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Zhang Q, Liu Y, Ren L, Li J, Lin W, Lou L, Wang M, Li C, Jiang Y. Proteomic analysis of DEN and CCl 4-induced hepatocellular carcinoma mouse model. Sci Rep 2024; 14:8013. [PMID: 38580754 PMCID: PMC10997670 DOI: 10.1038/s41598-024-58587-6] [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: 11/26/2023] [Accepted: 04/01/2024] [Indexed: 04/07/2024] Open
Abstract
Hepatocellular carcinoma (HCC) seriously threatens human health, mostly developed from liver fibrosis or cirrhosis. Since diethylnitrosamine (DEN) and carbon tetrachloride (CCl4)-induced HCC mouse model almost recapitulates the characteristic of HCC with fibrosis and inflammation, it is taken as an essential tool to investigate the pathogenesis of HCC. However, a comprehensive understanding of the protein expression profile of this model is little. In this study, we performed proteomic analysis of this model to elucidate its proteomic characteristics. Compared with normal liver tissues, 432 differentially expressed proteins (DEPs) were identified in tumor tissues, among which 365 were up-regulated and 67 were down-regulated. Through Gene Ontology (GO) analysis, Ingenuity Pathway Analysis (IPA), protein-protein interaction networks (PPI) analysis and Gene-set enrichment analysis (GSEA) analysis of DEPs, we identified two distinguishing features of DEN and CCl4-induced HCC mouse model in protein expression, the upregulation of actin cytoskeleton and branched-chain amino acids metabolic reprogramming. In addition, matching DEPs from the mouse model to homologous proteins in the human HCC cohort revealed that the DEN and CCl4-induced HCC mouse model was relatively similar to the subtype of HCC with poor prognosis. Finally, combining clinical information from the HCC cohort, we screened seven proteins with prognostic significance, SMAD2, PTPN1, PCNA, MTHFD1L, MBOAT7, FABP5, and AGRN. Overall, we provided proteomic data of the DEN and CCl4-induced HCC mouse model and highlighted the important proteins and pathways in it, contributing to the rational application of this model in HCC research.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Yuhui Liu
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Liangliang Ren
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Junqing Li
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
- School of Basic Medical Science, Anhui Medical University, Hefei, 230032, China
| | - Weiran Lin
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Lijuan Lou
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Minghan Wang
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Chaoying Li
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China
| | - Ying Jiang
- State Key Laboratory of Medicle Proteomics, Beijing Institute of Lifeomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing, 102206, China.
- School of Basic Medical Science, Anhui Medical University, Hefei, 230032, China.
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2
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Meng Y, Huang K, Shi M, Huo Y, Han L, Liu B, Li Y. Research Advances in the Role of the Tropomyosin Family in Cancer. Int J Mol Sci 2023; 24:13295. [PMID: 37686101 PMCID: PMC10488083 DOI: 10.3390/ijms241713295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Cancer is one of the most difficult diseases for human beings to overcome. Its development is closely related to a variety of factors, and its specific mechanisms have been a hot research topic in the field of scientific research. The tropomyosin family (Tpm) is a group of proteins closely related to the cytoskeleton and actin, and recent studies have shown that they play an important role in various cancers, participating in a variety of biological activities, including cell proliferation, invasion, and migration, and have been used as biomarkers for various cancers. The purpose of this review is to explore the research progress of the Tpm family in tumorigenesis development, focusing on the molecular pathways associated with them and their relevant activities involved in tumors. PubMed and Web of Science databases were searched for relevant studies on the role of Tpms in tumorigenesis and development and the activities of Tpms involved in tumors. Data from the literature suggest that the Tpm family is involved in tumor cell proliferation and growth, tumor cell invasion and migration, tumor angiogenesis, tumor cell apoptosis, and immune infiltration of the tumor microenvironment, among other correlations. It can be used as a potential biomarker for early diagnosis, follow-up, and therapeutic response of some tumors. The Tpm family is involved in cancer in a close relationship with miRNAs and LncRNAs. Tpms are involved in tumor tissue invasion and migration as a key link. On this basis, TPM is frequently used as a biomarker for various cancers. However, the specific molecular mechanism of its involvement in cancer progression has not been explained clearly, which remains an important direction for future research.
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Affiliation(s)
- Yucheng Meng
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (Y.M.); (K.H.); (M.S.); (Y.H.); (L.H.)
| | - Ke Huang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (Y.M.); (K.H.); (M.S.); (Y.H.); (L.H.)
