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Suleman M, Khattak A, Akbar F, Rizwan M, Tayyab M, Yousaf M, Khan A, Albekairi NA, Agouni A, Crovella S. Analysis of E2F1 single-nucleotide polymorphisms reveals deleterious non-synonymous substitutions that disrupt E2F1-RB protein interaction in cancer. Int J Biol Macromol 2024; 260:129559. [PMID: 38242392 DOI: 10.1016/j.ijbiomac.2024.129559] [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: 05/13/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Cancer is a medical condition that is caused by the abnormal growth and division of cells, leading to the formation of tumors. The E2F1 and RB pathways are critical in regulating cell cycle, and their dysregulation can contribute to the development of cancer. In this study, we analyzed experimentally reported SNPs in E2F1 and assessed their effects on the binding affinity with RB. Out of 46, nine mutations were predicted as deleterious, and further analysis revealed four highly destabilizing mutations (L206W, R232C, I254T, A267T) that significantly altered the protein structure. Molecular docking of wild-type and mutant E2F1 with RB revealed a docking score of -242 kcal/mol for wild-type, while the mutant complexes had scores ranging from -217 to -220 kcal/mol. Molecular simulation analysis revealed variations in the dynamics features of both mutant and wild-type complexes due to the acquired mutations. Furthermore, the total binding free energy for the wild-type E2F1-RB complex was -64.89 kcal/mol, while those of the L206W, R232C, I254T, and A267T E2F1-RB mutants were -45.90 kcal/mol, -53.52 kcal/mol, -55.67 kcal/mol, and -61.22 kcal/mol, respectively. Our study is the first to extensively analyze E2F1 gene mutations and identifies candidate mutations for further validation and potential targeting for cancer therapeutics.
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Affiliation(s)
- Muhammad Suleman
- Laboratory of Animal Research Center (LARC) Qatar University, Doha, Qatar; Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Aishma Khattak
- Department of Bioinformatics, Shaheed Benazir butto women university Peshawar, Pakistan
| | - Fazal Akbar
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Muhammad Rizwan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Muhammad Tayyab
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar.
| | - Muhammad Yousaf
- Centre for Animal Sciences and Fisheries, University of Swat, Swat, Pakistan.
| | - Abbas Khan
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh 11451, Saudi Arabia.
| | - Abdelali Agouni
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar.
| | - Sergio Crovella
- Laboratory of Animal Research Center (LARC) Qatar University, Doha, Qatar.
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2
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Ahsan T, Shoily SS, Ahmed T, Sajib AA. Role of the redox state of the Pirin-bound cofactor on interaction with the master regulators of inflammation and other pathways. PLoS One 2023; 18:e0289158. [PMID: 38033031 PMCID: PMC10688961 DOI: 10.1371/journal.pone.0289158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/10/2023] [Indexed: 12/02/2023] Open
Abstract
Persistent cellular stress induced perpetuation and uncontrolled amplification of inflammatory response results in a shift from tissue repair toward collateral damage, significant alterations of tissue functions, and derangements of homeostasis which in turn can lead to a large number of acute and chronic pathological conditions, such as chronic heart failure, atherosclerosis, myocardial infarction, neurodegenerative diseases, diabetes, rheumatoid arthritis, and cancer. Keeping the vital role of balanced inflammation in maintaining tissue integrity in mind, the way to combating inflammatory diseases may be through identification and characterization of mediators of inflammation that can be targeted without hampering normal body function. Pirin (PIR) is a non-heme iron containing protein having two different conformations depending on the oxidation state of the iron. Through exploration of the Pirin interactome and using molecular docking approaches, we identified that the Fe2+-bound Pirin directly interacts with BCL3, NFKBIA, NFIX and SMAD9 with more resemblance to the native binding pose and higher affinity than the Fe3+-bound form. In addition, Pirin appears to have a function in the regulation of inflammation, the transition between the canonical and non-canonical NF-κB pathways, and the remodeling of the actin cytoskeleton. Moreover, Pirin signaling appears to have a critical role in tumor invasion and metastasis, as well as metabolic and neuro-pathological complications. There are regulatory variants in PIR that can influence expression of not only PIR but also other genes, including VEGFD and ACE2. Disparity exists between South Asian and European populations in the frequencies of variant alleles at some of these regulatory loci that may lead to differential occurrence of Pirin-mediated pathogenic conditions.
