2023] [Accepted: 01/17/2024] [Indexed: 02/01/2024]
Abstract
Gastric cancer remains a highly prevalent malignancy worldwide with its molecular features poorly understood. To gain full insight into its genetic landscape, we performed whole-transcriptome sequencing on human tumors and adjacent non-tumors to predict the function of microRNA, long coding RNA, circular RNA, and mRNA, as well as estimate their correlation with gastric cancer characteristics through construction of ceRNA, WGCNA and PPI network. Functional enrichment analysis annotated nucleic acid binding, enzyme activity and binding related to differentially expressed miRNAs (dif-miRNAs); energy binding and enzyme binding related to dif-lncRNAs; protein binding and enzyme activity related to dif-circRNAs; protein digestion and absorption related to dif-mRNAs. The expression of key miR-135a-5p, lncRNAs-MSTRG.48856.1, ENST00000569981, MSTRG.22826.1, ENST00000564492, circRNAs-CCSER2, FNDC3B, CORO1C, FAM214A were validated by real-time PCR. The ceRNA network filtered 14 miRNAs, 30 lncRNAs, and 6 mRNA in the lncRNA-ceRNA axis and 8 miRNAs, 9 circRNAs, and 3 mRNA in the circRNA-ceRNA axis. Genes involved in ceRNA were annotated to be closely related to tumor material synthesis and metabolism. The WGCNA network filtered gene clusters related to TNM traits and extracted the hub genes CLDN10, CD177, newGene_35523, newGene_51201, CEACAM7, and newGene_46634. These genes were associated with cell proliferation, metabolism, and enzyme activity regulation. The PPI network analyzed the stable interaction relationships of the hub genes. Our research provides a valuable resource for understanding the molecular mechanisms of gastric cancer from the perspective of tumor metabolism.
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Affiliation(s)
- Meng Zhu
- College of Basic Medicine, Ningxia Medical University, 1160 Shengli Street, Yinchuan, Ningxia 750004, China
| | - Zenghui Zhu
- College of Basic Medicine, Ningxia Medical University, 1160 Shengli Street, Yinchuan, Ningxia 750004, China
| | - Ning Zhang
- Department of Pathology, General Hospital of Ningxia Medical University, 804 Shengli Street, Yinchuan, Ningxia 750004, China.
| | - Jingwei Ma
- The Second Department of Surgical Oncology, General Hospital of Ningxia Medical University, 804 Shengli Street, Yinchuan, Ningxia 750004, China
| | - Ningbo Huang
- College of Basic Medicine, Ningxia Medical University, 1160 Shengli Street, Yinchuan, Ningxia 750004, China
| | - Shuixiang He
- Department of Gastroenterology, First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi 710061, China
| | - Xinlan Lu
- Department of Gastroenterology, First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, Shaanxi 710061, China.
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Lee JH, Choi JH, Lee KM, Lee MW, Ku JL, Oh DC, Shin YH, Kim DH, Cho IR, Paik WH, Ryu JK, Kim YT, Lee SH, Lee SK. Antiproliferative Activity of Piceamycin by Regulating Alpha-Actinin-4 in Gemcitabine-Resistant Pancreatic Cancer Cells. Biomol Ther (Seoul) 2024; 32:123-135. [PMID: 38148558 PMCID: PMC10762279 DOI: 10.4062/biomolther.2023.109] [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: 06/07/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 12/28/2023] Open
Abstract
Although gemcitabine-based regimens are widely used as an effective treatment for pancreatic cancer, acquired resistance to gemcitabine has become an increasingly common problem. Therefore, a novel therapeutic strategy to treat gemcitabine-resistant pancreatic cancer is urgently required. Piceamycin has been reported to exhibit antiproliferative activity against various cancer cells; however, its underlying molecular mechanism for anticancer activity in pancreatic cancer cells remains unexplored. Therefore, the present study evaluated the antiproliferation activity of piceamycin in a gemcitabine-resistant pancreatic cancer cell line and patient-derived pancreatic cancer organoids. Piceamycin effectively inhibited the proliferation and suppressed the expression of alpha-actinin-4, a gene that plays a pivotal role in tumorigenesis and metastasis of various cancers, in gemcitabine-resistant cells. Long-term exposure to piceamycin induced cell cycle arrest at the G0/G1 phase and caused apoptosis. Piceamycin also inhibited the invasion and migration of gemcitabine-resistant cells by modulating focal adhesion and epithelial-mesenchymal transition biomarkers. Moreover, the combination of piceamycin and gemcitabine exhibited a synergistic antiproliferative activity in gemcitabine-resistant cells. Piceamycin also effectively inhibited patient-derived pancreatic cancer organoid growth and induced apoptosis in the organoids. Taken together, these findings demonstrate that piceamycin may be an effective agent for overcoming gemcitabine resistance in pancreatic cancer.