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730030, China
| | - Mingxuan Shi
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (Y.M.); (K.H.); (M.S.); (Y.H.); (L.H.)
| | - Yifei Huo
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (Y.M.); (K.H.); (M.S.); (Y.H.); (L.H.)
| | - Liang Han
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (Y.M.); (K.H.); (M.S.); (Y.H.); (L.H.)
| | - Bin Liu
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (Y.M.); (K.H.); (M.S.); (Y.H.); (L.H.)
| | - Yi Li
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (Y.M.); (K.H.); (M.S.); (Y.H.); (L.H.)
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3
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Carraro C, Bonaguro L, Schulte-Schrepping J, Horne A, Oestreich M, Warnat-Herresthal S, Helbing T, De Franco M, Haendler K, Mukherjee S, Ulas T, Gandin V, Goettlich R, Aschenbrenner AC, Schultze JL, Gatto B. Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state. eLife 2022; 11:e78012. [PMID: 36043458 PMCID: PMC9433094 DOI: 10.7554/elife.78012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development of 3-chloropiperidines, a new class of candidate anticancer agents. Combined analyses of transcriptome and chromatin accessibility elucidated the mechanisms underlying sensitivity to test agents. Furthermore, we implemented a new versatile strategy for the integration of RNA- and ATAC-seq (Assay for Transposase-Accessible Chromatin) data, able to accelerate and extend the standalone analyses of distinct omic layers. This platform guided the construction of a perturbation-informed basal signature predicting cancer cell lines' sensitivity and to further direct compound development against specific tumor types. Overall, this approach offers a scalable pipeline to support the early phases of drug discovery, understanding of mechanisms, and potentially inform the positioning of therapeutics in the clinic.
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Affiliation(s)
- Caterina Carraro
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Arik Horne
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Marie Oestreich
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
| | - Stefanie Warnat-Herresthal
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
| | - Tim Helbing
- Institute of Organic Chemistry, Justus Liebig University GiessenGiessenGermany
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Kristian Haendler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
- Institute of Human Genetics, University of LübeckLübeckGermany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- MRC Biostatistics Unit, University of CambridgeCambridgeUnited Kingdom
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
| | - Valentina Gandin
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
| | - Richard Goettlich
- Institute of Organic Chemistry, Justus Liebig University GiessenGiessenGermany
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical CenterNijmegenNetherlands
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V.BonnGermany
- Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of BonnBonnGermany
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of BonnBonnGermany
| | - Barbara Gatto
- Department of Pharmaceutical and Pharmacological Sciences, University of PadovaPadovaItaly
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Khalil K, Eon A, Janody F. Cell Architecture-Dependent Constraints: Critical Safeguards to Carcinogenesis. Int J Mol Sci 2022; 23:8622. [PMID: 35955754 PMCID: PMC9369145 DOI: 10.3390/ijms23158622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Animal cells display great diversity in their shape. These morphological characteristics result from crosstalk between the plasma membrane and the force-generating capacities of the cytoskeleton macromolecules. Changes in cell shape are not merely byproducts of cell fate determinants, they also actively drive cell fate decisions, including proliferation and differentiation. Global and local changes in cell shape alter the transcriptional program by a multitude of mechanisms, including the regulation of physical links between the plasma membrane and the nuclear envelope and the mechanical modulation of cation channels and signalling molecules. It is therefore not surprising that anomalies in cell shape contribute to several diseases, including cancer. In this review, we discuss the possibility that the constraints imposed by cell shape determine the behaviour of normal and pro-tumour cells by organizing the whole interconnected regulatory network. In turn, cell behaviour might stabilize cells into discrete shapes. However, to progress towards a fully transformed phenotype and to acquire plasticity properties, pro-tumour cells might need to escape these cell shape restrictions. Thus, robust controls of the cell shape machinery may represent a critical safeguard against carcinogenesis.
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Affiliation(s)
- Komal Khalil
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Master Programme in Oncology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Alice Eon
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
- Magistère Européen de Génétique, Université Paris Cité, 5 Rue Thomas Mann, 75013 Paris, France
| | - Florence Janody
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal; (K.K.); (A.E.)