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Affiliation(s)
- Tamim Ahsan
- Molecular Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, Bangladesh
| | - Sabrina Samad Shoily
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Tasnim Ahmed
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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3
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Zhou Q, Wang J, Zhang H, Sun L, Liu J, Meng L, Li J. Tumor-derived exosomes RNA expression profiling identifies the prognosis, immune characteristics, and treatment in HR+/HER2-breast cancer. Aging (Albany NY) 2023; 15:8471-8486. [PMID: 37647033 PMCID: PMC10497011 DOI: 10.18632/aging.204986] [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: 02/27/2023] [Accepted: 07/15/2023] [Indexed: 09/01/2023]
Abstract
Exosomes play crucial roles in intercellular communication and are involved in the onset and progression of various types of cancers, including breast cancer. However, the RNA composition of breast cancer-derived exosomes has not been comprehensively explored. We conducted microarray assays on exosomes isolated from breast cancer and healthy breast epithelial cells from three patients with hormone receptor (HR) +/ human epidermal growth factor receptor (HER2) - breast cancer and identified 817 differentially expressed genes (DEGs). Among these, 315 upregulated tumor-derived exosome genes (UTEGs) were used to classify HR+/HER2- breast cancers into two categories, revealing a difference in survival rates between the groups. We developed and validated a novel prognostic exosome score (ES) model consisting of four UTEGs that provides a refined prognosis prediction in HR+/HER2-breast cancer. ES reflects various immune-related features, including somatic variation, immunogenicity, and tumor immune infiltrate composition. Our findings indicate a considerable positive correlation between the ES and drug sensitivity values for vincristine, paclitaxel, and docetaxel. However, ES was remarkably higher in the endocrine therapy non-responder group than in the responder group. Immunohistochemistry confirmed the remarkable expression of the four model genes in tumor tissues, and their expression in MCF-7 cell exosomes was higher than that in MCF10A cells, as verified via qPCR. In summary, tumor-derived exosome genes provide novel insights into the subtyping, prognosis, and treatment of HR+/HER2-breast cancer.
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Affiliation(s)
- Qi Zhou
- Department of Breast Surgery, People’s Hospital of Tangshan, Tangshan 063001, Hebei, China
| | - Jing Wang
- Department of Breast Center, People’s Hospital of Tangshan, Tangshan 063001, Hebei, China
| | - Haiping Zhang
- Department of Breast Surgery, People’s Hospital of Tangshan, Tangshan 063001, Hebei, China
| | - Lu Sun
- Department of Oncology, Tangshan People’s Hospital, Tangshan 063001, Hebei, China
| | - Jingjing Liu
- Department of Oncology, Tangshan People’s Hospital, Tangshan 063001, Hebei, China
| | - Lingchao Meng
- Department of Pathology, Tangshan People’s Hospital, Tangshan 063001, Hebei, China
| | - Jingwu Li
- The Cancer Institute, Tangshan People’s Hospital, Tangshan 063001, Hebei, China
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4
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Penas C, Arroyo-Berdugo Y, Apraiz A, Rasero J, Muñoa-Hoyos I, Andollo N, Cancho-Galán G, Izu R, Gardeazabal J, Ezkurra PA, Subiran N, Alvarez-Dominguez C, Alonso S, Bosserhoff AK, Asumendi A, Boyano MD. Pirin is a prognostic marker of human melanoma that dampens the proliferation of malignant cells by downregulating JARID1B/KDM5B expression. Sci Rep 2023; 13:9561. [PMID: 37308689 DOI: 10.1038/s41598-023-36684-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/08/2023] [Indexed: 06/14/2023] Open
Abstract