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Affiliation(s)
- Jee-Hyung Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin Ho Choi
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Kyung-Min Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Min Woo Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Ja-Lok Ku
- Department of Biomedical Sciences, Korean Cell Line Bank, Laboratory of Cell Biology and Cancer Research Institute, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yern-Hyerk Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Dae Hyun Kim
- Dxome Co. Ltd., Seongnam 13558, Republic of Korea
| | - In Rae Cho
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Woo Hyun Paik
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Ji Kon Ryu
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Yong-Tae Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Sang Hyub Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University Hospital, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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Ram Soren K, Tripathi S, Hembram M, Kumar N, Konda K A, Gupta NC, Bharadwaj C, Prasad Dixit G. Network interactions with functional roles and evolutionary relationships for BURP domain-containing proteins in chickpea and model species. Bioinformation 2023; 19:1197-1211. [PMID: 38250539 PMCID: PMC10794749 DOI: 10.6026/973206300191197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
The functional significance and evolutionary relationships of BURP domain-containing genes unique to plants is of interest. Network analysis reveals different associations of BURP proteins with other proteins and functional terms, throwing light on their involvement in various biological processes and pathways. The gene expression data reveals that BURP genes are affected by salinity stress, reflecting diverse expression patterns in roots and shoots.
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Affiliation(s)
| | | | | | - Neeraj Kumar
- ICAR-Division of genetics, IARI, New Delhi, India
| | | | - NC Gupta
- National Institute of Plant Biotechnology, New Delhi, India
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Fernando PC, Mabee PM, Zeng E. Protein-protein interaction network module changes associated with the vertebrate fin-to-limb transition. Sci Rep 2023; 13:22594. [PMID: 38114646 PMCID: PMC10730527 DOI: 10.1038/s41598-023-50050-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Evolutionary phenotypic transitions, such as the fin-to-limb transition in vertebrates, result from modifications in related proteins and their interactions, often in response to changing environment. Identifying these alterations in protein networks is crucial for a more comprehensive understanding of these transitions. However, previous research has not attempted to compare protein-protein interaction (PPI) networks associated with evolutionary transitions, and most experimental studies concentrate on a limited set of proteins. Therefore, the goal of this work was to develop a network-based platform for investigating the fin-to-limb transition using PPI networks. Quality-enhanced protein networks, constructed by integrating PPI networks with anatomy ontology data, were leveraged to compare protein modules for paired fins (pectoral fin and pelvic fin) of fishes (zebrafish) to those of the paired limbs (forelimb and hindlimb) of mammals (mouse). This also included prediction of novel protein candidates and their validation by enrichment and homology analyses. Hub proteins such as shh and bmp4, which are crucial for module stability, were identified, and their changing roles throughout the transition were examined. Proteins with preserved roles during the fin-to-limb transition were more likely to be hub proteins. This study also addressed hypotheses regarding the role of non-preserved proteins associated with the transition.
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Affiliation(s)
- Pasan C Fernando
- Department of Plant Sciences, University of Colombo, Colombo, Sri Lanka.
| | - Paula M Mabee
- Department of Biology, University of South Dakota, Vermillion, SD, USA
- National Ecological Observatory Network, Battelle, 1625 38th St. #100, Boulder, CO, 80301, USA
| | - Erliang Zeng
- Departments of Preventive & Community Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA.
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA.
- Departments of Biostatistics, College of Public Health, University of Iowa, Iowa City, IA, USA.
- Departments of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, USA.
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