- IPATIMUP—Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
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5
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Gill MR, Jarman PJ, Hearnden V, Fairbanks SD, Bassetto M, Maib H, Palmer J, Ayscough KR, Thomas JA, Smythe C. A Ruthenium(II) Polypyridyl Complex Disrupts Actin Cytoskeleton Assembly and Blocks Cytokinesis. Angew Chem Int Ed Engl 2022; 61:e202117449. [PMID: 35416386 PMCID: PMC9323417 DOI: 10.1002/anie.202117449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/05/2022]
Abstract
The dinuclear RuII complex [(Ru(phen)2)2(tpphz)]4+ (phen=1,10‐phenanthroline, tpphz=tetrapyridophenazine) “RuRuPhen” blocks the transformation of G‐actin monomers to F‐actin filaments with no disassembly of pre‐formed F‐actin. Molecular docking studies indicate multiple RuRuPhen molecules bind to the surface of G‐actin but not the binding pockets of established actin polymerisation inhibitors. In cells, addition of RuRuPhen causes rapid disruption to actin stress fibre organisation, compromising actomyosin contractility and cell motility; due to this effect RuRuPhen interferes with late‐stage cytokinesis. Immunofluorescent microscopy reveals that RuRuPhen causes cytokinetic abscission failure by interfering with endosomal sorting complexes required for transport (ESCRT) complex recruitment.
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Affiliation(s)
- Martin R. Gill
- Department of Chemistry Faculty of Science and Engineering Swansea University UK
| | - Paul J. Jarman
- Department of Biomedical Science University of Sheffield UK
| | - Vanessa Hearnden
- Department of Materials Science and Engineering University of Sheffield UK
| | | | - Marcella Bassetto
- Department of Chemistry Faculty of Science and Engineering Swansea University UK
| | - Hannes Maib
- Department of Biomedical Science University of Sheffield UK
| | - John Palmer
- Department of Biomedical Science University of Sheffield UK
| | | | | | - Carl Smythe
- Department of Biomedical Science University of Sheffield UK
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6
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Gill MR, Jarman PJ, Hearnden V, Fairbanks SD, Bassetto M, Maib H, Palmer J, Ayscough KR, Thomas JA, Smythe C. A Ruthenium(II) Polypyridyl Complex Disrupts Actin Cytoskeleton Assembly and Blocks Cytokinesis. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202117449. [PMID: 38505667 PMCID: PMC10947085 DOI: 10.1002/ange.202117449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Indexed: 11/10/2022]
Abstract
The dinuclear RuII complex [(Ru(phen)2)2(tpphz)]4+ (phen=1,10-phenanthroline, tpphz=tetrapyridophenazine) "RuRuPhen" blocks the transformation of G-actin monomers to F-actin filaments with no disassembly of pre-formed F-actin. Molecular docking studies indicate multiple RuRuPhen molecules bind to the surface of G-actin but not the binding pockets of established actin polymerisation inhibitors. In cells, addition of RuRuPhen causes rapid disruption to actin stress fibre organisation, compromising actomyosin contractility and cell motility; due to this effect RuRuPhen interferes with late-stage cytokinesis. Immunofluorescent microscopy reveals that RuRuPhen causes cytokinetic abscission failure by interfering with endosomal sorting complexes required for transport (ESCRT) complex recruitment.
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Affiliation(s)
- Martin R. Gill
- Department of ChemistryFaculty of Science and EngineeringSwansea UniversityUK
| | - Paul J. Jarman
- Department of Biomedical ScienceUniversity of SheffieldUK
| | - Vanessa Hearnden
- Department of Materials Science and EngineeringUniversity of SheffieldUK
| | | | - Marcella Bassetto
- Department of ChemistryFaculty of Science and EngineeringSwansea UniversityUK
| | - Hannes Maib
- Department of Biomedical ScienceUniversity of SheffieldUK
| | - John Palmer
- Department of Biomedical ScienceUniversity of SheffieldUK
| | | | | | - Carl Smythe
- Department of Biomedical ScienceUniversity of SheffieldUK
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7
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Chakraborty S, Nandy A, Ghosh S, Das NK, Parveen S, Datta S, Mukherjee S. Protein-templated gold nanoclusters as specific bio-imaging probes for the detection of Hg(ii) ions in in vivo and in vitro systems: discriminating between MDA-MB-231 and MCF10A cells. Analyst 2021; 146:1455-1463. [DOI: 10.1039/d0an02108c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sub-nanomolar selective detection of Hg(ii) ions by protein (Human Serum Albumin, HSA) templated gold nanoclusters (AuNCs), both in in vitro as well as in vivo environments and specific endocytose behaviour towards breast cancer (BC) cell lines.
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Affiliation(s)
- Subhajit Chakraborty
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462 066
- India
| | - Atanu Nandy
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462 066
- India
| | - Subhadip Ghosh
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462 066
- India
| | - Nirmal Kumar Das
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462 066
- India
| | - Sameena Parveen
- Department of Biological Sciences
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462 066
- India
| | - Sunando Datta
- Department of Biological Sciences
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462 066
- India
| | - Saptarshi Mukherjee
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462 066
- India
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