Originally considered to act as a transcriptional co-factor, Pirin has recently been reported to play a role in tumorigenesis and the malignant progression of many tumors. Here, we have analyzed the diagnostic and prognostic value of Pirin expression in the early stages of melanoma, and its role in the biology of melanocytic cells. Pirin expression was analyzed in a total of 314 melanoma biopsies, correlating this feature with the patient's clinical course. Moreover, PIR downregulated primary melanocytes were analyzed by RNA sequencing, and the data obtained were validated in human melanoma cell lines overexpressing PIR by functional assays. The immunohistochemistry multivariate analysis revealed that early melanomas with stronger Pirin expression were more than twice as likely to develop metastases during the follow-up. Transcriptome analysis of PIR downregulated melanocytes showed a dampening of genes involved in the G1/S transition, cell proliferation, and cell migration. In addition, an in silico approach predicted that JARID1B as a potential transcriptional regulator that lies between PIR and its downstream modulated genes, which was corroborated by co-transfection experiments and functional analysis. Together, the data obtained indicated that Pirin could be a useful marker for the metastatic progression of melanoma and that it participates in the proliferation of melanoma cells by regulating the slow-cycling JARID1B gene.
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Affiliation(s)
- Cristina Penas
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain
| | - Yoana Arroyo-Berdugo
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain
| | - Aintzane Apraiz
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain
| | - Javier Rasero
- Department of Psychology, Carnegie Mellon University, Pittsburg, PA, 15213, USA
| | - Iraia Muñoa-Hoyos
- Department of Physiology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain
| | - Noelia Andollo
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain
| | | | - Rosa Izu
- Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain
- Department of Dermatology, Basurto University Hospital, 48013, Bilbo, Spain
| | - Jesús Gardeazabal
- Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain
- Department of Dermatology, Cruces University Hospital, 48903, Barakaldo, Spain
| | - Pilar A Ezkurra
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain
| | - Nerea Subiran
- Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain
- Department of Physiology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain
| | - Carmen Alvarez-Dominguez
- MEDONLINE Multidisciplinary Research Group, Faculty of Health Sciences and Faculty of Education, International University of La Rioja, 26006, Logroño, Spain
| | - Santos Alonso
- Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, UPV/EHU, 48940, Leioa, Spain
| | - Anja K Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander University of Erlangen-Nürnberg, 91054, Erlangen, Germany
- Comprehensive Cancer Center (CCC) Erlangen-EMN, 91054, Erlangen, Germany
| | - Aintzane Asumendi
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain
- Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain
| | - María D Boyano
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, UPV/EHU, 48940, Leioa, Spain.
- Biocruces Bizkaia Health Research Institute, 48903, Barakaldo, Spain.
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5
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Dual-RNAseq Analysis Unravels Virus-Host Interactions of MetSV and Methanosarcina mazei. Viruses 2022; 14:v14112585. [PMID: 36423194 PMCID: PMC9694453 DOI: 10.3390/v14112585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/05/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Methanosarcina spherical virus (MetSV), infecting Methanosarcina species, encodes 22 genes, but their role in the infection process in combination with host genes has remained unknown. To study the infection process in detail, infected and uninfected M. mazei cultures were compared using dual-RNAseq, qRT-PCRs, and transmission electron microscopy (TEM). The transcriptome analysis strongly indicates a combined role of virus and host genes in replication, virus assembly, and lysis. Thereby, 285 host and virus genes were significantly regulated. Within these 285 regulated genes, a network of the viral polymerase, MetSVORF6, MetSVORF5, MetSVORF2, and the host genes encoding NrdD, NrdG, a CDC48 family protein, and a SSB protein with a role in viral replication was postulated. Ultrastructural analysis at 180 min p.i. revealed many infected cells with virus particles randomly scattered throughout the cytoplasm or attached at the cell surface, and membrane fragments indicating cell lysis. Dual-RNAseq and qRT-PCR analyses suggested a multifactorial lysis reaction in potential connection to the regulation of a cysteine proteinase, a pirin-like protein and a HicB-solo protein. Our study's results led to the first preliminary infection model of MetSV infecting M. mazei, summarizing the key infection steps as follows: replication, assembly, and host cell lysis.
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Azam H, Pierro L, Reina M, Gallagher WM, Prencipe M. Emerging role for the Serum Response Factor (SRF) as a potential therapeutic target in cancer. Expert Opin Ther Targets 2022; 26:155-169. [PMID: 35114091 DOI: 10.1080/14728222.2022.2032652] [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: 11/04/2022]
Abstract
INTRODUCTION The Serum Response Factor (SRF) is a transcription factor involved in three hallmarks of cancer: the promotion of cell proliferation, cell death resistance and invasion and metastasis induction. Many studies have demonstrated a leading role in the development and progression of multiple cancer types, thus highlighting the potential of SRF as a prognostic biomarker and therapeutic target, especially for cancers with poor prognosis. AREAS COVERED This review examines the role of SRF in several cancers in promoting cellular processes associated with cancer development and progression. SRF co-factors and signalling pathways are discussed as possible targets to inhibit SRF in a tissue and cancer-specific way. Small-molecule inhibitors of SRF, such as the CCGs series of compounds and lestaurtinib, which could be used as cancer therapeutics, are also discussed. EXPERT OPINION Targeting of SRF and its co-factors represents a promising therapeutic approach. Further understanding of the molecular mechanisms behind the action of SRF could provide a pipeline of novel molecular targets and therapeutic combinations for cancer. Basket clinical trials and the use of SRF immunohistochemistry as companion diagnostics will help testing of these new targets in patients.
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Affiliation(s)
- Haleema Azam
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute, University College Dublin, Belfield, D4, Dublin, Ireland.,UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, D4, Dublin, Ireland
| | - Lisa Pierro
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute, University College Dublin, Belfield, D4, Dublin, Ireland.,UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, D4, Dublin, Ireland
| | - Martina Reina
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute, University College Dublin, Belfield, D4, Dublin, Ireland.,UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, D4, Dublin, Ireland
| | - William M Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute, University College Dublin, Belfield, D4, Dublin, Ireland.,UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, D4, Dublin, Ireland
| | - Maria Prencipe
- Cancer Biology and Therapeutics Laboratory, UCD Conway Institute, University College Dublin, Belfield, D4, Dublin, Ireland.,UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, D4, Dublin, Ireland
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7
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Zhang Y, Knatko EV, Higgins M, Dayalan Naidu S, Smith G, Honda T, de la Vega L, Dinkova-Kostova AT. Pirin, an Nrf2-Regulated Protein, Is Overexpressed in Human Colorectal Tumors. Antioxidants (Basel) 2022; 11:262. [PMID: 35204145 PMCID: PMC8868368 DOI: 10.3390/antiox11020262] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022] Open
Abstract
The evolutionary conserved non-heme Fe-containing protein pirin has been implicated as an important factor in cell proliferation, migration, invasion, and tumour progression of melanoma, breast, lung, cervical, prostate, and oral cancers. Here we found that pirin is overexpressed in human colorectal cancer in comparison with matched normal tissue. The overexpression of pirin correlates with activation of transcription factor nuclear factor erythroid 2 p45-related factor 2 (Nrf2) and increased expression of the classical Nrf2 target NAD(P)H:quinone oxidoreductase 1 (NQO1), but interestingly and unexpectedly, not with expression of the aldo-keto reductase (AKR) family members AKR1B10 and AKR1C1, which are considered to be the most overexpressed genes in response to Nrf2 activation in humans. Using pharmacologic and genetic approaches to either downregulate or upregulate Nrf2, we show that pirin is regulated by Nrf2 in human and mouse cells and in the mouse colon in vivo. The small molecule pirin inhibitor TPhA decreased the viability of human colorectal cancer (DLD1) cells, but this decrease was independent of the levels of pirin. Our study demonstrates the Nrf2-dependent regulation of pirin and encourages the pursuit for specific pirin inhibitors.
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Affiliation(s)
- Ying Zhang
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; (Y.Z.); (E.V.K.); (M.H.); (S.D.N.); (G.S.); (L.d.l.V.)
| | - Elena V. Knatko
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; (Y.Z.); (E.V.K.); (M.H.); (S.D.N.); (G.S.); (L.d.l.V.)
| | - Maureen Higgins
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; (Y.Z.); (E.V.K.); (M.H.); (S.D.N.); (G.S.); (L.d.l.V.)
| | - Sharadha Dayalan Naidu
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; (Y.Z.); (E.V.K.); (M.H.); (S.D.N.); (G.S.); (L.d.l.V.)
| | - Gillian Smith
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; (Y.Z.); (E.V.K.); (M.H.); (S.D.N.); (G.S.); (L.d.l.V.)
| | - Tadashi Honda
- Department of Chemistry, Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, NY 11794, USA;
| | - Laureano de la Vega
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; (Y.Z.); (E.V.K.); (M.H.); (S.D.N.); (G.S.); (L.d.l.V.)
| | - Albena T. Dinkova-Kostova
- Jacqui Wood Cancer Centre, Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK; (Y.Z.); (E.V.K.); (M.H.); (S.D.N.); (G.S.); (L.d.l.V.)
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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8
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Luo D, Zhao D, Zhang M, Hu C, Li H, Zhang S, Chen X, Huttad L, Li B, Jin C, Lin C, Han B. Alternative Splicing-Based Differences Between Hepatocellular Carcinoma and Intrahepatic Cholangiocarcinoma: Genes, Immune Microenvironment, and Survival Prognosis. Front Oncol 2021; 11:731993. [PMID: 34760694 PMCID: PMC8574058 DOI: 10.3389/fonc.2021.731993] [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: 06/28/2021] [Accepted: 09/29/2021] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing (AS) event is a novel biomarker of tumor tumorigenesis and progression. However, the comprehensive analysis of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) is lacking. Differentially expressed analysis was used to identify the differentially expressed alternative splicing (DEAS) events between HCC or ICC tissues and their normal tissues. The correlation between DEAS events and functional analyses or immune features was evaluated. The cluster analysis based on DEAS can accurately reflect the differences in the immune microenvironment between HCC and ICC. Forty-five immune checkpoints and 23 immune features were considered statistically significant in HCC, while only seven immune checkpoints and one immune feature in ICC. Then, the prognostic value of DEAS events was studied, and two transcripts with different basic cell functions (proliferation, cell cycle, invasion, and migration) were produced by ADHFE1 through alternative splicing. Moreover, four nomograms were established in conjunction with relevant clinicopathological factors. Finally, we found two most significant splicing factors and further showed their protein crystal structure. The joint analysis of the AS events in HCC and ICC revealed novel insights into immune features and clinical prognosis, which might provide positive implications in HCC and ICC treatment.
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Affiliation(s)
- Dingan Luo
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Deze Zhao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Mao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chuan Hu
- Medical College, Qingdao University, Qingdao, China
| | - Haoran Li
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shun Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaowu Chen
- Asian Liver Center, Department of Surgery, Medical School of Stanford University, Stanford, CA, United States
| | - Lakshmi Huttad
- Asian Liver Center, Department of Surgery, Medical School of Stanford University, Stanford, CA, United States
| | - Bailiang Li
- Department of Radiation Oncology, Medical School of Stanford University, Stanford, CA, United States
| | - Cheng Jin
- Department of Radiation Oncology, Medical School of Stanford University, Stanford, CA, United States
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Bing Han
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
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9
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Peng Q, Wen T, Liu D, Wang S, Jiang X, Zhao S, Huang G. DSN1 is a prognostic biomarker and correlated with clinical characterize in breast cancer. Int Immunopharmacol 2021; 101:107605. [PMID: 34238686 DOI: 10.1016/j.intimp.2021.107605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 11/20/2022]
Abstract
DSN1 affects cell cycle progression and is associated with clinical-pathological features in colorectal and hepatocellular carcinomas. However, the biological function of DSN1 in breast cancer is still indistinct. In this study, we comprehensively analyzed the correlation between DSN1 expression in different molecular subtypes or stages of breast cancer and investigated the prognostic value of DSN1 in databases such as Oncomine, Cancer Cell Line Encyclopedia, UALCAN, Human Protein Atlas, Kaplan-Meier Plotter, OncoLnc, GEPIA. Moreover, we investigated the correlation of DSN1 with tumor-infiltrating immune cells in the different tumor microenvironments via Tumor Immune Estimation Resource database and explore DSN1 co-expression networks in breast cancer via LinkedOmics analysis, NetworkAnalyst database analysis. Finally, we also performed our immunohistochemical experiments to explore the expression of DSN1 in different stages or subtypes of breast cancer. The findings in this article shed light on the essential role of DSN1 in breast cancers as well as suggested that the upregulation of DSN1 expression was strongly associated with poor prognosis and decreased survival in breast cancer, and there were significant differences in its expression in different pathological subtypes and stages of breast cancer.
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Affiliation(s)
- Qing Peng
- Department of VIP clinic, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, PR China.
| | - Tingyu Wen
- Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Dongyang Liu
- Division of General Surgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, PR China.
| | - Suguo Wang
- Department of VIP clinic, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, PR China
| | - Xinting Jiang
- Department of VIP clinic, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, PR China
| | - Shiju Zhao
- Department of VIP clinic, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, PR China.
| | - Gaozhong Huang
- Department of VIP clinic, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, PR China.
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10
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Suleman M, Tahir Ul Qamar M, Saleem S, Ahmad S, Ali SS, Khan H, Akbar F, Khan W, Alblihy A, Alrumaihi F, Waseem M, Allemailem KS. Mutational Landscape of Pirin and Elucidation of the Impact of Most Detrimental Missense Variants That Accelerate the Breast Cancer Pathways: A Computational Modelling Study. Front Mol Biosci 2021; 8:692835. [PMID: 34262943 PMCID: PMC8273169 DOI: 10.3389/fmolb.2021.692835] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022] Open
Abstract
Pirin (PIR) protein is highly conserved in both prokaryotic and eukaryotic organisms. Recently, it has been identified that PIR positively regulates breast cancer cell proliferation, xenograft tumor formation, and metastasis, through an enforced transition of G1/S phase of the cell cycle by upregulation of E2F1 expression at the transcriptional level. Keeping in view the importance of PIR in many crucial cellular processes in humans, we used a variety of computational tools to identify non-synonymous single-nucleotide polymorphisms (SNPs) in the PIR gene that are highly deleterious for the structure and function of PIR protein. Out of 173 SNPs identified in the protein, 119 are non-synonymous, and by consensus, 24 mutations were confirmed to be deleterious in nature. Mutations such as V257A, I28T, and I264S were unveiled as highly destabilizing due to a significant stability fold change on the protein structure. This observation was further established through molecular dynamics (MD) simulation that demonstrated the role of the mutation in protein structure destability and affecting its internal dynamics. The findings of this study are believed to open doors to investigate the biological relevance of the mutations and drugability potential of the protein.
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Affiliation(s)
- Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | | | - Shoaib Saleem
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Syed Shujait Ali
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Haji Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Fazal Akbar
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Wajid Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Adel Alblihy
- Medical Center, King Fahad Security College (KFSC), Riyadh, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Muhammad Waseem
- Faculty of Rehabilitation and Allied Health Science, Riphah International University, Islamabad, Pakistan
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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Zu ML, Duan Y, Xie JB, Qi YS, Xie P, Borjigidai A, Piao XL. Gypenoside LI arrests the cell cycle of breast cancer in G0/G1 phase by down-regulating E2F1. JOURNAL OF ETHNOPHARMACOLOGY 2021; 273:114017. [PMID: 33716078 DOI: 10.1016/j.jep.2021.114017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Gynostemma pentaphyllum (Thunb.) Makino, a traditional medicine in China, has been widely used for the treatment of various diseases. Gypenoside LI (Gyp LI) is a major constituent from steamed G. pentaphyllum. Previous studies have shown that gypnenoside LI possess inhibitory effect on the growth of many cancer cells. However, its pharmacological effect in breast cancer and the mechanism have not been reported yet. AIM OF THE STUDY To investigate the anti-breast cancer activity of gypenoside LI and underlying mechanisms of gypenoside LI in MDA-MB-231 and MCF-7 cells. MATERIAL/METHODS The cytotoxicity of gypenoside LI was determined by MTT, colony-formation and three-dimensional spheroid assay. The migration, cell apoptosis and the cell cycle were investigated through cell morphology observation, flow cytometry analysis and key proteins detection. The anticancer mechanisms of gypenoside LI were detected by RNA sequencing (RNA-seq) and Gene Set Enrichment Analysis (GSEA) transcriptome analysis. RESULTS Gypenoside LI inhibited cell proliferation, migration, induced cell apoptosis and cell cycle arrest. Gypenoside LI arrested cell cycle at G0/G1 phase by regulating E2F1. It also inhibited tumor proliferation by regulating the expression of ERCC6L. Interestingly, we found that E2F1 siRNA also down-regulated the expression of ERCC6L. Gypenoside LI showed potential anti-breast cancer cells activity, especially on triple-negative breast cancer cells. CONCLUSIONS These data indicate that gypenoside LI could inhibit human breast cancer cells through inhibiting proliferation and migration, inducing apoptosis, arresting cell cycle at G0/G1 phase by regulating E2F1. It could be used as potential multi-target chemopreventive agents for cancer.
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Affiliation(s)
- Ma-Li Zu
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Yu Duan
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Jin-Bo Xie
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Yan-Shuang Qi
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Peng Xie
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China
| | - Almaz Borjigidai
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China.
| | - Xiang-Lan Piao
- Key Laboratory of Ethnomedicine of Ministry of Education, Center on Translational Neuroscience, School of Pharmacy, Minzu University of China, Beijing, 100081, PR China.
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12
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Role of Pirin, an Oxidative Stress Sensor Protein, in Epithelial Carcinogenesis. BIOLOGY 2021; 10:biology10020116. [PMID: 33557375 PMCID: PMC7915911 DOI: 10.3390/biology10020116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/08/2021] [Accepted: 01/14/2021] [Indexed: 12/12/2022]
Abstract
Pirin is an oxidative stress (OS) sensor belonging to the functionally diverse cupin superfamily of proteins. Pirin is a suggested quercetinase and transcriptional activator of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway. Its biological role in cancer development remains a novel area of study. This review presents accumulating evidence on the contribution of Pirin in epithelial cancers, involved signaling pathways, and as a suggested therapeutic target. Finally, we propose a model in which Pirin is upregulated by physical, chemical or biological factors involved in OS and cancer development.
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Shen C, Li J, Chang S, Che G. [Advancement of E2F1 in Common Tumors]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:921-926. [PMID: 33070516 PMCID: PMC7583875 DOI: 10.3779/j.issn.1009-3419.2020.101.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
细胞周期相关转录因子E2F1(E2F transcription factor 1)是细胞周期相关转录因子E2F家族成员之一,主要参与包括细胞周期进展、DNA修复、DNA复制、细胞分化,增殖和凋亡等多种细胞过程。E2F1在全身多种肿瘤组织和细胞中呈高表达,起着促癌基因的作用,E2F1表达上调与肿瘤的发生、发展、转移及预后密切相关。因此,E2F1有望成为肿瘤治疗的新靶点。本文就E2F1在目前常见肿瘤中的最新研究进展做一综述。
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Affiliation(s)
- Cheng Shen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jue Li
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Shuai Chang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
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